Background on plotJacobson() function

RCSC paradigm Jacobson plot CECPfuns package Plots and graphs

1.xi.23 This is very early work in progress and will evolve a lot over the next week and then get into CECPfuns R package on github.

Chris Evans https://www.psyctc.org/R_blog/ (PSYCTC.org)https://www.psyctc.org/psyctc/
2023-11-01

[This started as an Rblog post on 1.xi.23. It is work in progress and will evolve a lot over the next weeks. When it’s ready it will be added to the CECPfuns R package on github. Latest updates 13.xi.23]

Show code
### this is just getting the data and then  adding a few artificial points
if (interactive()) {
  load(file = "./_posts/2023-11-01-plotjacobson/tmpTib") # running interactively 
} else {
  load(file = "tmpTib") # in the full Rblog
}
tibDat <- tmpTib
tmpTibDat <- tibble(id = c(997, 998, 999),
                    firstScore = c(.5, .1, 1.1),
                    lastScore = c(2, .7, .1))
bind_rows(tmpTibDat,
          tibDat) -> tibDat
rm(tmpTib)
rm(tmpTibDat)

RCI <- getRCIfromSDandAlpha(sd(tibDat$firstScore), rel = 0.943242)
CSC <- 1.26
# minPossScore <- NA
# maxPossScore <- NA
# baselineScores <- tibDat$firstScore
# finalScores <- tibDat$lastScore
# pointNames <- tibDat$id
# goodScorePos <- FALSE
# 
# tibble(baselineScores = baselineScores,
#        finalScores = finalScores,
#        pointNames = pointNames) -> tmpTib

### now we can define the function
getJacobsonPlot <- function(baselineScores, 
                          finalScores, 
                          pointNames = NA, # can be used to label points
                          namesNotPoints = FALSE, # only use labels, no points
                          nameRCIDetOnly = FALSE, # only label deteriorators
                          namesSize = 2, # sets the font size for labels
                          CSC = NA, # the CSC value to use
                          RCI = NA, # the RCI value to use
                          minPossScore = 0, 
                          maxPossScore = 4, 
                          goodScorePos = FALSE, # set to TRUE/T if a better score is positive
                          omitNHS = FALSE, # use to omit scores starting in non-help-seeking range
                          title = NULL, # to override the default title
                          subtitle = NULL, # ditto for subtitle
                          titleJustificn = .5, # centre justifies titles, 0 for L, 1 for R
                          xLab = NULL, # overrides the default x axis label 
                          yLab = NULL, # overrides the default y axis label
                          noLegend = FALSE, # removes legends for colours
                          labelCSClines = FALSE, # set to TRUE/T to label CSC lines with CSC value
                          areaColourScheme = c("NONE", # mapping to use, see notes, schemes are:
                                               "RCSC5",
                                               "DIRECTION",
                                               "RCI3",
                                               "CSC4",
                                               "RCSC7",
                                               "RCSC10",
                                               "POLYGONS"), 
                          legendNameAreas = "Area mapping", # set title for area legend
                          pointColourScheme = c("RCSC5",
                                                "RCI3",
                                                "DIRECTION",
                                                "CSC4",
                                                "RCSC7",
                                                "RCSC10",
                                                "NONE"), # chose point colour mapping, as above
                          legendNamePoints = "Point mapping", # title for point colours
                          ### now lots of mappings used by the above colour mappings
                          coloursDirection = c("red", 
                                               "green", 
                                               "black"),
                          ### you can override the labels to local choice and language
                          labelsDirection = c("Deterioration", 
                                              "Improvement", 
                                              "No change"),
                          coloursRCI3 = c("grey", 
                                          "red", 
                                          "green"),
                          labelsRCI3 = c("No reliable change", 
                                         "Reliable deterioration", 
                                         "Reliable improvement"),
                          coloursCSC4 = c("green", 
                                          "red", 
                                          "orange", 
                                          "skyblue1"),
                          labelsCSC4 = c("High to low", 
                                         "Low to high", 
                                         "Stayed high", 
                                         "Stayed low"),
                          coloursRCSC5 = c("grey", 
                                           "red", 
                                           "skyblue1", 
                                           "green", 
                                           "chartreuse4"),
                          labelsRCSC5 = c("No reliable change", 
                                          "Reliable deterioration", 
                                          "Reliable improvement, stayed high", 
                                          "Reliable improvement, high to low ('Recovered')", 
                                          "Reliable improvement, stayed low"),
                          ### it's essentially impossible to code labels for the RCSC
                          ### that would be independent of the cueing of the scores
                          ### hence different labels (but same colours and order)
                          ### for positively cued measures
                          labelsRCSC5pos = c("No reliable change", 
                                             "Reliable deterioration", 
                                             "Reliable improvement, stayed high", 
                                             "Reliable improvement, low to high ('Recovered')", 
                                             "Reliable improvement, stayed low"),
                          coloursRCSC7 = c("grey", 
                                           "orange", 
                                           "red", 
                                           "sienna2", 
                                           "palegreen", 
                                           "green", 
                                           "skyblue1"),
                          labelsRCSC7 = c("No reliable change", 
                                          "Reliable deterioration, stayed high", 
                                          "Reliable deterioration, low to high", 
                                          "Reliable deterioration, stayed low", 
                                          "Reliable improvement, stayed high", 
                                          "Reliable improvement, high to low ('Recovered')", 
                                          "Reliable improvement, stayed low"),
                          labelsRCSC7pos = c("No reliable change", 
                                             "Reliable deterioration, stayed low", 
                                             "Reliable deterioration, high to low", 
                                             "Reliable deterioration, stayed high", 
                                             "Reliable improvement, stayed low", 
                                             "Reliable improvement, low to high ('Recovered')", 
                                             "Reliable improvement, stayed high"),
                          coloursRCSC10 = c("yellow", #1
                                            "blue", #2
                                            "purple", #3
                                            "grey", #4
                                            "orange", #5
                                            "red", #6
                                            "violetred4", #7
                                            "palegreen", #8
                                            "green", #9
                                            "chartreuse4"), #10
                          labelsRCSC10 = c("No reliable change, stayed high", #1
                                           "No reliable change, high to low", #2
                                           "No reliable change, low to high", #3
                                           "No reliable change, stayed low", #4
                                           "Reliable deterioration, stayed high", #5 
                                           "Reliable deterioration, low to high", #6
                                           "Reliable deterioration, stayed low", #7
                                           "Reliable improvement, stayed high", #8
                                           "Reliable improvement, high to low ('Recovered')", #9
                                           "Reliable improvement, stayed low"), #10
                          labelsRCSC10pos = c("No reliable change, stayed low", #1p
                                              "No reliable change, low to high", #2p
                                              "No reliable change, high to low", #3p
                                              "No reliable change, stayed high", #4p
                                              "Reliable deterioration, stayed low", #5p
                                              "Reliable deterioration, low to high", #6p
                                              "Reliable deterioration, stayed high", #7p
                                              "Reliable improvement, stayed low", #8p
                                              "Reliable improvement, low to high ('Recovered')", #9p
                                              "Reliable improvement, stayed high"), #10p
                          ### you can also add mapping to point shapes
                          pointShapeScheme = c("NONE",
                                               "DIRECTION",
                                               "RCI3"),
                          ### these allow you to override the default mapping to 
                          ### a square and arrows pointing the appropriate ways
                          ### NULL leaves the default mapping in place
                          ### I really don't advise overriding these but you can!
                          pointShapeNoRelChange = NULL,
                          pointShapeRelDet = NULL,
                          pointShapeRelImp = NULL,
                          ### the following arguments control the aesthetics
                          pointSize = 1,
                          ### the default alpha settings allow both points and areas to be coloured
                          pointAlpha = 1, # 1 is no transparency, 0 is no colour
                          areaAlpha = .3, # ditto, .3 is probably OK for a pale coloured ground
                          ### aesthetics for the no-change diagonal line
                          lineTypeNoChange = 1, # default is solid line
                          lineWidthNoChange = .5, # default is ggplot default line thickness
                          lineColourNoChange = 1, # default is black
                          ### same for the CSC lines
                          lineTypeCSC = 1, 
                          lineWidthCSC = .5, 
                          lineColourCSC = 1, 
                          ### same for the RCI lines
                          lineTypeRCI = 1,
                          lineWidthRCI = .5,
                          lineColourRCI = 1,
                          themeToUse = theme_bw(), # set ggplot theme to use, unquoted
                          ### I can't imagine changing these myself but ...
                          ### these allow you to override the theme's colours
                          plotColour = NULL, # background colour of the plot area itself, e.g. "white"
                          borderColour = NULL, # and same for the border around it
                          ### you might want to use these to suppress messages and warnings
                          noMessages = FALSE, # suppress messages
                          noWarnings = FALSE, # suppress my warnings (not other R ones)
                          ### these are probably only useful to help me debug things
                          printVariables = FALSE, # will give a print out of all internal variables
                          warningsToErrors = FALSE, # makes warnings into errors, i.e. 
                          ### this is really only for someone drilling into the code
                          ### it labels all twelve area polygons with their numbers
                          labelAllPolygons = FALSE,
                          ### arguments not implemented yet
                          greyScale = FALSE # may be implemented to force B&W/greyscale
){
  ### 
  ### function to give single group Jacobson plot given vectors of pre and post scores
  ### and fixed CSC and RCI
  ### default, with goodScorePos == FALSE, is distress/dysfunction scoring i.e. higher scores worse
  ### but can override that by using goodScorePos == TRUE
  ### by default the function expects to be told minimum and maximum scores on the measure
  ### these are simple numerical min and max, i.e. ignores whether scale is positive or negative 
  ### those default to zero and four as per original CORE scoring but can be overridden (doh!)
  ### fixing either or both minPossScore and maxPossScore to NULL means the observed minimum
  ### and maximum will be used, not recommended and may produce odd scale labelling
  ###
  ### get the arguments before anything is changed
  listArgs <- as.list(match.call(expand.dots = FALSE)[-1])

  ### handle warningsToErrors before other arguments
  ### test it
  if (!is.logical(warningsToErrors)){
    stop("You have given warningsToErrors as something other than a logical value (TRUE, FALSE, T or F).  Sorry: please go back and fix this.")
  }
  if (length(warningsToErrors) != 1) {
    stop("The argument warningsToErrors must be a single logical value.  Sorry: please go back and fix this.")
  }
  
  oldWarn <- getOption("warn")
  if (warningsToErrors) {
    options("warn" = 2)
  }
  
  ### handle noMessages before other arguments
  ### test it
  if (!is.logical(noMessages)){
    stop("You have given noMessages as something other than a logical value (TRUE, FALSE, T or F).  Sorry: please go back and fix this.")
  }
  if (length(noMessages) != 1) {
    stop("The argument noMessages must be a single logical value.  Sorry: please go back and fix this.")
  }
  
  ### handle noWarnings before other arguments
  ### test it
  if (!is.logical(noWarnings)){
    stop("You have given noWarnings as something other than a logical value (TRUE, FALSE, T or F).  Sorry: please go back and fix this.")
  }
  if (length(noWarnings) != 1) {
    stop("The argument noWarnings must be a single logical value.  Sorry: please go back and fix this.")
  }
  
  ### now match the arguments which are switch choices, these will have the default match.arg error trapping
  ###
  areaColourScheme <- str_to_upper(match.arg(areaColourScheme))
  pointColourScheme <- str_to_upper(match.arg(pointColourScheme))
  pointShapeScheme <- match.arg(pointShapeScheme) ### all three options start differently so can do this:
  pointShapeScheme <- str_to_upper(pointShapeScheme)
  ###
  ### sanity testing of other arguments
  ###
  if (length(baselineScores) != length(finalScores)) {
    stop("Length of baseline and final scores must be the same")
  }
  if (!is.numeric(baselineScores)) {
    stop("Baseline scores must be numeric")
  }
  if (!is.numeric(finalScores)) {
    stop("Final scores must be numeric")
  }  
  if (!is.na(pointNames[1]) & (length(pointNames) != length(baselineScores))) {
    stop("When given, the length of labels (pointNames) must be same as lengths of scores")
  }
  if (!is.na(pointNames[1]) & is.numeric(pointNames)) {
    if (!noWarnings) {
      warning("You have given a numeric vector for pointNames.  If you have many numbers this will be a mess!")
    }
    pointNames <- as.character(pointNames)
  }
  if (!is.na(pointNames[1]) & !(any(is.character(pointNames),
                                    is.factor(pointNames),
                                    is.numeric(pointNames)))) {
    stop("You have given pointNames as something other than numeric (discouraged), character or factor. Sorry: please go back and fix this.")
  }
  if (!is.logical(namesNotPoints)){
    stop("You have given namesNotPoints as something other than a logical value (TRUE, FALSE, T or F).  Sorry: please go back and fix this.")
  }
  if (length(namesNotPoints) != 1) {
    stop("The argument namesNotPoints must be a single logical value.  Sorry: please go back and fix this.")
  }
  if (!is.logical(nameRCIDetOnly)){
    stop("You have given nameRCIDetOnly as something other than a logical value (TRUE, FALSE, T or F).  Sorry: please go back and fix this.")
  }
  if (length(nameRCIDetOnly) != 1) {
    stop("The argument nameRCIDetOnly must be a single logical value.  Sorry: please go back and fix this.")
  }
  if (!is.numeric(namesSize)) {
    stop("The value for namesSize must be numeric. Sorry: please go back and fix this.")
  }
  if (length(namesSize) != 1) {
    stop("The argument namesSize must be a single number. Sorry: please go back and fix this.")
  }
  if (namesSize < 0) {
    stop("The value for namesSize must be a positive number. Sorry: please go back and fix this.")
  }
  if (!is.na(CSC) & !is.numeric(CSC)){
    stop("You have given CSC as something other than a numeric value.  Sorry: please go back and fix this.")
  }
  if (length(CSC) != 1) {
    stop("The argument CSC must be a single numeric value.  Sorry: please go back and fix this.")
  }
  if (!is.na(RCI) & !is.numeric(RCI)){
    stop("You have given RCI as something other than a numeric value.  Sorry: please go back and fix this.")
  }
  if (length(RCI) != 1) {
    stop("The argument RCI must be a single numeric value.  Sorry: please go back and fix this.")
  }
  if (is.na(minPossScore)){
    stop("You have not given a value for minPossScore (NA is the default).  Sorry, but I set that default to force users to choose the appropriate value.  It must be the lowest numeric value possible for the score, not the worst score (which would be the lowest number possible for a positively cued measure).  Sorry: please go back and fix this.")
  }
  if (is.na(minPossScore) & !is.numeric(minPossScore)){
    stop("You have given minPossScore as something other than a numeric value.  Sorry: please go back and fix this.")
  }
  if (length(minPossScore) != 1) {
    stop("The argument minPossScore must be a single numeric value.  Sorry: please go back and fix this.")
  }
  if (is.na(maxPossScore)){
    stop("You have not given a value for maxPossScore (NA is the default).  Sorry, but I set that default to force users to choose the appropriate value.  It must be the highest numeric value possible for the score, not the best score (which would be the lowest number possible for a positively cued measure).  Sorry: please go back and fix this.")
  }
  if (!is.na(maxPossScore) & !is.numeric(maxPossScore)){
    stop("You have given maxPossScore as something other than a numeric value.  Sorry: please go back and fix this.")
  }
  if (length(maxPossScore) != 1) {
    stop("The argument maxPossScore must be a single numeric value.  Sorry: please go back and fix this.")
  }
  if (maxPossScore < minPossScore) {
    msg <- paste0("You have given minPossScore as ",
                  minPossScore,
                  " and maxPossScore as ",
                  maxPossScore,
                  "\nbut these must be in order of actual scores not cueing of scores.",
                  "\ni.e. maxPossScore must be higher than minPossScore whether higher scores are better or worse than lower scores.  Sorry: please go back and fix this.")
    stop(msg)
  }
  if (!is.na(CSC) & (CSC < minPossScore |
                     CSC > maxPossScore)) {
    msg <- paste0("You have given CSC as ",
                  CSC,
                  " and minPossScore as ",
                  minPossScore,
                  " and maxPossScore as ",
                  maxPossScore,
                  "\nbut CSC must lie between the possible scores.  Sorry: please go back and fix this.")
    stop(msg)
  }
  if (!is.logical(goodScorePos)){
    stop("You have given goodScorePos as something other than a logical value (TRUE, FALSE, T or F).  Sorry: please go back and fix this.")
  }
  if (length(goodScorePos) != 1) {
    stop("The argument goodScorePos must be a single logical value.  Sorry: please go back and fix this.")
  }
  if (!is.logical(omitNHS)){
    stop("You have given omitNHS as something other than a logical value (TRUE, FALSE, T or F).  Sorry: please go back and fix this.")
  }
  if (length(omitNHS) != 1) {
    stop("The argument omitNHS must be a single logical value.  Sorry: please go back and fix this.")
  }
  
  if (!is.null(title) & !is.character(title)) {
    stop("If you are giving a title it must be a single character value.  Sorry: please go back and fix this.")
  }
  if (!is.null(title) & length(title) != 1) {
    stop("If you are giving a title it must be a single value.  Sorry: please go back and fix this.")
  }
  if (!is.null(subtitle) & !is.character(subtitle)) {
    stop("If you are giving a subtitle it must be a single character value.  Sorry: please go back and fix this.")
  }
  if (!is.null(subtitle) & length(subtitle) != 1) {
    stop("If you are giving a subtitle it must be a single value.  Sorry: please go back and fix this.")
  }
  if (!is.numeric(titleJustificn)) {
    stop("The argument titleJustificn must be a single number. Sorry: please go back and fix this.")
  }
  if (length(titleJustificn) != 1) {
    stop("The argument titleJustificn must be a single number. Sorry: please go back and fix this.")
  }
  if (!(titleJustificn %in% c(0, .5, 1))) {
    msg <- paste0("You gave titleJustificn as ",
                  titleJustificn,
                  "but it must be one of: 0 (left justified), .5 (centred) or 1 (right justified). Sorry: please go back and fix this.")
    stop(msg)
  }
  if (!is.null(xLab) & !is.character(xLab)) {
    stop("If you are giving a label for the x axis it must be a single character value.  Sorry: please go back and fix this.")
  }
  if (!is.null(xLab) & length(xLab) != 1) {
    stop("If you are giving a label for the x axis it must be a single value.  Sorry: please go back and fix this.")
  }
  if (!is.null(yLab) & !is.character(yLab)) {
    stop("If you are giving a label for the y axis it must be a single character value.  Sorry: please go back and fix this.")
  }
  if (!is.null(yLab) & length(yLab) != 1) {
    stop("If you are giving a label for the y axis it must be a single value.  Sorry: please go back and fix this.")
  }
  if (!is.logical(noLegend)){
    stop("You have given noLegend as something other than a logical value (TRUE, FALSE, T or F).  Sorry: please go back and fix this.")
  }
  if (length(noLegend) != 1) {
    stop("The argument noLegend must be a single logical value.  Sorry: please go back and fix this.")
  }  
  if (!is.logical(labelCSClines)){
    stop("You have given labelCSClines as something other than a logical value (TRUE, FALSE, T or F).  Sorry: please go back and fix this.")
  }
  if (length(labelCSClines) != 1) {
    stop("The argument labelCSClines must be a single logical value.  Sorry: please go back and fix this.")
  } 
  if (!is.null(legendNameAreas) & !is.character(legendNameAreas)) {
    stop("If you are giving a new label to the area legend it must be a single character value.  Sorry: please go back and fix this.")
  }
  if (!is.null(legendNameAreas) & length(legendNameAreas) != 1) {
    stop("If you are giving a new label to the area legend it must be a single value.  Sorry: please go back and fix this.")
  }
  if (!is.null(legendNamePoints) & !is.character(legendNamePoints)) {
    stop("If you are giving a new label to the point legend it must be a single character value.  Sorry: please go back and fix this.")
  }
  if (!is.null(legendNamePoints) & length(legendNamePoints) != 1) {
    stop("If you are giving a new label to the point it must be a single value.  Sorry: please go back and fix this.")
  }
  if (!is.character(coloursDirection)) {
    stop("The argument coloursDirection must be a character vector of length three.  Sorry: please go back and fix this.")
  }
  if (length(coloursDirection) != 3) {
    stop("The argument coloursDirection must be a character vector of length three.  Sorry: please go back and fix this.")
  }
  if (!is.character(labelsDirection)) {
    stop("The argument labelsDirection must be a character vector of length three.  Sorry: please go back and fix this.")
  }
  if (length(labelsDirection) != 3) {
    stop("The argument labelsDirection must be a character vector of length three.  Sorry: please go back and fix this.")
  }
  if (!is.character(coloursRCI3)) {
    stop("The argument coloursRCI3 must be a character vector of length three.  Sorry: please go back and fix this.")
  }
  if (length(coloursRCI3) != 3) {
    stop("The argument coloursRCI3 must be a character vector of length three.  Sorry: please go back and fix this.")
  }
  if (!is.character(labelsRCI3)) {
    stop("The argument labelsRCI3 must be a character vector of length three.  Sorry: please go back and fix this.")
  }
  if (length(labelsRCI3) != 3) {
    stop("The argument labelsRCI3 must be a character vector of length three.  Sorry: please go back and fix this.")
  }
  if (!is.character(coloursCSC4)) {
    stop("The argument coloursCSC4 must be a character vector of length four.  Sorry: please go back and fix this.")
  }
  if (length(coloursCSC4) != 4) {
    stop("The argument coloursCSC4 must be a character vector of length four.  Sorry: please go back and fix this.")
  }
  if (!is.character(labelsCSC4)) {
    stop("The argument labelsCSC4 must be a character vector of length four.  Sorry: please go back and fix this.")
  }
  if (length(labelsCSC4) != 4) {
    stop("The argument labelsCSC4 must be a character vector of length four.  Sorry: please go back and fix this.")
  }
  if (!is.character(coloursRCSC5)) {
    stop("The argument labelsCSC4 must be a character vector of length five.  Sorry: please go back and fix this.")
  }
  if (length(coloursRCSC5) != 5) {
    stop("The argument coloursRCSC5 must be a character vector of length five.  Sorry: please go back and fix this.")
  }
  if (!is.character(labelsRCSC5)) {
    stop("The argument labelsRCSC5 must be a character vector of length five.  Sorry: please go back and fix this.")
  }
  if (length(labelsRCSC5) != 5) {
    stop("The argument labelsRCSC5 must be a character vector of length five.  Sorry: please go back and fix this.")
  }
  if (!is.character(labelsRCSC5pos)) {
    stop("The argument labelsRCSC5pos must be a character vector of length five.  Sorry: please go back and fix this.")
  }
  if (length(labelsRCSC5pos) != 5) {
    stop("The argument labelsRCSC5pos must be a character vector of length five.  Sorry: please go back and fix this.")
  }
  if (!is.character(coloursRCSC7)) {
    stop("The argument coloursRCSC7 must be a character vector of length seven.  Sorry: please go back and fix this.")
  }
  if (length(coloursRCSC7) != 7) {
    stop("The argument coloursRCSC7 must be a character vector of length seven.  Sorry: please go back and fix this.")
  }
  if (!is.character(labelsRCSC7)) {
    stop("The argument labelsRCSC7 must be a character vector of length seven.  Sorry: please go back and fix this.")
  }
  if (length(labelsRCSC7) != 7) {
    stop("The argument labelsRCSC7 must be a character vector of length seven.  Sorry: please go back and fix this.")
  }
  if (!is.character(labelsRCSC7pos)) {
    stop("The argument labelsRCSC7pos must be a character vector of length seven.  Sorry: please go back and fix this.")
  }
  if (length(labelsRCSC7pos) != 7) {
    stop("The argument labelsRCSC7pos must be a character vector of length seven.  Sorry: please go back and fix this.")
  }
  if (!is.character(coloursRCSC10)) {
    stop("The argument coloursRCSC10 must be a character vector of length ten.  Sorry: please go back and fix this.")
  }
  if (length(coloursRCSC10) != 10) {
    stop("The argument coloursRCSC10 must be a character vector of length ten.  Sorry: please go back and fix this.")
  }
  if (!is.character(labelsRCSC10)) {
    stop("The argument labelsRCSC10 must be a character vector of length ten.  Sorry: please go back and fix this.")
  }
  if (length(labelsRCSC10) != 10) {
    stop("The argument labelsRCSC10 must be a character vector of length ten.  Sorry: please go back and fix this.")
  }
  if (!is.character(labelsRCSC10pos)) {
    stop("The argument labelsRCSC10pos must be a character vector of length ten.  Sorry: please go back and fix this.")
  }
  if (length(labelsRCSC10pos) != 10) {
    stop("The argument labelsRCSC10pos must be a character vector of length ten.  Sorry: please go back and fix this.")
  }
  if (!is.null(pointShapeNoRelChange)) {
    if (length(pointShapeNoRelChange) != 1) {
      stop("The argument pointShapeNoRelChange must be an integer between 0 and 25 (inclusive). Sorry: please go back and fix this.")
    }    
    if (is.numeric(pointShapeNoRelChange)) {
      if (!(pointShapeNoRelChange %in% 1:25)) {
        stop("The argument pointShapeNoRelChange must be an integer between 0 and 25 (inclusive). Sorry: please go back and fix this.")
      }
    }
  }
  if (!is.null(pointShapeRelDet)) {
    if (length(pointShapeRelDet) != 1) {
      stop("The argument pointShapeRelDet must be an integer between 0 and 25 (inclusive). Sorry: please go back and fix this.")
    }    
    if (is.numeric(pointShapeRelDet)) {
      if (!(pointShapeRelDet %in% 1:25)) {
        stop("The argument pointShapeRelDet must be an integer between 0 and 25 (inclusive). Sorry: please go back and fix this.")
      }
    }
  }
  if (!is.null(pointShapeRelImp)) {
    if (length(pointShapeRelImp) != 1) {
      stop("The argument pointShapeRelImp must be an integer between 0 and 25 (inclusive). Sorry: please go back and fix this.")
    }    
    if (is.numeric(pointShapeRelImp)) {
      if (!(pointShapeRelImp %in% 1:25)) {
        stop("The argument pointShapeRelImp must be an integer between 0 and 25 (inclusive). Sorry: please go back and fix this.")
      }
    }
  }
  if (!is.numeric(pointSize)) {
    stop("The argument pointSize must be an integer between 0 and 25 (inclusive). Sorry: please go back and fix this.")
  }
  if (length(pointSize) != 1) {
    stop("The argument pointSize must be an integer between 0 and 25 (inclusive). Sorry: please go back and fix this.")
  }
  if (pointSize < 0) {
    stop("The argument pointSize must be a positive number. Sorry: please go back and fix this.")
  }
  if (!is.numeric(pointAlpha)) {
    stop("The argument pointAlpha must be a number between 0 and 1 (inclusive). Sorry: please go back and fix this.")
  }
  if (length(pointAlpha) != 1) {
    stop("The argument pointAlpha must be a number between 0 and 1 (inclusive). Sorry: please go back and fix this.")
  }
  if (pointAlpha < 0 | pointAlpha > 1) {
    stop("The argument pointAlpha must be a number between 0 and 1 (inclusive). Sorry: please go back and fix this.")
  }
  if (!is.numeric(areaAlpha)) {
    stop("The argument areaAlpha must be a number between 0 and 1 (inclusive). Sorry: please go back and fix this.")
  }
  if (length(areaAlpha) != 1) {
    stop("The argument areaAlpha must be a number between 0 and 1 (inclusive). Sorry: please go back and fix this.")
  }
  if (areaAlpha < 0 | areaAlpha > 1) {
    stop("The argument areaAlpha must be a number between 0 and 1 (inclusive). Sorry: please go back and fix this.")
  }
  
  if (!is.numeric(lineTypeNoChange) & !is.character(lineTypeNoChange)) {
    stop("The argument lineTypeNoChange must be a character or number. Sorry: please go back and fix this.")
  }
  if (length(lineTypeNoChange) != 1) {
    stop("The argument lineTypeNoChange must be a single value. Sorry: please go back and fix this.")
  }
  if (!is.numeric(lineWidthNoChange)) {
    stop("The argument lineWidthNoChange must be a number. Sorry: please go back and fix this.")
  }
  if (length(lineWidthNoChange) != 1) {
    stop("The argument lineWidthNoChange must be a single number. Sorry: please go back and fix this.")
  }
  if (!is.numeric(lineColourNoChange) & !is.character(lineColourNoChange)) {
    stop("The argument lineColourNoChange must be a character or number. Sorry: please go back and fix this.")
  }
  if (length(lineColourNoChange) != 1) {
    stop("The argument lineColourNoChange must be a single number or character. Sorry: please go back and fix this.")
  }
  if (!is.numeric(lineTypeCSC) & !is.character(lineTypeCSC)) {
    stop("The argument lineTypeCSC must be a character or number. Sorry: please go back and fix this.")
  }
  if (length(lineTypeCSC) != 1) {
    stop("The argument lineTypeCSC must be a single number or character. Sorry: please go back and fix this.")
  }
  if (!is.numeric(lineWidthCSC)) {
    stop("The argument lineWidthCSC must be a number. Sorry: please go back and fix this.")
  }
  if (length(lineWidthCSC) != 1) {
    stop("The argument lineWidthCSC must be a single number. Sorry: please go back and fix this.")
  }
  if (!is.numeric(lineColourCSC) & !is.character(lineColourCSC)) {
    stop("The argument lineColourCSC must be a character or number. Sorry: please go back and fix this.")
  }
  if (length(lineColourCSC) != 1) {
    stop("The argument lineColourCSC must be a single number or character. Sorry: please go back and fix this.")
  }
  if (!is.numeric(lineTypeRCI) & !is.character(lineTypeRCI)) {
    stop("The argument lineTypeRCI must be a character or number. Sorry: please go back and fix this.")
  }
  if (length(lineTypeRCI) != 1) {
    stop("The argument lineTypeRCI must be a single number or character. Sorry: please go back and fix this.")
  }
  if (!is.numeric(lineWidthRCI)) {
    stop("The argument lineWidthRCI must be a number. Sorry: please go back and fix this.")
  }
  if (length(lineWidthRCI) != 1) {
    stop("The argument lineWidthRCI must be a single number. Sorry: please go back and fix this.")
  }
  if (!is.numeric(lineColourRCI) & !is.character(lineColourRCI)) {
    stop("The argument lineColourRCI must be a character or number. Sorry: please go back and fix this.")
  }
  if (length(lineColourRCI) != 1) {
    stop("The argument lineColourRCI must be a single number or character. Sorry: please go back and fix this.")
  }
  if (!is.list(themeToUse)) {
    stop("The argument themeToUse must be a list (actually a ggplot theme but I can't test for that!). Sorry: please go back and fix this.")
  }
  if (!is.logical(labelAllPolygons)){
    stop("You have given labelAllPolygons as something other than a logical value (TRUE, FALSE, T or F).  Sorry: please go back and fix this.")
  }
  if (!is.null(plotColour) & !is.character(plotColour)) {
    stop("If used, the argument plotColour must be a single character value.  Sorry: please go back and fix this.")
  }
  if (!is.null(plotColour) & length(plotColour) != 1) {
    stop("If used, the argument plotColour must be a single character value not a vector.  Sorry: please go back and fix this.")
  }
  if (!is.null(borderColour) & !is.character(borderColour)) {
    stop("If used, the argument borderColour must be a single character value.  Sorry: please go back and fix this.")
  }
  if (!is.null(plotColour) & length(plotColour) != 1) {
    stop("If used, the argument borderColour must be a single character value not a vector.  Sorry: please go back and fix this.")
  }
  if (!is.logical(printVariables)) {
    stop("The argument printVariables must be a logical, i.e. TRUE | FALSE | T | F.  Sorry: please go back and fix this.")
  }
  if (length(printVariables) != 1) {
    stop("The argument printVariables must be a single logical value, not a vector.  Sorry: please go back and fix this.")
  }
  if (length(labelAllPolygons) != 1) {
    stop("The argument labelAllPolygons must be a single logical value.  Sorry: please go back and fix this.")
  }
  if (!is.logical(greyScale)){
    stop("You have given greyScale as something other than a logical value (TRUE, FALSE, T or F).  Sorry: please go back and fix this.")
  }
  if (length(greyScale) != 1) {
    stop("The argument greyScale must be a single logical value.  Sorry: please go back and fix this.")
  }
  ### must have shape and point colour schemes the same if both set
  if (pointShapeScheme != "NONE" & pointColourScheme != "NONE") {
    if (pointShapeScheme != pointColourScheme) {
      errTxt <- paste0("The plot is confusing if pointShapeScheme and pointColourScheme are not the same.",
                       "\n You input: \npointShapeScheme = ",
                       pointShapeScheme,
                       " and pointColourScheme = ",
                       pointColourScheme,
                       "\n either set one of them to 'NONE' or set both to the same value.")
      stop(errTxt)
    }
  }
  
  
  ### trying to allow theme setting in the arguments
  oldTheme <- theme_get()
  theme_set(themeToUse)
  
  ### 
  ### start to handle the arguments
  ###

  ###
  ### set point shapes
  ### makes sense to do this before handling the data?
  ###
  if(pointShapeScheme == "NONE"){
    ### default point shape scheme is by RCI with filled circles
    pointShape <- 16
    vecPointShapes <- rep(pointShape, 3)
    ### obviously could have done that in one line but makes principle clear
  } else {
    ### alternative point shape scheme is by variables shapes in tmpTib (later)
    ### with these shapes
    if(is.null(pointShapeNoRelChange)) {
      pointShapeNoRelChange <- 23
    }
    if(is.null(pointShapeRelDet)) {
      if(!goodScorePos) {
        pointShapeRelDet <- 24
      } else {
        pointShapeRelDet <- 25
      }
    }
    if(is.null(pointShapeRelImp)) {
      if(!goodScorePos) {
        pointShapeRelImp <- 25
      } else {
        pointShapeRelImp <- 24
      }
    }
    ### set the mapping to be used in scale_shape_manual()
    vecPointShapes <- c(pointShapeRelDet , pointShapeRelImp, pointShapeNoRelChange)
    if(pointShapeScheme == "NONE") {
      names(vecPointShapes) <- rep("default", 3)
      vecShapeLabels <- rep("", 3)
    }
    if(pointShapeScheme == "DIRECTION") {
      names(vecPointShapes) <- c("Det", "Imp", "NoChange")
      vecShapeLabels = labelsDirection
    }
    if(pointShapeScheme == "RCI3") {
      names(vecPointShapes) <- c("RelDet", "RelImp", "NoRelChange")
      vecShapeLabels <- labelsRCI3
    }
  }
  
  ### 
  ### OK now handle the data
  ###
   
  ### start of main function to use the score data
  ###
  ### start with names for points if supplied or not
  if(length(pointNames) > 1) {
    pointNames <- as.character(pointNames) 
  } else {
    pointNames <- as.character(1:length(baselineScores))
  }
  
  ### get score range (may come in useful positioning things on plot)
  scoreRange <- abs(maxPossScore - minPossScore)
  
  ### OK now build the data
  tibble(pointNames = pointNames,
         firstScore = baselineScores,
         lastScore = finalScores,
         goodScorePos = goodScorePos) -> tmpTib
  
  ### deal with situations of not having been given a CSC or RCI (or both missing)
  if(is.na(CSC) & is.na(RCI)){
    # transfer pertinent arguments which are really only:
    # tmpTib, minPoss & maxPoss, noChangeline and default point and direction arguments
    # JacobsonPlotNoRCSC() 
    return()
  } 
  ### deal with not having been given an RCI
  if(is.na(RCI)){
    # JacobsonPlotNoRCI() # transfer pertinent arguments
    return()
  }
  if(is.na(CSC)){
    # JacobsonPlotNoCSC() # transfer pertinent arguments
    return()
  }
  
  ###
  ### now get the missing data summary information
  ###
  Original_n <- nrow(tmpTib)
  tmpTib %>%
    reframe(FirstMissing = getNNA(firstScore),
            LastMissing = getNNA(lastScore),
            ### now we are in the full RCSC situation with a CSC and RCI, so ...
            nStartTroubled = if_else(goodScorePos, 
                                     sum(firstScore <= CSC, na.rm = TRUE),
                                     sum(firstScore >= CSC, na.rm = TRUE)),
            nStartOK = Original_n - nStartTroubled) %>%
    pivot_longer(cols = everything()) -> tmpTibMissing
  
  tmpTib %>%
    ### get rid of those with missing scores
    drop_na() -> tmpTib
  Complete <- nrow(tmpTib)
  Incomplete <- Original_n - Complete
  
  tibble(Original_n = Original_n,
         Incomplete = Incomplete,
         Complete = Complete) %>% 
    pivot_longer(cols = everything()) -> tmpTib2
  
  bind_rows(tmpTibMissing,
            tmpTib2) %>%
    rename(n = value,
           What = name) %>%
    mutate(What = ordered(What,
                          levels = c("Original_n",
                                     "FirstMissing",
                                     "LastMissing",
                                     "Incomplete",
                                     "Complete",
                                     "nStartOK",
                                     "nStartTroubled"),
                          labels = c("Original data",
                                     "Missing first score",
                                     "Missing last score",
                                     "Incomplete (either score missing)",
                                     "Complete data",
                                     "Started in non-help-seeking range",
                                     "Started in help-seeking range"
                                     ))) %>%
    arrange(What) -> tmpTibMissing
  
  tmpTibMissing %>%
    filter(What == "Started in help-seeking range") %>%
    select(n) %>%
    pull() -> nHelpSeeking
  
  rm(tmpTib2)
  ### finished summarising missing data
  
  ### start processing the data
  tmpTib %>%
    mutate(RCIcrit = RCI,
           CSCcrit = CSC, 
           firstLastChange = lastScore - firstScore) -> tmpTib
  
  ### I don't like this but ...
  if (omitNHS) {
    tmpTib %>%
      mutate(startHS = if_else(goodScorePos, 
                              firstScore <= CSCcrit,
                              firstScore >= CSCcrit)) %>%
      filter(startHS) -> tmpTib
  }
  
### can now build the default subtitle
  if(is.null(subtitle)) {
    subtitle = paste0("Showing ", 
                      Complete,
                      " with first and last scores from ",
                      Original_n,
                      " rows in the dataset;\n",
                      nHelpSeeking,
                      " in help-seeking score range, ",
                      nrow(tmpTib),
                      " used.")
  }
  
  tmpTib %>%
    mutate(### get direction
           direction3 = case_when(firstLastChange == 0 ~ "NoChange",
                                  goodScorePos & firstLastChange < 0 ~ "Det",
                                  goodScorePos & firstLastChange > 0 ~ "Imp",
                                  !goodScorePos & firstLastChange < 0 ~ "Imp",
                                  !goodScorePos & firstLastChange > 0 ~ "Det"),
           ### now get RCI categories: 
           RCIchange = if_else(abs(firstLastChange) < RCIcrit, "NoRelChange", paste0("Rel", direction3)),
           firstCSCstatus = case_when(!goodScorePos & firstScore >= CSCcrit ~ "HS", 
                                      !goodScorePos & firstScore < CSCcrit ~ "NHS",
                                      goodScorePos & firstScore < CSCcrit ~ "HS", 
                                      goodScorePos & firstScore >= CSCcrit ~ "NHS"),
           lastCSCstatus = case_when(!goodScorePos & lastScore >= CSCcrit ~ "HS", 
                                     !goodScorePos & lastScore < CSCcrit ~ "NHS",
                                     goodScorePos & lastScore < CSCcrit ~ "HS", 
                                     goodScorePos & lastScore >= CSCcrit ~ "NHS"),
           CSC4 = paste0(firstCSCstatus, "To", lastCSCstatus),
           RCSC5 = case_when(
             RCIchange == "NoRelChange" ~ "NoRelChange",
             RCIchange == "RelDet"  ~ "RelDet",
             RCIchange == "RelImp" & CSC4 == "HSToHS" ~ "RelImpHSToHS",
             RCIchange == "RelImp" & CSC4 == "HSToNHS" ~ "RelImpHSToNHS",
             RCIchange == "RelImp" & CSC4 == "NHSToNHS" ~ "RelImpNHSToNHS"),
           RCSC7 = case_when(
             RCIchange == "NoRelChange" ~ "NoRelChange",
             RCIchange == "RelDet" & CSC4 == "HSToHS" ~ "RelDetHSToHS",
             RCIchange == "RelDet" & CSC4 == "NHSToNHS" ~ "RelDetNHSToNHS",
             RCIchange == "RelDet" & CSC4 == "NHSToHS" ~ "RelDetNHSToHS",
             RCIchange == "RelImp" & CSC4 == "HSToHS" ~ "RelImpHSToHS",
             RCIchange == "RelImp" & CSC4 == "HSToNHS" ~ "RelImpHSToNHS",
             RCIchange == "RelImp" & CSC4 == "NHSToNHS" ~ "RelImpNHSToNHS"),
           RCSC10 = case_when(
             RCIchange == "NoRelChange" & CSC4 == "HSToHS" ~ "NoRelChangeHSToHS",
             RCIchange == "NoRelChange" & CSC4 == "HSToNHS" ~ "NoRelChangeHSToNHS",
             RCIchange == "NoRelChange" & CSC4 == "NHSToNHS" ~ "NoRelChangeNHSToNHS",
             RCIchange == "NoRelChange" & CSC4 == "NHSToHS" ~ "NoRelChangeNHSToHS",
             RCIchange == "RelDet" & CSC4 == "HSToHS" ~ "RelDetHSToHS",
             RCIchange == "RelDet" & CSC4 == "NHSToHS" ~ "RelDetNHSToHS",
             RCIchange == "RelDet" & CSC4 == "NHSToNHS" ~ "RelDetNHSToNHS",
             RCIchange == "RelImp" & CSC4 == "HSToHS" ~ "RelImpHSToHS",
             RCIchange == "RelImp" & CSC4 == "HSToNHS" ~ "RelImpHSToNHS",
             RCIchange == "RelImp" & CSC4 == "NHSToNHS" ~ "RelImpNHSToNHS")) -> tmpTib
  
  ### handle shapes
  if(pointShapeScheme == "NONE") {
    tmpTib %>%
    mutate(Shapes = "default") -> tmpTib
  } else {
    tmpTib %>%
      mutate(Shapes = case_when(pointShapeScheme == "DIRECTION" ~ direction3,
                              pointShapeScheme == "RCI3" ~ RCIchange)) -> tmpTib
  }
  ### now set up the shapes to use
  ### handle nameRCIDetOnly, i.e. labelling only of reliably deteriorated
  if(nameRCIDetOnly){
    tmpTib %>%
      ### recode pointNames so only reliable deteriorators have an ID/name
      mutate(pointNames = if_else(RCIchange != "RelDet", "", pointNames)) -> tmpTib
  }
  
  ### build tibAreas
  tribble(
    ~iPolygon, ~namePolygon, ~RCI, ~direction, ~start, ~end, ~CSC4,
    1, "RelDetHighToHigh",         "RelDet",      "Det", "High", "High", "StayedHigh",
    2, "NoRelChangeDetHighToHigh", "NoRelChange", "Det", "High", "High", "StayedHigh",
    3, "NoRelChangeImpHighToHigh", "NoRelChange", "Imp", "High", "High", "StayedHigh",
    4, "RelImpHighToHigh",         "RelImp",      "Imp", "High", "High", "StayedHigh",
    5, "RelImpHighToLow",          "RelImp",      "Imp", "High", "Low",   "HighToLow",
    6, "RelImpLowToLow",           "RelImp",      "Imp", "Low",  "Low",   "StayedLow",
    7, "NoRelChangeImpLowToLow",   "NoRelChange", "Imp", "Low",  "Low",   "StayedLow",
    8, "NoRelChangeDetLowToLow",   "NoRelChange", "Det", "Low",  "Low",   "StayedLow",
    9, "RelDetLowToLow",           "RelDet",      "Det", "Low",  "Low",   "StayedLow",
    10, "RelDetLowToHigh",         "RelDet",      "Det", "Low",  "High",  "LowToHigh",
    11, "NoRelChangeDetLowToHigh",  "NoRelChange", "Det", "Low",  "High",  "LowToHigh",
    12, "NoRelChangeImpHighToLow", "NoRelChange", "Imp", "High", "Low",   "HighToLow") %>%
    mutate(areaAlpha = rep(areaAlpha, 12)) -> tibAreas1

  ### handle goodScorePos for direction
  if(goodScorePos) {
    tibAreas1 %>%
      mutate(direction = case_when(
        direction == "Det" ~ "Imp",
        direction == "Imp" ~ "Det")) -> tibAreas1
  }
    ### handle goodScorePos for RCI
  if(goodScorePos) {
    tibAreas1 %>%
      mutate(RCI = case_when(
        RCI == "RelDet" ~ "RelImp",
        RCI == "RelImp" ~ "RelDet",
        RCI == "NoRelChange" ~ "NoRelChange")) -> tibAreas1
  }
  
  # RCSC5 for areas:  
  if(!goodScorePos) {
    tmpVecRCSC5 <- c("RelDet", #1
                     "NoRelChange", #2
                     "NoRelChange", #3
                     "RelImpHighToHigh", #4
                     "RelImpHighToLow", #5
                     "RelImpLowToLow", #6
                     "NoRelChange", #7
                     "NoRelChange", #8
                     "RelDet", #9
                     "RelDet", #10
                     "NoRelChange", #11
                     "NoRelChange" #12
    )
  } else {
    tmpVecRCSC5 <- c("RelImpHighToHigh", #1
                     "NoRelChange", #2
                     "NoRelChange", #3
                     "RelDet", #4
                     "RelDet", #5
                     "RelDet", #6
                     "NoRelChange", #7
                     "NoRelChange", #8
                     "RelImpLowToLow", #9
                     "RelImpLowToHigh", #10
                     "NoRelChange", #11
                     "NoRelChange" #12
    ) 
  }
  tibAreas1 %>%
    mutate(RCSC5 = tmpVecRCSC5) -> tibAreas1
  
  # RCSC7 for areas: 
  if(!goodScorePos) {
    tmpVecRCSC7 <- c("RelDetHSToHS", #1
                     "NoRelChange", #2
                     "NoRelChange", #3
                     "RelImpHSToHS", #4
                     "RelImpHSToNHS", #5
                     "RelImpNHSToNHS", #6
                     "NoRelChange", #7
                     "NoRelChange", #8
                     "RelDetNHSToNHS", #9
                     "RelDetNHSToHS", #10
                     "NoRelChange", #11
                     "NoRelChange" #12
    ) 
  } else {
    tmpVecRCSC7 <- c("RelImpNHSToNHS", #1
                     "NoRelChange", #2
                     "NoRelChange", #3
                     "RelDetNHSToNHS", #4
                     "RelDetNHSToHS", #5
                     "RelDetHSToHS", #6
                     "NoRelChange", #7
                     "NoRelChange", #8
                     "RelImpHSToHS", #9
                     "RelImpHSToNHS", #10
                     "NoRelChange", #11
                     "NoRelChange" #12
    )
  }
  tibAreas1 %>%
    mutate(RCSC7 = tmpVecRCSC7) -> tibAreas1
  
  # RCSC10 for areas: 
  if(!goodScorePos) {
    tmpVecRCSC10 <- c("RelDetHSToHS",  #1 
                      "NoRelChangeHSToHS", #2 
                      "NoRelChangeHSToHS", #3
                      "RelImpHSToHS", #4
                      "RelImpHSToNHS", #5
                      "RelImpNHSToNHS", #6
                      "NoRelChangeNHSToNHS", #7
                      "NoRelChangeNHSToNHS", #8
                      "RelDetNHSToNHS", #9
                      "RelDetNHSToHS",  #10,
                      "NoRelChangeNHSToHS", #11
                      # and finally for #12
                      "NoRelChangeHSToNHS")
  } else {
    tmpVecRCSC10 <- c("RelImpNHSToNHS",  #1 
                      "NoRelChangeNHSToNHS", #2 
                      "NoRelChangeNHSToNHS", #3
                      "RelDetNHSToNHS", #4
                      "RelDetNHSToHS", #5
                      "RelDetHSToHS", #6
                      "NoRelChangeHSToHS", #7
                      "NoRelChangeHSToHS", #8
                      "RelImpHSToHS", #9
                      "RelImpHSToNHS",  #10,
                      "NoRelChangeHSToNHS", #11
                      # and finally for #12
      "NoRelChangeNHSToHS")
  }
  tibAreas1 %>%
    mutate(RCSC10 = tmpVecRCSC10) -> tibAreas1
  
  ### get names in correct order
  tibAreas1 %>%
    pull(namePolygon) -> vecAreas
  tibAreas1 %>%
    mutate(namePolygon = ordered(namePolygon,
                                 levels = vecAreas,
                                 labels = vecAreas)) -> tibAreas1
  
  ### use that to build the 12 tiling polygons
  ### I've done this rather clumsily, longhand!
  # 1 relDetHighToHigh
  dfPolygonRelDetHighToHigh <- data.frame(x = c(CSC,       maxPossScore - RCI, CSC),
                                          y = c(CSC + RCI, maxPossScore,       maxPossScore))
  # 2 noRelChangeDetHighToHigh
  dfPolygonNoRelChangeDetHighToHigh <- data.frame(x = c(CSC, maxPossScore, maxPossScore - RCI, CSC),
                                                  y = c(CSC,  maxPossScore, maxPossScore, CSC + RCI))
  # 3 noRelChangeImpHighToHigh
  dfPolygonNoRelChangeImpHighToHigh <- data.frame(x = c(CSC, CSC + RCI, maxPossScore,       maxPossScore),
                                                  y = c(CSC, CSC,       maxPossScore - RCI, maxPossScore))
  # 4 relImpHighToHigh
  dfPolygonRelImpHighToHigh <- data.frame(x = c(CSC + RCI, maxPossScore, maxPossScore),
                                          y = c(CSC,       CSC,          maxPossScore - RCI))
  # 5 relImpHighToLow
  dfPolygonRelImpHighToLow <- data.frame(x = c(CSC,          CSC,       CSC + RCI, maxPossScore, maxPossScore),
                                         y = c(minPossScore, CSC - RCI, CSC,       CSC,          minPossScore))
  # 6 relImpLowToLow
  dfPolygonRelImpLowToLow <- data.frame(x = c(minPossScore + RCI, CSC,                CSC),
                                        y = c(minPossScore,       minPossScore, CSC - RCI))
  # 7 noRelChangeImpLowToLow
  dfPolygonNoRelChangeImpLowToLow <- data.frame(x = c(minPossScore, minPossScore + RCI, CSC, CSC),
                                                y = c(minPossScore, minPossScore,       CSC - RCI, CSC))
  # 8 noRelChangeDetLowToLow
  dfPolygonNoRelChangeDetLowToLow <- data.frame(x = c(minPossScore, CSC, CSC - RCI, minPossScore),
                                                y = c(minPossScore, CSC, CSC,       RCI))
  # 9 relDetLowToLow
  dfPolygonRelDetLowToLow <- data.frame(x = c(minPossScore, CSC - RCI, minPossScore),
                                        y = c(RCI,          CSC,       CSC))
  # 10 relDetLowToHigh
  dfPolygonRelDetLowToHigh <- data.frame(x = c(minPossScore, CSC - RCI, CSC,       CSC,          minPossScore),
                                         y = c(CSC,          CSC,       CSC + RCI, maxPossScore, maxPossScore))
  # 11 noRelChangeDetLowToHigh
  dfPolygonNoRelChangeDetLowToHigh <- data.frame(x = c(CSC - RCI, CSC, CSC),
                                                 y = c(CSC,       CSC, CSC + RCI))
  # 12 noRelChangeImpHighToLow
  dfPolygonNoRelChangeImpHighToLow <- data.frame(x = c(CSC,       CSC, CSC + RCI),
                                                 y = c(CSC - RCI, CSC, CSC))
  
  tibAreas1 %>%
    rowwise() %>%
    mutate(nameFile = paste0("dfPolygon", namePolygon),
           tmpList = list(get(nameFile))) %>%
    ungroup() %>%
    unnest(tmpList) %>%
    group_by(iPolygon) %>%
    mutate(xCentre = mean(x),
           yCentre = mean(y)) %>%
    ungroup() %>%
    select(-nameFile) -> tibAreas
  ### finished creating tibAreas
  ###
  ### area schemes
  ###
  ### default is to use same alpha for all 12 areas
  vec12alphas <- rep(areaAlpha, 12)
  if(areaColourScheme == "NONE") {
    areaColourScheme <- "ALLWHITE"
    vec12colours <- rep("white", 12)
    vecAreaColours <- vec12colours
    vecAreaLabels <- rep("", 12)
    tibAreas %>%
      mutate(Areas = "") -> tibAreas
  }
  if(areaColourScheme == "POLYGONS") {
    tibAreas %>%
      ### set the variable to use for the areas
      mutate(Areas = namePolygon) -> tibAreas
    vecAreaColours <- c("#8DD3C7", "#FFFFB3", "#BEBADA", 
                        "#FB8072", "#80B1D3", "#FDB462",
                        "#B3DE69", "#FCCDE5", "#D9D9D9", 
                        "#BC80BD", "#CCEBC5", "#FFED6F")
    ### now the area legend labels
    vecAreaLabels <- vecAreas
  }
  if(areaColourScheme == "DIRECTION") {
    tibAreas %>%
      ### set the variable to use for the areas
      mutate(Areas = direction) -> tibAreas
    vecAreaColours <- coloursDirection
    names(vecAreaColours) <- c("Det", "Imp", "NoChange")
    ### now the legend label
    vecAreaLabels <- labelsDirection
    names(vecAreaLabels) <- c("Det", "Imp", "NoChange")
  }
  if(areaColourScheme == "RCI3") {
    tibAreas %>%
      ### set the variable to use for the Areas
      mutate(Areas = RCI) -> tibAreas
    vecAreaColours <- coloursRCI3
    ### now the legend labels
    vecAreaLabels <- labelsRCI3
    ### and name the colours
    names(vecAreaColours) <- c("NoRelChange", "RelDet", "RelImp")
  }
  if(areaColourScheme == "CSC4") {
    tibAreas %>%
      ### set the variable to use for the Areas
      mutate(Areas = CSC4) -> tibAreas
    vecAreaColours <- coloursCSC4
    names(vecAreaColours) <- c("HighToLow", "LowToHigh", "StayedHigh", "StayedLow")
    ### now the legend label
    vecAreaLabels <- labelsCSC4
    names(vecAreaLabels) <- c("HighToLow", "LowToHigh", "StayedHigh", "StayedLow")
    if(goodScorePos) {
      vecAreaColours <- coloursCSC4
      names(vecAreaColours) <- c("LowToHigh", "HighToLow", "StayedLow", "StayedHigh")
    }
  }  
  
  if(areaColourScheme == "RCSC5") {
    tibAreas %>%
      ### set the variable to use for the areas
      mutate(Areas = RCSC5) -> tibAreas
    vecAreaColours <- coloursRCSC5
    ### now the legend labels
    vecAreaLabels <- labelsRCSC5
    if (goodScorePos) {
      vecAreaLabels <- labelsRCSC5pos
    }
  }  
  if(areaColourScheme == "RCSC7") {
    ### set the order of the colours
    orderColours <- c("NoRelChange",
                      "RelDetHSToHS",
                      "RelDetNHSToHS",
                      "RelDetNHSToNHS",
                      "RelImpHSToHS",
                      "RelImpHSToNHS",
                      "RelImpNHSToNHS")
    tibAreas %>%
      ### set the variable to use for the areas
      mutate(Areas = RCSC7) -> tibAreas
    vecAreaColours <- coloursRCSC7
    names(vecAreaColours) <- orderColours
    ### now the legend labels
    vecAreaLabels <- labelsRCSC7
    names(vecAreaLabels) <- orderColours
    if (goodScorePos) {
      vecAreaLabels <- labelsRCSC7pos
      names(vecAreaLabels) <- orderColours
    }
  }  
  if(areaColourScheme == "RCSC10") {
    ### set order for colours
    orderColours <- c("NoRelChangeHSToHS",
                      "NoRelChangeHSToNHS",
                      "NoRelChangeNHSToHS",
                      "NoRelChangeNHSToNHS",
                      "RelDetHSToHS",
                      "RelDetNHSToHS",
                      "RelDetNHSToNHS",
                      "RelImpHSToHS",
                      "RelImpHSToNHS",
                      "RelImpNHSToNHS")
    tibAreas %>%
      ### set the variable to use for the areas
      mutate(Areas = RCSC10) -> tibAreas
    vecAreaColours <- coloursRCSC10
    names(vecAreaColours) <- orderColours
    ### now the legend label
    vecAreaLabels <- labelsRCSC10
    names(vecAreaLabels) <- orderColours
    if (goodScorePos) {
      vecAreaLabels <- labelsRCSC10pos
      names(vecAreaLabels) <- orderColours
    }
  }  
  
  ###
  ### line types
  ###
  if (is.null(lineTypeCSC)) {
    lineTypeCSC = 1
  }
  if (is.null(lineTypeNoChange)) {
    lineTypeNoChange = 1
  }
  if (is.null(lineTypeRCI)) {
    lineTypeRCI = 1
  }
  ### line colours
  if (is.null(lineColourCSC)) {
    lineColourCSC = 1
  }
  if (is.null(lineColourNoChange)) {
    lineColourNoChange = 1
  }
  if (is.null(lineColourRCI)) {
    lineColourRCI = 1
  }
  ### line widths
  if (is.null(lineWidthCSC)) {
    lineWidthCSC = .4
  }
  if (is.null(lineWidthNoChange)) {
    lineWidthNoChange = .4
  }
  if (is.null(lineWidthRCI)) {
    lineWidthRCI = .4
  }
  
  ###
  ### axis labels
  ###
  if(is.null(xLab)) {
    xLab <- "Baseline score"
  }
  if(is.null(yLab)) {
    yLab <- "Last score"
  }
  if(is.null(title)) {
    title <- "Jacobson plot"
  }

  
  ###
  ### set point colours 
  ###
  if(pointColourScheme == "NONE") {
    tmpTib %>%
      ### set the variable to use for the points
      mutate(Points = "black") -> tmpTib
    
    vecPointColours <- rep("black", 3)
    names(vecPointColours) <- rep("black", 3)
    ### now the legend labels
    if (pointShapeScheme == "DIRECTION") {
      vecPointLabels <- c("No change", "Deterioration", "Improvement")
    } else {
      vecPointLabels <- c("No reliable change", "Reliable deterioration", "Reliable improvement")
    }
  }
  if(pointColourScheme == "DIRECTION") {
    tmpTib %>%
      ### set the variable to use for the points
      mutate(Points = direction3) -> tmpTib
    vecPointColours <- coloursDirection
    names(vecPointColours) <- c("Det", "Imp", "NoChange")
    ### now the legend labels
    vecPointLabels <- labelsDirection
    names(vecPointLabels) <- c("Det", "Imp", "NoChange")
  }
  if(pointColourScheme == "RCI3") {
    tmpTib %>%
      ### set the variable to use for the points
      mutate(Points = RCIchange) -> tmpTib
    vecPointColours <- coloursRCI3
    names(vecPointColours) <- c("NoRelChange", "RelDet", "RelImp")
    ### now the legend label
    vecPointLabels <- labelsRCI3
    names(vecPointLabels) <- c("NoRelChange", "RelDet", "RelImp")
  }
  
  if(pointColourScheme == "CSC4") {
    tmpTib %>%
      ### set the variable to use for the points
      mutate(Points = CSC4) -> tmpTib
    vecPointColours <- coloursCSC4
    names(vecPointColours) <- c("HSToNHS", "NHSToHS", "HSToHS", "NHSToNHS")
    ### now the legend label
    vecPointLabels <- labelsCSC4 
    names(vecPointLabels) <- c("HSToNHS", "NHSToHS", "HSToHS", "NHSToNHS")
  }  
  
  if(pointColourScheme == "RCSC5") {
    tmpTib %>%
      ### set the variable to use for the points
      mutate(Points = RCSC5) -> tmpTib
    ### create vector of levels for negative cueing
    vecPointsRCSC5 <- c("NoRelChange",
                        "RelDet",
                        "RelImpHSToHS",
                        "RelImpHSToNHS",
                        "RelImpNHSToNHS")
    ### create vector for colours
    vecPointColours <- coloursRCSC5
    ### name/label that vector
    names(vecPointColours) <- vecPointsRCSC5
    ### now the legend label
    vecPointLabels <- labelsRCSC5
    names(vecPointLabels) <- vecPointsRCSC5
    if (goodScorePos) {
      ### create vector of levels for positive cueing
      vecPointsRCSC5 <- c("NoRelChange",
                          "RelDet",
                          "RelImpNHSToNHS",
                          "RelImpHSToNHS",
                          "RelImpHSToHS")
      ### create vector for colours
      vecPointColours <- coloursRCSC5
      ### name/label that vector
      names(vecPointColours) <- vecPointsRCSC5
      ### now the legend label
      vecPointLabels <- labelsRCSC5
      names(vecPointLabels) <- vecPointsRCSC5
    }
  }
  
  if(pointColourScheme == "RCSC7") {
    tmpTib %>%
      ### set the variable to use for the points
      mutate(Points = RCSC7) -> tmpTib
    ### get vector of levels
    vecPointsRCSC7 <- c("NoRelChange",
                        "RelDetHSToHS",
                        "RelDetNHSToHS",
                        "RelDetNHSToNHS",                                         
                        "RelImpHSToHS",
                        "RelImpHSToNHS",
                        "RelImpNHSToNHS")
    vecPointsRCSC7 <- ordered(vecPointsRCSC7,
                              levels = vecPointsRCSC7,
                              labels = vecPointsRCSC7)
    ### create vector for colours
    vecPointColours <- coloursRCSC7
    ### name/label that vector as this is what ggplot uses to map colours
    names(vecPointColours) <- vecPointsRCSC7
    ### now the legend label
    if(!goodScorePos) {
      vecPointLabels <- labelsRCSC7
      names(vecPointLabels) <- vecPointsRCSC7
    } else {
      vecPointLabels <- labelsRCSC7pos
      names(vecPointLabels) <- vecPointsRCSC7  
    }
  }
  
  if(pointColourScheme == "RCSC10") {
    tmpTib %>%
      ### set the variable to use for the points
      mutate(Points = RCSC10) -> tmpTib
    ### get vector of levels
    vecPointsRCSC10 <- c("NoRelChangeHSToHS",
                         "NoRelChangeHSToNHS",
                         "NoRelChangeNHSToHS",
                         "NoRelChangeNHSToNHS",
                         "RelDetHSToHS",
                         "RelDetNHSToHS",
                         "RelDetNHSToNHS",                                         
                         "RelImpHSToHS",
                         "RelImpHSToNHS",
                         "RelImpNHSToNHS")
    if(!goodScorePos) {
      ### create vector for colours
      vecPointColours <- coloursRCSC10
      ### name/label that vector
      names(vecPointColours) <- vecPointsRCSC10
      ### similar for the legend labels
      vecPointLabels <- labelsRCSC10
      names(vecPointLabels) <- vecPointsRCSC10
    } else {
       ### create vector for colours
      vecPointColours <- coloursRCSC10
      ### name/label that vector
      names(vecPointColours) <- vecPointsRCSC10
      vecPointLabels <- labelsRCSC10pos
      names(vecPointLabels) <- vecPointsRCSC10
    }
  } 
  ### finally (!) start to build the plot    
  ggplot(data = tmpTib,
         aes(x = firstScore, y = lastScore)) +
    ### we never want a legend for alpha so kill that now 
    guides(alpha = "none") -> tmpPlot
  
  ### set background and surround colours
  if(!is.null(plotColour)) {
    # plot area
    tmpPlot +
      theme(panel.background = element_rect(fill = plotColour)) -> tmpPlot
  }
  if(!is.null(borderColour)) {
    # plot area
    tmpPlot +
      theme(plot.background = element_rect(fill = borderColour)) -> tmpPlot
  }
  
  ### plot areas 
  if (areaColourScheme != "ALLWHITE") {
    tmpPlot +
      geom_polygon(data = tibAreas,
                aes(x = x, y = y, group = namePolygon, fill = Areas),
                alpha = areaAlpha) +
      scale_fill_manual(name = legendNameAreas,
                        values = vecAreaColours,
                        labels = vecAreaLabels,
                        guide = guide_legend(order = 1)) +
      ### allow use of new scales for colour and fill later
      ggnewscale::new_scale_colour() +
      ggnewscale::new_scale_fill() -> tmpPlot
  }

  ### ### lines
  ### add leading diagonal of no change
  tmpPlot +
    geom_abline(slope = 1, intercept = 0,
                linetype = lineTypeNoChange,
                colour = lineColourNoChange,
                linewidth = lineWidthNoChange) -> tmpPlot
  
  ### put in CSC lines
  tmpPlot +
    geom_vline(xintercept = CSC,
               linetype = lineTypeCSC,
               colour = lineColourCSC,
               linewidth = lineWidthCSC) +
    geom_hline(yintercept = CSC,
               linetype = lineTypeCSC,
               colour = lineColourCSC,
               linewidth = lineWidthCSC) -> tmpPlot
  
  ### add RCI tramlines
  tmpPlot +
    geom_abline(slope = 1, intercept = -RCI,
                linetype = lineTypeRCI,
                colour = lineColourRCI,
                linewidth = lineWidthRCI) +
    geom_abline(slope = 1, intercept = RCI,
                linetype = lineTypeRCI,
                colour = lineColourRCI,
                linewidth = lineWidthRCI) -> tmpPlot
  ### generate point mapping
  ### labelled points
  if(namesNotPoints) {
    if(!nameRCIDetOnly | is.null(nameRCIDetOnly)) {
      ### only makes sense to label fewer than 50 points
      if (Complete < 50) {
        tmpPlot +
          ggrepel::geom_text_repel(aes(colour = RCIchange,
                                       label = pointNames),
                                   size = namesSize) -> tmpPlot
      } else {
        ### got fewer than 50 points so label them
        tmpPlot +
          geom_text(aes(colour = RCIchange,
                        label = pointNames),
                    size = namesSize) -> tmpPlot
      }
    }
    if (nameRCIDetOnly){
      tmpPlot +
        ggrepel::geom_text_repel(aes(colour = RCIchange,
                                     label = pointNames),
                                 size = namesSize) -> tmpPlot
    }
  }
  if (!namesNotPoints){
    ### this needs to be different if no point colour used
    if (pointColourScheme != "NONE") {
      tmpPlot +
        geom_point(data = tmpTib,
                   aes(colour = Points,
                       fill = Points,
                       shape = Shapes),
                   alpha = pointAlpha,
                   size = pointSize) -> tmpPlot
    } else {
      ### no colour scheme so:
      tmpPlot +
        geom_point(data = tmpTib,
                   aes(shape = Shapes),
                   alpha = pointAlpha,
                   size = pointSize,
                   colour = "black",
                   fill = "black") -> tmpPlot
      ### I think fill and colour will default to black OK?
    }
  }
  
  ### scales
  tmpPlot +
    scale_x_continuous(name = xLab,
                       limits = c(minPossScore, maxPossScore),
                       expand = c(0, 0) ) +
    scale_y_continuous(name = yLab,
                       limits = c(minPossScore, maxPossScore),
                       expand = c(0, 0) ) +
    ggtitle(title,
            subtitle = subtitle) +
    ### crucial setting to get square plot
    theme(aspect.ratio = 1) +
    theme(plot.title = element_text(hjust = titleJustificn),
          plot.subtitle = element_text(hjust = titleJustificn)) -> tmpPlot
  
  if(labelCSClines & !is.na(CSC)) { ### @@@
    tmpPlot +
      ### these label the CSC lines.  I'm not sure they're very  informative or aesthetic.
      geom_text(label = paste0("CSC = ",
                               CSC),
                # "\nfor last scores"),
                x = scoreRange / 70,
                y = CSC + (scoreRange / 70),
                hjust = 0,
                size = 3) +
      geom_text(label = paste0("CSC = ",
                               CSC),
                # "\nfor baseline scores"),
                x = CSC + (scoreRange / 70),
                y = maxPossScore - (scoreRange / 70),
                hjust = 0,
                size = 3) -> tmpPlot
  }
  
  ### deal with legends to plot
  
  ### noLegend trumps all then ...
  ### otherwise select by n_distinct
  ### if n_distinct > 0 only for area use fill and no other
  ### if n_distinct > 0 for area and point but not shape do fill (area) and colour (points)
  ### if n_distinct > 0 for all three 
  if (noLegend) {
    tmpPlot +
      guides(colour = "none",
             fill = "none",
             shape = "none") -> tmpPlot
  } else {
    ### do some counting to decide which guides you need and which legends
    tibAreas %>%
      summarise(nAreaColours = n_distinct(Areas)) %>%
      select(nAreaColours) %>%
      pull() -> nAreaColours
    tmpTib %>% 
      summarise(nPointColours = n_distinct(Points)) %>%
      select(nPointColours) %>%
      pull() -> nPointColours
    tmpTib %>%
      summarise(nPointShapes = n_distinct(Shapes)) %>%
      select(nPointShapes) %>%
      pull() -> nPointShapes

    if (max(nAreaColours, nPointColours, nPointShapes) == 1){
      # got no variance so no legends
      tmpPlot +
        guides(fill = "none",
               colour = "none",
               shape = "none") -> tmpPlot
    }
    if (nAreaColours > 1 & max(nPointColours, nPointShapes) == 1){
      # only got areas so legend only for fill
      ### rethink the whole setting of colour, fill & shape maps
      ### they are done by using named values in a vector
      ### name by the levels of the things you are mapping i.e. direction, RCI etc.
      ### values are values to use, i.e. colours/fills and shapes
      ### set up the named vectors when you know the schemes
      tmpPlot +
        scale_fill_manual(legendNameAreas,
                          values = vecAreaColours,
                          labels = vecAreaLabels) +
        scale_colour_manual(legendNamePoints,
                      values = vecPointColours,
                      labels = vecPointLabels) +
        guides(colour = "none",
               shape = "none") -> tmpPlot
    }
    if (nPointShapes > 1 & max(nPointColours, nAreaColours) == 1){
      # only got shapes
      tmpPlot +
        scale_shape_manual(legendNamePoints,
                           values = vecPointShapes,
                           labels = vecShapeLabels) +
        scale_fill_manual(legendNamePoints,
                    values = vecPointColours,
                    labels = vecPointLabels) +
        scale_colour_manual(legendNamePoints,
                            values = vecPointColours,
                            labels = vecPointLabels) +
        guides(colour = "none",
               fill = "none") -> tmpPlot  
    }
    if (nPointColours > 1 & max(nAreaColours, nPointShapes) == 1){
      # only got point colours
      tmpPlot +
        scale_colour_manual(legendNamePoints,
                      values = vecPointColours,
                      labels = vecPointLabels) +
        guides(fill = "none",
               shape = "none") -> tmpPlot
    }
    if (nPointShapes > 1 & nPointColours > 1 & nAreaColours == 1){
      # keep legend for colour and shape
      tmpPlot +
        scale_shape_manual(legendNamePoints,
                           values = vecPointShapes,
                           labels = vecPointLabels) +
        scale_colour_manual(legendNamePoints,
                      values = vecPointColours,
                      labels = vecPointLabels) +
        ### have to add fill as using filled points
        scale_fill_manual(legendNamePoints,
                      values = vecPointColours,
                      labels = vecPointLabels) -> tmpPlot
    }
    if (nPointShapes == 1 & nPointColours > 1 & nAreaColours > 1){
      # keep legend for fill and colour
      tmpPlot +
        scale_colour_manual(legendNamePoints,
                      values = vecPointColours,
                      labels = vecPointLabels) +
        guides(fill = "none",
               shape = "none") -> tmpPlot
    }
    if (nPointShapes > 1 & nPointColours == 1 & nAreaColours > 1){
      # using area colours and point shapes
      tmpPlot +
        scale_shape_manual(legendNamePoints,
                           values = vecPointShapes,
                           labels = vecPointLabels) +
        scale_colour_manual(legendNamePoints,
                      values = vecPointColours,
                      labels = vecPointLabels) +
        ### have to add fill as using filled points
        scale_fill_manual(legendNamePoints,
                          values = vecPointColours,
                          labels = vecPointLabels) +
        guides(fill = "none",
               colour = "none") -> tmpPlot
    }
    if (nPointShapes > 1 & nPointColours > 1 & nAreaColours > 1){
      # keep legends for all three, fill colour and shape
      tmpPlot +
        scale_shape_manual(legendNamePoints,
                           values = vecPointShapes,
                           labels = vecPointLabels) +
        scale_colour_manual(legendNamePoints,
                      values = vecPointColours,
                      labels = vecPointLabels) +
        ### have to add fill as using filled points
        scale_fill_manual(legendNamePoints,
                      values = vecPointColours,
                      labels = vecPointLabels) +
        guides(fill = "none") -> tmpPlot
        
    }
  }
  
  if(labelAllPolygons){
    tmpPlot +
      ### if labelling centroids of each polygon ...
      geom_text(data = tibAreas,
                aes(x = xCentre, y = yCentre, label = iPolygon),
                size = 4) -> tmpPlot
  }
  
  if (printVariables) {
    options(width = 240)
    ### define functions
    getClasses <- function(x){
      ### collapse classes of x
      vecClass <- class(get(x))
      if (length(vecClass) == 1) {
        return( vecClass)
      }
      vecTmp <- paste(vecClass[1 : (length(vecClass) - 1)], collapse = ", ")
      paste0(vecTmp, ", ", vecClass[length(vecClass)])
    }
    collapseVec <- function(x){
      if (is.atomic(get(x))) {
        paste(get(x), collapse = ", ")
      } else {
        "NA"
      }
    }
    descVars <- function(vec) {
      tibble(var = vec) %>%
        rowwise() %>%
        mutate(classes = getClasses(var),
               atomic = is.atomic(get(var)),
               length = if_else(atomic, as.character(length(get(var))), "NA"),
               values = collapseVec(var)) %>%
        arrange(atomic, classes) %>%
        print(n = Inf)
        # flextable() %>%
        # autofit() %>%
        # print()
    }
    
    print(" ")
    print("Here are all the arguments from the call:")
    print(" ")
    print(listArgs)
    print(" ")
    print("And here are all the internal variables at the end of the function:")
    print(" ")
    vecLs <- ls()
    print(vecLs)
    print(" ")
    print("And here is the information about them")
    print(" ")
    descVars(vecLs)
    print(" ")
    # vecLs <- setdiff(vecLs, c("getJacobsonPlot", "tmpPlot"))
    # lapply(vecLs, function(x){print(get(x))})
    print("tmpTib has these columns:")
    print(colnames(tmpTib))
    print("...and these values:")
    tmpTib %>%
      print(n = Inf)
    print(" ")
    print("tibAreas has these columns:")
    print(colnames(tibAreas))
    print("... and these values:")
    tibAreas %>%
      print(n = Inf)
  }
  
  ### reset option to original if reset
  options("warn" = oldWarn)
  theme_set(oldTheme)
  ### finally, return the completed plot
  tmpPlot
}

Introduction

getJacobsonPlot() is the basic function to create a Jacobson plot (a.k.a. RCSC plot) from, at minimum, starting scores and final scores as two vectors and the minimum and maximum possible scores on the measure.

Here is an example plot using only the necessary arguments and leaving all the others at their default settings. The data are real CORE-OM data scored on the 0 to 4 scoring. I have added three points falling into categories of the RCSC5 system that didn’t occur in the real data (one reliable deterioration, stayed low, one reliable deterioration, low to high and one reliable improvement, stayed low.)

Show code
getJacobsonPlot(baselineScores = tibDat$firstScore, 
                finalScores = tibDat$lastScore, 
                CSC = 1.26, 
                RCI = 0.3983001,
                minPossScore = 0, 
                maxPossScore = 4)

So far so underwhelming: not a terribly good plot. However, what I hope makes the function really useful for a wide variety of possible users is that it can label points by their shape (for direction of change and reliable change (“RCI3”) and can label the points, and the areas of the plot, by a set of categorisations:

Probably as important as that plethora of mappings the function handles the cueing of the measure, i.e. whether high scores indicate worse or better state. Finally, the function has a large huge number of arguments to the function that enable the user to change many aspects of the plot such as colour mappings, types and thickness of lines and, though I think it’s unlikely this is ever going to be necessary, point shapes. More importantly, all the text values: title, subtitle, mapping legend names, category labels and the two axis labels have sensible defaults but all can be changed to whatever you want, in whatever language and character set, depending on your local R, you would need.

Category systems

As noted above the category systems I have implemented are:
1. Direction (i.e. just a scattergram of first and last scores labelling direction of change)

  1. RCI3: the classic threesome of reliable improvement, no reliable change and reliable deterioration

  2. CSC4: the simple CSC foursome of HighToHigh, LowToHigh, HighToLow, LowToLow

  3. The RCSC categories that use both RCI and CSC:

    • RCSC5: NoRelChange, RelDet, RelImpHighToLow (“Recovered”), RelImpHighToHigh, RelImpLowToLow (using the obvious abbreviations and assuming negatively cued measure)

    • RCSC7: RelDetHighToHigh, RelDetLowToHigh, RelDetLowToLow, NoRelChange, RelImpHighToHigh, RelImpHighToLow (“Recovered”), RelImpLowToLow

    • RCSC10: RelDetHighToHigh, RelDetLowToHigh, RelDetLowToLow, NoRelChangeHighToHigh, NoRelChangeLowToHigh, NoRelChangeHighToLow, NoRelChangeLowToLow, RelImpHighToHigh, RelImpHighToLow (“recovered”), RelImpLowToLow.

The categories can be marked on the plot by:

  1. Colouring the areas of the plot

  2. Colouring the points

  3. Changing the shapes of the points (but only for direction or for RCI3)

Cueing of the score: goodScorePos

This shows the impact of that goodScorePos argument using the same data which are actually cued negatively

Show code
getJacobsonPlot(baselineScores = tibDat$firstScore, 
             finalScores = tibDat$lastScore, 
             subtitle = "Positively cued scoring: 4 = best, 0 = worst; original data",
             CSC = 1.26, 
             RCI = 0.3983001,
             minPossScore = 0, 
             maxPossScore = 4,
             goodScorePos = TRUE,
             areaColourScheme = "DIRECTION",
             pointColourScheme = "DIRECTION",
             pointSize = 1.8)

That also introduces another argument: areaAlpha: on some screens than others the red points are visible on top of the red area but the green points are not very visible. There are two arguments that control the alpha (transparency) of the points and areas: pointAlpha and areaAlpha. The default value of pointAlpha is 1, i.e. no transparency, the default value of areaAlpha is .3, i.e. 30% transparency which for my vision system and screen at least is working for the red “deterioration” but not the green “improvement”. Let’s trying pushing the area transparency down to .1.

Show code
getJacobsonPlot(baselineScores = tibDat$firstScore, 
             finalScores = tibDat$lastScore, 
             subtitle = "Positively cued scoring: 4 = best, 0 = worst; original data",
             CSC = 1.26, 
             RCI = 0.3983001,
             minPossScore = 0, 
             maxPossScore = 4,
             goodScorePos = TRUE,
             areaColourScheme = "DIRECTION",
             pointColourScheme = "DIRECTION",
             pointSize = 1.8,
             areaAlpha = .1)

OK (at least to my visual system and monitors!) I hope that illustrates that many things can be tweaked to get better images.

Categories: direction, RCI, CSC and RCSC

Direction

Direction is the simplest. I think people are only going to use this when they have neither a usable RCI nor a usable CSC.

Show code
#1
getJacobsonPlot(baselineScores = tibDat$firstScore, 
             finalScores = tibDat$lastScore, 
             title = "Direction categories, by point colour",
             subtitle = "",
             CSC = 1.26, 
             RCI = 0.3983001,
             minPossScore = 0, 
             maxPossScore = 4,
             goodScorePos = FALSE,
             pointColourScheme = "DIRECTION",
             areaColourScheme = "NONE",
             pointSize = 1.7,
             lineTypeCSC = 0,
             lineTypeRCI = 0) -> tmpPlot1
tmpPlot1
Show code
#2
getJacobsonPlot(baselineScores = tibDat$firstScore, 
             finalScores = tibDat$lastScore, 
             title = "Direction categories, by area colour",
             subtitle = "",
             CSC = 1.26, 
             RCI = 0.3983001,
             minPossScore = 0, 
             maxPossScore = 4,
             goodScorePos = FALSE,
             pointColourScheme = "NONE",
             areaColourScheme = "DIRECTION",
             pointSize = 1.7,
             lineTypeCSC = 0,
             lineTypeRCI = 0) -> tmpPlot2
tmpPlot2

That shows one slightly counterintuitive issue: when mapping direction of change by point there are three categories: deteriorated, unchanged and improved but if mapping by the area of the plot there are only two categories as the unchanged points don’t lie in either area but on the boundary between the areas.

Show code
#3
getJacobsonPlot(baselineScores = tibDat$firstScore, 
             finalScores = tibDat$lastScore, 
             title = "Direction categories, by point shapes",
             subtitle = "",
             CSC = 1.26, 
             RCI = 0.3983001,
             minPossScore = 0, 
             maxPossScore = 4,
             goodScorePos = FALSE,
             pointColourScheme = "NONE",
             areaColourScheme = "NONE",
             pointShapeScheme = "DIRECTION",
             pointSize = 1.7,
             lineTypeCSC = 0,
             lineTypeRCI = 0) -> tmpPlot3
tmpPlot3
Show code
#4
getJacobsonPlot(baselineScores = tibDat$firstScore, 
             finalScores = tibDat$lastScore, 
             title = "Direction categories, by point and area colours",
             subtitle = "Default alpha (transparency) for area and point\nallows points to be seen on same colour areas",
             CSC = 1.26, 
             RCI = 0.3983001,
             minPossScore = 0, 
             maxPossScore = 4,
             goodScorePos = FALSE,
             pointColourScheme = "DIRECTION",
             areaColourScheme = "DIRECTION",
             pointShapeScheme = "NONE",
             pointSize = 1.7,
             lineTypeCSC = 0,
             lineTypeRCI = 0) -> tmpPlot4
tmpPlot4
Show code
#5
getJacobsonPlot(baselineScores = tibDat$firstScore, 
             finalScores = tibDat$lastScore, 
             title = "Direction categories, by area colours and point shapes",
             subtitle = "",
             CSC = 1.26, 
             RCI = 0.3983001,
             minPossScore = 0, 
             maxPossScore = 4,
             goodScorePos = FALSE,
             pointColourScheme = "NONE",
             areaColourScheme = "DIRECTION",
             pointShapeScheme = "DIRECTION",
             pointSize = 1.7,
             lineTypeCSC = 0,
             lineTypeRCI = 0) -> tmpPlot5
tmpPlot5
Show code
#6
getJacobsonPlot(baselineScores = tibDat$firstScore, 
             finalScores = tibDat$lastScore, 
             title = "Direction categories, by point colours and shapes",
             subtitle = "",
             CSC = 1.26, 
             RCI = 0.3983001,
             minPossScore = 0, 
             maxPossScore = 4,
             goodScorePos = FALSE,
             pointColourScheme = "DIRECTION",
             areaColourScheme = "NONE",
             pointShapeScheme = "DIRECTION",
             pointSize = 1.7,
             lineTypeCSC = 0,
             lineTypeRCI = 0) -> tmpPlot6
tmpPlot6
Show code
#7
getJacobsonPlot(baselineScores = tibDat$firstScore, 
             finalScores = tibDat$lastScore, 
             title = "Direction categories, by area and point colours and point shapes",
             subtitle = "",
             CSC = 1.26, 
             RCI = 0.3983001,
             minPossScore = 0, 
             maxPossScore = 4,
             goodScorePos = FALSE,
             pointColourScheme = "DIRECTION",
             areaColourScheme = "DIRECTION",
             pointShapeScheme = "DIRECTION",
             pointSize = 1.5,
             lineTypeCSC = 0,
             lineTypeRCI = 0) -> tmpPlot7
tmpPlot7
Show code
# figure <- ggpubr::ggarrange(tmpPlot1, tmpPlot2, tmpPlot3,
#                             tmpPlot4, tmpPlot5, tmpPlot6, tmpPlot7,
#                     # labels = c("A", "B", "C"),
#                     ncol = 2, nrow = 4)
# figure

RCI categories “RCI3”

This is just the conventional three level RCI categorisation.

Show code
getJacobsonPlot(baselineScores = tibDat$firstScore, 
                finalScores = tibDat$lastScore, 
                title = "RCI categories, by point colour",
                subtitle = "",
                CSC = 1.26, 
                RCI = 0.3983001,
                minPossScore = 0, 
                maxPossScore = 4,
                goodScorePos = FALSE,
                pointColourScheme = "RCI3",
                areaColourScheme = "NONE",
                pointSize = 1.7,
                noLegend = FALSE) -> tmpPlot1
tmpPlot1
Show code
getJacobsonPlot(baselineScores = tibDat$firstScore, 
                finalScores = tibDat$lastScore, 
                title = "RCI categories, by area colour",
                subtitle = "",
                CSC = 1.26, 
                RCI = 0.3983001,
                minPossScore = 0, 
                maxPossScore = 4,
                goodScorePos = FALSE,
                pointColourScheme = "NONE",
                areaColourScheme = "RCI3",
                pointSize = 1.7,
                noLegend = FALSE) -> tmpPlot2
tmpPlot2
Show code
getJacobsonPlot(baselineScores = tibDat$firstScore, 
                finalScores = tibDat$lastScore, 
                title = "RCI categories, by point shapes",
                subtitle = "",
                CSC = 1.26, 
                RCI = 0.3983001,
                minPossScore = 0, 
                maxPossScore = 4,
                goodScorePos = FALSE,
                pointColourScheme = "NONE",
                areaColourScheme = "NONE",
                pointShapeScheme = "RCI3",
                pointSize = 1.7,
                noLegend = FALSE) -> tmpPlot3
tmpPlot3
Show code
getJacobsonPlot(baselineScores = tibDat$firstScore, 
                finalScores = tibDat$lastScore, 
                title = "RCI categories, by point and area colours",
                subtitle = "Default alpha (transparency) for area and point\nallows points to be seen on same colour areas",
                CSC = 1.26, 
                RCI = 0.3983001,
                minPossScore = 0, 
                maxPossScore = 4,
                goodScorePos = FALSE,
                pointColourScheme = "RCI3",
                areaColourScheme = "RCI3",
                pointShapeScheme = "NONE",
                pointSize = 1.7,
                noLegend = FALSE) -> tmpPlot4
tmpPlot4
Show code
getJacobsonPlot(baselineScores = tibDat$firstScore, 
                finalScores = tibDat$lastScore, 
                title = "RCI categories, by area colours and point shapes",
                subtitle = "",
                CSC = 1.26, 
                RCI = 0.3983001,
                minPossScore = 0, 
                maxPossScore = 4,
                goodScorePos = FALSE,
                pointColourScheme = "NONE",
                areaColourScheme = "RCI3",
                pointShapeScheme = "RCI3",
                pointSize = 1.7,
                noLegend = FALSE) -> tmpPlot5
tmpPlot5
Show code
getJacobsonPlot(baselineScores = tibDat$firstScore, 
                finalScores = tibDat$lastScore, 
                title = "RCI categories, by point colours and shapes",
                subtitle = "",
                CSC = 1.26, 
                RCI = 0.3983001,
                minPossScore = 0, 
                maxPossScore = 4,
                goodScorePos = FALSE,
                pointColourScheme = "RCI3",
                areaColourScheme = "NONE",
                pointShapeScheme = "RCI3",
                pointSize = 1.7,
                noLegend = FALSE) -> tmpPlot6
tmpPlot6
Show code
getJacobsonPlot(baselineScores = tibDat$firstScore, 
                finalScores = tibDat$lastScore, 
                title = "RCI categories, by area and point colours and point shapes",
                subtitle = "",
                CSC = 1.26, 
                RCI = 0.3983001,
                minPossScore = 0, 
                maxPossScore = 4,
                goodScorePos = FALSE,
                pointColourScheme = "RCI3",
                areaColourScheme = "RCI3",
                pointShapeScheme = "RCI3",
                pointSize = 1.5,
                noLegend = FALSE) -> tmpPlot7
tmpPlot7
Show code
# figure <- ggpubr::ggarrange(tmpPlot1, tmpPlot2, tmpPlot3,
#                             tmpPlot4, tmpPlot5, tmpPlot6, tmpPlot7,
#                             # labels = c("A", "B", "C"),
#                             ncol = 2, nrow = 4)
# figure

RCSC categories “RCSC5”

RCSC categorisations combine the RCI categories with the CSC categories giving a maximum of 10 categories (as it’s not possible to have clinically significant deterioration with reliable deterioration nor vice versa.)

I think what I am calling RCSC5 is the most commonly used RCSC categorisation which lumps all the “no reliable deterioration” and “reliable deterioration” categories, i.e. letting those RCI categories trump the CSC categories but distinguishing the three CSC categories within those showing reliable improvement and terming those who were in the reliable and clinically improved polygon as “recovered” (a term I dislike as it seems to me both to ignore the “recovery” movement and hugely overstate what we can derive from the measures we are using).

You could set pointShapeScheme to “DIRECTION” here but I think the only shape mapping to use logically is “RCI3” as that’s crucial to all the RCSC categorisations. I’ve used “RCI3” here when the title says mapping to point shape as well as area or point colour.

Show code
#1
getJacobsonPlot(baselineScores = tibDat$firstScore, 
                finalScores = tibDat$lastScore, 
                title = "RCSC5 categories, by point colour",
                subtitle = "",
                CSC = 1.26, 
                RCI = 0.3983001,
                minPossScore = 0, 
                maxPossScore = 4,
                goodScorePos = FALSE,
                pointColourScheme = "RCSC5",  # @@@@@@@
                areaColourScheme = "NONE",
                pointSize = 1.7) -> tmpPlot1
tmpPlot1
Show code
#2
getJacobsonPlot(baselineScores = tibDat$firstScore, 
                finalScores = tibDat$lastScore, 
                title = "RCSC5 categories, by area colour",
                subtitle = "",
                CSC = 1.26, 
                RCI = 0.3983001,
                minPossScore = 0, 
                maxPossScore = 4,
                goodScorePos = FALSE,
                pointColourScheme = "NONE",
                areaColourScheme = "RCSC5",
                pointSize = 1.7) -> tmpPlot2
tmpPlot2
Show code
#3
getJacobsonPlot(baselineScores = tibDat$firstScore, 
                finalScores = tibDat$lastScore, 
                title = "RCSC5 categories, by point and area colours",
                subtitle = "",
                CSC = 1.26, 
                RCI = 0.3983001,
                minPossScore = 0, 
                maxPossScore = 4,
                goodScorePos = FALSE,
                pointColourScheme = "RCSC5",
                areaColourScheme = "RCSC5",
                pointShapeScheme = "NONE",
                pointSize = 1.7) -> tmpPlot3
tmpPlot3
Show code
#4
getJacobsonPlot(baselineScores = tibDat$firstScore, 
                finalScores = tibDat$lastScore, 
                title = "RCSC5 categories, by area colours and point shapes",
                subtitle = "",
                CSC = 1.26, 
                RCI = 0.3983001,
                minPossScore = 0, 
                maxPossScore = 4,
                goodScorePos = FALSE,
                pointColourScheme = "NONE",
                areaColourScheme = "RCSC5",
                pointShapeScheme = "RCI3",
                pointSize = 1.7) -> tmpPlot4
tmpPlot4
Show code
# figure <- ggpubr::ggarrange(tmpPlot1, tmpPlot2, tmpPlot3, 
#                             tmpPlot4,  
#                             ncol = 1, nrow = 4)
# figure

RCSC categories “RCSC7”

Like what I call “RCSC5” this allows the “no reliable change” to trump the CSC categories. However, unlike RCSC5 it splits the reliably deteriorated into three categories. Again, mapping to shape here only uses the reliable change categories.

Show code
#1
getJacobsonPlot(baselineScores = tibDat$firstScore, 
                finalScores = tibDat$lastScore, 
                title = "RCSC7 categories, by point colour",
                subtitle = "",
                CSC = 1.26, 
                RCI = 0.3983001,
                minPossScore = 0, 
                maxPossScore = 4,
                goodScorePos = FALSE,
                pointColourScheme = "RCSC7",
                areaColourScheme = "NONE",
                pointSize = 1.7) -> tmpPlot1
tmpPlot1
Show code
#2
getJacobsonPlot(baselineScores = tibDat$firstScore, 
                finalScores = tibDat$lastScore, 
                title = "RCSC7 categories, by area colour",
                subtitle = "",
                CSC = 1.26, 
                RCI = 0.3983001,
                minPossScore = 0, 
                maxPossScore = 4,
                goodScorePos = FALSE,
                pointColourScheme = "NONE",
                areaColourScheme = "RCSC7",
                pointSize = 1.7) -> tmpPlot2
tmpPlot2
Show code
#3
getJacobsonPlot(baselineScores = tibDat$firstScore, 
                finalScores = tibDat$lastScore, 
                title = "RCSC7 categories, by point and area colours",
                subtitle = "",
                CSC = 1.26, 
                RCI = 0.3983001,
                minPossScore = 0, 
                maxPossScore = 4,
                goodScorePos = FALSE,
                pointColourScheme = "RCSC7",
                areaColourScheme = "RCSC7",
                pointShapeScheme = "NONE",
                pointSize = 1.7) -> tmpPlot3
tmpPlot3
Show code
# figure <- ggpubr::ggarrange(tmpPlot1, tmpPlot2, tmpPlot3, 
#                             # labels = c("A", "B", "C"),
#                             ncol = 1, nrow = 3)
# figure

RCSC categories “RCSC10”

I think this is a bit mad but I have created it! I haven’t bothered showing it coupled with direction or RCI3 by point shape as I think that really would be getting mad!

Show code
#1
getJacobsonPlot(baselineScores = tibDat$firstScore, 
                finalScores = tibDat$lastScore, 
                title = "RCSC10 categories, by point colour",
                subtitle = "",
                CSC = 1.26, 
                RCI = 0.3983001,
                minPossScore = 0, 
                maxPossScore = 4,
                goodScorePos = FALSE,
                pointColourScheme = "RCSC10",
                areaColourScheme = "NONE",
                pointSize = 1.7) -> tmpPlot1
tmpPlot1
Show code
#2
getJacobsonPlot(baselineScores = tibDat$firstScore, 
                finalScores = tibDat$lastScore, 
                title = "RCSC10 categories, by area colour",
                subtitle = "",
                CSC = 1.26, 
                RCI = 0.3983001,
                minPossScore = 0, 
                maxPossScore = 4,
                goodScorePos = FALSE,
                pointColourScheme = "NONE",
                areaColourScheme = "RCSC10",
                pointSize = 1.7) -> tmpPlot2
tmpPlot2
Show code
#4
getJacobsonPlot(baselineScores = tibDat$firstScore, 
                finalScores = tibDat$lastScore, 
                title = "RCSC10 categories, by point and area colours",
                subtitle = "",
                CSC = 1.26, 
                RCI = 0.3983001,
                minPossScore = 0, 
                maxPossScore = 4,
                goodScorePos = FALSE,
                pointColourScheme = "RCSC10",
                areaColourScheme = "RCSC10",
                pointShapeScheme = "NONE",
                pointSize = 1.7) -> tmpPlot3
tmpPlot3
Show code
# figure <- ggpubr::ggarrange(tmpPlot1, tmpPlot2, tmpPlot3, 
#                             # labels = c("A", "B", "C"),
#                             ncol = 1, nrow = 3)
# figure

All the arguments for getJacobsonPlot()

Here is the function definition showing the full set of arguments. You’ll see that most have default values. I’ll go through all the arguments below, by their groups, after demonstrating some of the category mappings.

getJacobsonPlot <- function(baselineScores, 
                          finalScores, 
                          pointNames = NA, # can be used to label points
                          namesNotPoints = FALSE, # only use labels, no points
                          nameRCIDetOnly = FALSE, # only label deteriorators
                          namesSize = 2, # sets the font size for labels
                          CSC = NA, # the CSC value to use
                          RCI = NA, # the RCI value to use
                          minPossScore = 0, 
                          maxPossScore = 4, 
                          goodScorePos = FALSE, # set to TRUE/T if a better score is positive
                          omitNHS = FALSE, # use to omit scores starting in non-help-seeking range
                          title = NULL, # to override the default title
                          subtitle = NULL, # ditto for subtitle
                          titleJustificn = .5, # centre justifies titles, 0 for L, 1 for R
                          xLab = NULL, # overrides the default x axis label 
                          yLab = NULL, # overrides the default y axis label
                          noLegend = FALSE, # removes legends for colours
                          labelCSClines = FALSE, # set to TRUE/T to label CSC lines with CSC value
                          areaColourScheme = c("NONE", # mapping to use, see notes, schemes are:
                                               "RCSC5",
                                               "DIRECTION",
                                               "RCI3",
                                               "CSC4",
                                               "RCSC7",
                                               "RCSC10",
                                               "POLYGONS"), 
                          legendNameAreas = "Area mapping", # set title for area legend
                          pointColourScheme = c("RCSC5",
                                                "RCI3",
                                                "DIRECTION",
                                                "CSC4",
                                                "RCSC7",
                                                "RCSC10",
                                                "NONE"), # chose point colour mapping, as above
                          legendNamePoints = "Point mapping", # title for point colours
                          ### now lots of mappings used by the above colour mappings
                          coloursDirection = c("red", 
                                               "green", 
                                               "black"),
                          ### you can override the labels to local choice and language
                          labelsDirection = c("Deterioration", 
                                              "Improvement", 
                                              "No change"),
                          coloursRCI3 = c("grey", 
                                          "red", 
                                          "green"),
                          labelsRCI3 = c("No reliable change", 
                                         "Reliable deterioration", 
                                         "Reliable improvement"),
                          coloursCSC4 = c("green", 
                                          "red", 
                                          "orange", 
                                          "skyblue1"),
                          labelsCSC4 = c("High to low", 
                                         "Low to high", 
                                         "Stayed high", 
                                         "Stayed low"),
                          coloursRCSC5 = c("grey", 
                                           "red", 
                                           "skyblue1", 
                                           "green", 
                                           "chartreuse4"),
                          labelsRCSC5 = c("No reliable change", 
                                          "Reliable deterioration", 
                                          "Reliable improvement, stayed high", 
                                          "Reliable improvement, high to low ('Recovered')", 
                                          "Reliable improvement, stayed low"),
                          ### it's essentially impossible to code labels for the RCSC
                          ### that would be independent of the cueing of the scores
                          ### hence different labels (but same colours and order)
                          ### for positively cued measures
                          labelsRCSC5pos = c("No reliable change", 
                                             "Reliable deterioration", 
                                             "Reliable improvement, stayed high", 
                                             "Reliable improvement, low to high ('Recovered')", 
                                             "Reliable improvement, stayed low"),
                          coloursRCSC7 = c("grey", 
                                           "orange", 
                                           "red", 
                                           "sienna2", 
                                           "palegreen", 
                                           "green", 
                                           "skyblue1"),
                          labelsRCSC7 = c("No reliable change", 
                                          "Reliable deterioration, stayed high", 
                                          "Reliable deterioration, low to high", 
                                          "Reliable deterioration, stayed low", 
                                          "Reliable improvement, stayed high", 
                                          "Reliable improvement, high to low ('Recovered')", 
                                          "Reliable improvement, stayed low"),
                          labelsRCSC7pos = c("No reliable change", 
                                             "Reliable deterioration, stayed low", 
                                             "Reliable deterioration, high to low", 
                                             "Reliable deterioration, stayed high", 
                                             "Reliable improvement, stayed low", 
                                             "Reliable improvement, low to high ('Recovered')", 
                                             "Reliable improvement, stayed high"),
                          coloursRCSC10 = c("yellow", #1
                                            "blue", #2
                                            "purple", #3
                                            "grey", #4
                                            "orange", #5
                                            "red", #6
                                            "violetred4", #7
                                            "palegreen", #8
                                            "green", #9
                                            "chartreuse4"), #10
                          labelsRCSC10 = c("No reliable change, stayed high", #1
                                           "No reliable change, high to low", #2
                                           "No reliable change, low to high", #3
                                           "No reliable change, stayed low", #4
                                           "Reliable deterioration, stayed high", #5 
                                           "Reliable deterioration, low to high", #6
                                           "Reliable deterioration, stayed low", #7
                                           "Reliable improvement, stayed high", #8
                                           "Reliable improvement, high to low ('Recovered')", #9
                                           "Reliable improvement, stayed low"), #10
                          labelsRCSC10pos = c("No reliable change, stayed low", #1p
                                              "No reliable change, low to high", #2p
                                              "No reliable change, high to low", #3p
                                              "No reliable change, stayed high", #4p
                                              "Reliable deterioration, stayed low", #5p
                                              "Reliable deterioration, low to high", #6p
                                              "Reliable deterioration, stayed high", #7p
                                              "Reliable improvement, stayed low", #8p
                                              "Reliable improvement, low to high ('Recovered')", #9p
                                              "Reliable improvement, stayed high"), #10p
                          ### you can also add mapping to point shapes
                          pointShapeScheme = c("NONE",
                                               "DIRECTION",
                                               "RCI3"),
                          ### these allow you to override the default mapping to 
                          ### a square and arrows pointing the appropriate ways
                          ### NULL leaves the default mapping in place
                          ### I really don't advise overriding these but you can!
                          pointShapeNoRelChange = NULL,
                          pointShapeRelDet = NULL,
                          pointShapeRelImp = NULL,
                          ### the following arguments control the aesthetics
                          pointSize = 1,
                          ### the default alpha settings allow both points and areas to be coloured
                          pointAlpha = 1, # 1 is no transparency, 0 is no colour
                          areaAlpha = .3, # ditto, .3 is probably OK for a pale coloured ground
                          ### aesthetics for the no-change diagonal line
                          lineTypeNoChange = 1, # default is solid line
                          lineWidthNoChange = .5, # default is ggplot default line thickness
                          lineColourNoChange = 1, # default is black
                          ### same for the CSC lines
                          lineTypeCSC = 1, 
                          lineWidthCSC = .5, 
                          lineColourCSC = 1, 
                          ### same for the RCI lines
                          lineTypeRCI = 1,
                          lineWidthRCI = .5,
                          lineColourRCI = 1,
                          themeToUse = theme_bw(), # set ggplot theme to use, unquoted
                          ### I can't imagine changing these myself but ...
                          ### these allow you to override the theme's colours
                          plotColour = NULL, # background colour of the plot area itself, e.g. "white"
                          borderColour = NULL, # and same for the border around it
                          ### you might want to use these to suppress messages and warnings
                          noMessages = FALSE, # suppress messages
                          noWarnings = FALSE, # suppress my warnings (not other R ones)
                          ### these are probably only useful to help me debug things
                          printVariables = FALSE, # will give a print out of all internal variables
                          warningsToErrors = FALSE, # makes warnings into errors, i.e. 
                          ### this is really only for someone drilling into the code
                          ### it labels all twelve area polygons with their numbers
                          labelAllPolygons = FALSE,
                          ### arguments not implemented yet
                          greyScale = FALSE # may be implemented to force B&W/greyscale

Most of those can be ignored most of the time. The required arguments are: @@@

Arguments that have defaults, hence are optional, but which you will almost certainly wish to add, changing the defaults are as follows:

Optional arguments, not for categories

Other optional arguments fall into the following categories:

The next sections run through these groups of arguments and show their impacts on the plot.

Text options

As we saw, the subtitle argument allows you to add a subtitle using the default formatting of subtitles for the theme.

Other text control arguments are the title, titleJustificn, xLab and yLab arguments.

The title argument just allows you to replace the default title with anything of your own.

The titleJustificn argument does what it says: controls the justification of the title (and subtitle actually). Why anyone might want to use right justified title beats me but I think some journals do require left justifcation so titleJustificn = 0 would get that.

The xLab and yLab allow you to override the axis labels.

In principle these text components can be in any language your local implementation of R (and perhaps your operating system) can handle.

Show code
getJacobsonPlot(baselineScores = tibDat$firstScore, 
             finalScores = tibDat$lastScore, 
             CSC = 1.26, 
             RCI = 0.3983001,
             minPossScore = 0, 
             maxPossScore = 4,
             title = "Jacobson (RCSC) plot of data from Quito clinic",
             subtitle = paste0("n = ", nrow(tibDat), " clients"),
             titleJustificn = 1,
             xLab = "CORE-OM score at first session (= assessment)",
             yLab = "Last completed CORE-OM score")

Line type options

These can be used to change the line types used for the three categories of lines on the usual Jacobson plot:

For each of these the arguments are:

So the full list of these options is: lineTypeCSC, lineColourCSC, lineWidthCSC; lineTypeNoChange, lineColourNoChange, lineWidthNoChange; and lineTypeRCI, lineColourRCI, lineWidthRCI.

Here is a truly aesthetically horrible plot has removed the RCI tramlines by using lineTypeRCI = 0, turned the CSC lines red with lineColourCSC = “red” and dotted with lineTypeCSC = 3. I suspect that these options are only really useful when making plots to use for teaching.

Show code
getJacobsonPlot(baselineScores = tibDat$firstScore, 
             finalScores = tibDat$lastScore, 
             CSC = 1.26, 
             RCI = 0.3983001,
             minPossScore = 0, 
             maxPossScore = 4,
             lineTypeCSC = 3,
             lineWidthCSC = 0,
             lineColourCSC = "red",
             lineTypeNoChange = 2,
             lineWidthNoChange = 1,
             lineColourNoChange = "blue",
             lineTypeRCI = 0,
             lineWidthRCI = 0)

Point labelling

These options are best introduced with ID labelling but the argument could be used to label points by categories, e.g gender, therapist ID etc. though the realities of the plotting area are such that any variable used here should probably be of a maximum of three characters in width. I hope to write another function to handle categories rather differently using a legend or facetting. For the moment, using the one argument, ID and category labelling are mutually exclusively options unless you create a system like “M01”, “M02” etc. for male client IDs and “F01”, “F02” for female client IDs.

The pertinent arguments are:

Show code
getJacobsonPlot(baselineScores = tibDat$firstScore, 
             finalScores = tibDat$lastScore, 
             pointNames = as.character(tibDat$id), 
             pointColourScheme = "RCI3",
             namesNotPoints = TRUE, 
             nameRCIDetOnly = FALSE, 
             # namesSize = 2, 
             CSC = 1.26, 
             RCI = 0.3983001,
             minPossScore = 0, 
             maxPossScore = 4)

That illustrates a lot of problems with labels.

This next plot maps the RCI categories to plot areas rather than to point colours to at least have all the labels in black and it uses namesSize = 5 to make isolated labels much more readable than with the default namesSize of 2. However, it illustrates the overprinting issue!

Show code
getJacobsonPlot(baselineScores = tibDat$firstScore, 
             finalScores = tibDat$lastScore, 
             pointNames = as.character(tibDat$id), 
             areaColourScheme = "RCI3",
             namesNotPoints = TRUE, 
             nameRCIDetOnly = FALSE, 
             namesSize = 5, 
             CSC = 1.26, 
             RCI = 0.3983001,
             minPossScore = 0, 
             maxPossScore = 4)

This, with an artificially reduced dataset illustrates that ID labelling could work with small datasets.

Show code
goodScorePos <- FALSE
tibDat %>% 
  ### get only real data
  filter(id < 400) %>%
  mutate(firstLastChange = lastScore - firstScore,
         direction3 = case_when(firstLastChange == 0 ~ "NoChange",
                                  goodScorePos & firstLastChange < 0 ~ "Det",
                                  goodScorePos & firstLastChange > 0 ~ "Imp",
                                  !goodScorePos & firstLastChange < 0 ~ "Imp",
                                  !goodScorePos & firstLastChange > 0 ~ "Det"),
         RCIchange = if_else(abs(firstLastChange) < RCI, "NoRelChange", paste0("Rel", direction3)),
         firstCSCstatus = case_when(!goodScorePos & firstScore >= CSC ~ "HS", 
                                    !goodScorePos & firstScore < CSC ~ "NHS",
                                    goodScorePos & firstScore < CSC ~ "HS", 
                                    goodScorePos & firstScore >= CSC ~ "NHS"),
         lastCSCstatus = case_when(!goodScorePos & lastScore >= CSC ~ "HS", 
                                   !goodScorePos & lastScore < CSC ~ "NHS",
                                   goodScorePos & lastScore < CSC ~ "HS", 
                                   goodScorePos & lastScore >= CSC ~ "NHS"),
         CSC4 = paste0(firstCSCstatus, "To", lastCSCstatus),
         RCSC5 = case_when(
           RCIchange == "NoRelChange" ~ "NoRelChange",
           RCIchange == "RelDet"  ~ "RelDet",
           RCIchange == "RelImp" & CSC4 == "HSToHS" ~ "RelImpHSToHS",
           RCIchange == "RelImp" & CSC4 == "HSToNHS" ~ "RelImpHSToNHS",
           RCIchange == "RelImp" & CSC4 == "NHSToNHS" ~ "RelImpNHSToNHS")) %>%
  ### now reduce numbers
  group_by(RCSC5) %>%
  filter(row_number() < 6) -> tmpDat

getJacobsonPlot(baselineScores = tmpDat$firstScore, 
             finalScores = tmpDat$lastScore, 
             pointNames = as.character(tmpDat$id), 
             namesNotPoints = TRUE, 
             nameRCIDetOnly = FALSE, 
             areaColourScheme = "RCI3",
             pointColourScheme = "NONE",
             namesSize = 5, 
             CSC = 1.26, 
             RCI = 0.3983001,
             minPossScore = 0, 
             maxPossScore = 4)

Here, with totally artificial age labels, is an example labelling with age. These are totally artificial ages (though the data are real but demographics removed to protect confidentiality). I set them as:

And I allocated in a ratio 3:5:2.

Show code
tibDat %>% 
  ### get only real data
  filter(id < 400) %>%
  mutate(firstLastChange = lastScore - firstScore,
         direction3 = case_when(firstLastChange == 0 ~ "NoChange",
                                  goodScorePos & firstLastChange < 0 ~ "Det",
                                  goodScorePos & firstLastChange > 0 ~ "Imp",
                                  !goodScorePos & firstLastChange < 0 ~ "Imp",
                                  !goodScorePos & firstLastChange > 0 ~ "Det"),
         RCIchange = if_else(abs(firstLastChange) < RCI, "NoRelChange", paste0("Rel", direction3)),
         firstCSCstatus = case_when(!goodScorePos & firstScore >= CSC ~ "HS", 
                                    !goodScorePos & firstScore < CSC ~ "NHS",
                                    goodScorePos & firstScore < CSC ~ "HS", 
                                    goodScorePos & firstScore >= CSC ~ "NHS"),
         lastCSCstatus = case_when(!goodScorePos & lastScore >= CSC ~ "HS", 
                                   !goodScorePos & lastScore < CSC ~ "NHS",
                                   goodScorePos & lastScore < CSC ~ "HS", 
                                   goodScorePos & lastScore >= CSC ~ "NHS"),
         CSC4 = paste0(firstCSCstatus, "To", lastCSCstatus),
         RCSC5 = case_when(
           RCIchange == "NoRelChange" ~ "NoRelChange",
           RCIchange == "RelDet"  ~ "RelDet",
           RCIchange == "RelImp" & CSC4 == "HSToHS" ~ "RelImpHSToHS",
           RCIchange == "RelImp" & CSC4 == "HSToNHS" ~ "RelImpHSToNHS",
           RCIchange == "RelImp" & CSC4 == "NHSToNHS" ~ "RelImpNHSToNHS")) %>%
  ### now reduce numbers
  group_by(RCSC5) %>%
  filter(row_number() < 21) %>%
  ungroup() -> tmpDat

tmpDat %>%
  summarise(n = n()) %>%
  pull(n) -> tmpN

tmpDat %>%
  mutate(age = sample(c(rep("E", 3),
                        rep("A", 5),
                        rep("O", 2)), 
                      tmpN,
                      replace = TRUE)) -> tmpDat

getJacobsonPlot(baselineScores = tmpDat$firstScore, 
             finalScores = tmpDat$lastScore, 
             pointNames = tmpDat$age, 
             namesNotPoints = TRUE, 
             nameRCIDetOnly = FALSE, 
             namesSize = 3.5, 
             areaColourScheme = "RCI3",
             pointColourScheme = "NONE",
             CSC = 1.26, 
             RCI = 0.3983001,
             minPossScore = 0, 
             maxPossScore = 4)

Even here with n = 65 and more pruning out of points from the usually more occupied areas of the plot, overprinting is becoming a issue.

A service may be particularly interested in the IDs of reliable deteriorators. (Though I recommend if doing clinical audit, it is best to balance looking at deteriorators by looking at a similar number of clients who showed the best improvements.) This shows the IDs of the reliable deteriorators. (The IDs above 900 are artificial ones I added to the real data to ensure that all areas of the plot had at least one point.)

Show code
getJacobsonPlot(baselineScores = tibDat$firstScore,
             finalScores = tibDat$lastScore,
             pointNames = as.character(tibDat$id),
             namesNotPoints = TRUE,
             nameRCIDetOnly = TRUE,
             namesSize = 4,
             areaColourScheme = "RCI3",
             pointColourScheme = "NONE",
             CSC = 1.26,
             RCI = 0.3983001,
             minPossScore = 0,
             maxPossScore = 4)

Point labelling options

We have already seen that the label size can be varied with namesSize. (13.xi.23: I think I should add a choice of label colour and alpha/transparency and perhaps font and font characteristics.)

Point marker options

These are pretty esoteric but these three arguments control the mapping of direction of change to point shapes

In addition there are:

13.xi.23: ouch, something is overriding the remapping of the point shapes for no change but improvement and deterioration are working. Damn!

Show code
getJacobsonPlot(baselineScores = tibDat$firstScore, 
                finalScores = tibDat$lastScore, 
                CSC = 1.26, 
                RCI = 0.3983001,
                minPossScore = 0, 
                maxPossScore = 4,
                areaColourScheme = "RCI3",
                pointColourScheme = "RCI3",
                pointShapeScheme = "RCI3",
                pointShapeNoRelChange = "*",
                pointShapeRelDet = "D",
                pointShapeRelImp = "B", 
                pointSize = 2.5)

Legend options

13.xi.23 Ouch, more to do. Need to make it possible to override the default legend labels.

So for now the only option is noLegend which defaults to FALSE, which, as this shows, simply removes any legends.

Show code
getJacobsonPlot(baselineScores = tibDat$firstScore, 
                finalScores = tibDat$lastScore, 
                CSC = 1.26, 
                RCI = 0.3983001,
                minPossScore = 0, 
                maxPossScore = 4,
                pointSize = 2,
                noLegend = TRUE)

Saving the plot

By default the function returns the plot as a ggplot object. That means that if you don’t capture the returned plot, R will usually print it to whatever default printing is current for your R session, usually to the console. However, you can capture the ggplot object and do some post-processing of it, though this is probably for R afficionados. This next example illustrates using this to change some aspects of the plot by altering theme settings. Here I have changed some text colours (why you would want to do that is of course, unclear!). Some theme changes won’t impact on the plot, at least some arguments have been used to set things like area colours.

Show code
getJacobsonPlot(baselineScores = tibDat$firstScore, 
              finalScores = tibDat$lastScore, 
              CSC = 1.26, 
              RCI = 0.3983001,
              minPossScore = 0, 
              maxPossScore = 4) -> savedPlot

savedPlot +
  theme(text = element_text(colour = "blue"),
        axis.text = element_text(colour = "red"),
        plot.title = element_text(hjust = 0), 
        plot.subtitle = element_text(hjust = 0)) 

Probably more importantly this can be used to capture the plot and send it to another print option, e.g. to print it to a PDF, jpeg, png or tiff file. (Use R help for those formats if you aren’t familiar with doing that.)

Technicalities (geek stuff)

printVariables

[This needs a lot of work.]

I have written in an argument, printVariables, a logical value which defaults to FALSE. If TRUE it will print a lot (a lot) of information about the internal state of the function which might help me debug unexpected problems. Here’s what it tells me for the default run.

Show code
getJacobsonPlot(baselineScores = tibDat$firstScore, 
                finalScores = tibDat$lastScore, 
                CSC = 1.26, 
                RCI = 0.3983001,
                minPossScore = 0, 
                maxPossScore = 4,
                printVariables = TRUE) -> savedPlot
[1] " "
[1] "Here are all the arguments from the call:"
[1] " "
$baselineScores
tibDat$firstScore

$finalScores
tibDat$lastScore

$CSC
[1] 1.26

$RCI
[1] 0.3983001

$minPossScore
[1] 0

$maxPossScore
[1] 4

$printVariables
[1] TRUE

[1] " "
[1] "And here are all the internal variables at the end of the function:"
[1] " "
  [1] "areaAlpha"                         "areaColourScheme"                  "baselineScores"                    "borderColour"                      "collapseVec"                       "coloursCSC4"                      
  [7] "coloursDirection"                  "coloursRCI3"                       "coloursRCSC10"                     "coloursRCSC5"                      "coloursRCSC7"                      "Complete"                         
 [13] "CSC"                               "descVars"                          "dfPolygonNoRelChangeDetHighToHigh" "dfPolygonNoRelChangeDetLowToHigh"  "dfPolygonNoRelChangeDetLowToLow"   "dfPolygonNoRelChangeImpHighToHigh"
 [19] "dfPolygonNoRelChangeImpHighToLow"  "dfPolygonNoRelChangeImpLowToLow"   "dfPolygonRelDetHighToHigh"         "dfPolygonRelDetLowToHigh"          "dfPolygonRelDetLowToLow"           "dfPolygonRelImpHighToHigh"        
 [25] "dfPolygonRelImpHighToLow"          "dfPolygonRelImpLowToLow"           "finalScores"                       "getClasses"                        "goodScorePos"                      "greyScale"                        
 [31] "Incomplete"                        "labelAllPolygons"                  "labelCSClines"                     "labelsCSC4"                        "labelsDirection"                   "labelsRCI3"                       
 [37] "labelsRCSC10"                      "labelsRCSC10pos"                   "labelsRCSC5"                       "labelsRCSC5pos"                    "labelsRCSC7"                       "labelsRCSC7pos"                   
 [43] "legendNameAreas"                   "legendNamePoints"                  "lineColourCSC"                     "lineColourNoChange"                "lineColourRCI"                     "lineTypeCSC"                      
 [49] "lineTypeNoChange"                  "lineTypeRCI"                       "lineWidthCSC"                      "lineWidthNoChange"                 "lineWidthRCI"                      "listArgs"                         
 [55] "maxPossScore"                      "minPossScore"                      "nameRCIDetOnly"                    "namesNotPoints"                    "namesSize"                         "nAreaColours"                     
 [61] "nHelpSeeking"                      "noLegend"                          "noMessages"                        "noWarnings"                        "nPointColours"                     "nPointShapes"                     
 [67] "oldTheme"                          "oldWarn"                           "omitNHS"                           "Original_n"                        "plotColour"                        "pointAlpha"                       
 [73] "pointColourScheme"                 "pointNames"                        "pointShape"                        "pointShapeNoRelChange"             "pointShapeRelDet"                  "pointShapeRelImp"                 
 [79] "pointShapeScheme"                  "pointSize"                         "printVariables"                    "RCI"                               "scoreRange"                        "subtitle"                         
 [85] "themeToUse"                        "tibAreas"                          "tibAreas1"                         "title"                             "titleJustificn"                    "tmpPlot"                          
 [91] "tmpTib"                            "tmpTibMissing"                     "tmpVecRCSC10"                      "tmpVecRCSC5"                       "tmpVecRCSC7"                       "vec12alphas"                      
 [97] "vec12colours"                      "vecAreaColours"                    "vecAreaLabels"                     "vecAreas"                          "vecPointColours"                   "vecPointLabels"                   
[103] "vecPointShapes"                    "vecPointsRCSC5"                    "warningsToErrors"                  "xLab"                              "yLab"                             
[1] " "
[1] "And here is the information about them"
[1] " "
# A tibble: 107 × 5
# Rowwise: 
    var                               classes                 atomic length values                                                                                                                                                              
    <chr>                             <chr>                   <lgl>  <chr>  <chr>                                                                                                                                                               
  1 dfPolygonNoRelChangeDetHighToHigh data.frame              FALSE  NA     "NA"                                                                                                                                                                
  2 dfPolygonNoRelChangeDetLowToHigh  data.frame              FALSE  NA     "NA"                                                                                                                                                                
  3 dfPolygonNoRelChangeDetLowToLow   data.frame              FALSE  NA     "NA"                                                                                                                                                                
  4 dfPolygonNoRelChangeImpHighToHigh data.frame              FALSE  NA     "NA"                                                                                                                                                                
  5 dfPolygonNoRelChangeImpHighToLow  data.frame              FALSE  NA     "NA"                                                                                                                                                                
  6 dfPolygonNoRelChangeImpLowToLow   data.frame              FALSE  NA     "NA"                                                                                                                                                                
  7 dfPolygonRelDetHighToHigh         data.frame              FALSE  NA     "NA"                                                                                                                                                                
  8 dfPolygonRelDetLowToHigh          data.frame              FALSE  NA     "NA"                                                                                                                                                                
  9 dfPolygonRelDetLowToLow           data.frame              FALSE  NA     "NA"                                                                                                                                                                
 10 dfPolygonRelImpHighToHigh         data.frame              FALSE  NA     "NA"                                                                                                                                                                
 11 dfPolygonRelImpHighToLow          data.frame              FALSE  NA     "NA"                                                                                                                                                                
 12 dfPolygonRelImpLowToLow           data.frame              FALSE  NA     "NA"                                                                                                                                                                
 13 collapseVec                       function                FALSE  NA     "NA"                                                                                                                                                                
 14 descVars                          function                FALSE  NA     "NA"                                                                                                                                                                
 15 getClasses                        function                FALSE  NA     "NA"                                                                                                                                                                
 16 tmpPlot                           gg, ggplot              FALSE  NA     "NA"                                                                                                                                                                
 17 listArgs                          list                    FALSE  NA     "NA"                                                                                                                                                                
 18 tibAreas                          tbl_df, tbl, data.frame FALSE  NA     "NA"                                                                                                                                                                
 19 tibAreas1                         tbl_df, tbl, data.frame FALSE  NA     "NA"                                                                                                                                                                
 20 tmpTib                            tbl_df, tbl, data.frame FALSE  NA     "NA"                                                                                                                                                                
 21 tmpTibMissing                     tbl_df, tbl, data.frame FALSE  NA     "NA"                                                                                                                                                                
 22 oldTheme                          theme, gg               FALSE  NA     "NA"                                                                                                                                                                
 23 themeToUse                        theme, gg               FALSE  NA     "NA"                                                                                                                                                                
 24 borderColour                      NULL                    TRUE   0      ""                                                                                                                                                                  
 25 plotColour                        NULL                    TRUE   0      ""                                                                                                                                                                  
 26 pointShapeNoRelChange             NULL                    TRUE   0      ""                                                                                                                                                                  
 27 pointShapeRelDet                  NULL                    TRUE   0      ""                                                                                                                                                                  
 28 pointShapeRelImp                  NULL                    TRUE   0      ""                                                                                                                                                                  
 29 areaColourScheme                  character               TRUE   1      "ALLWHITE"                                                                                                                                                          
 30 coloursCSC4                       character               TRUE   4      "green, red, orange, skyblue1"                                                                                                                                      
 31 coloursDirection                  character               TRUE   3      "red, green, black"                                                                                                                                                 
 32 coloursRCI3                       character               TRUE   3      "grey, red, green"                                                                                                                                                  
 33 coloursRCSC10                     character               TRUE   10     "yellow, blue, purple, grey, orange, red, violetred4, palegreen, green, chartreuse4"                                                                                
 34 coloursRCSC5                      character               TRUE   5      "grey, red, skyblue1, green, chartreuse4"                                                                                                                           
 35 coloursRCSC7                      character               TRUE   7      "grey, orange, red, sienna2, palegreen, green, skyblue1"                                                                                                            
 36 labelsCSC4                        character               TRUE   4      "High to low, Low to high, Stayed high, Stayed low"                                                                                                                 
 37 labelsDirection                   character               TRUE   3      "Deterioration, Improvement, No change"                                                                                                                             
 38 labelsRCI3                        character               TRUE   3      "No reliable change, Reliable deterioration, Reliable improvement"                                                                                                  
 39 labelsRCSC10                      character               TRUE   10     "No reliable change, stayed high, No reliable change, high to low, No reliable change, low to high, No reliable change, stayed low, Reliable deterioration, stayed …
 40 labelsRCSC10pos                   character               TRUE   10     "No reliable change, stayed low, No reliable change, low to high, No reliable change, high to low, No reliable change, stayed high, Reliable deterioration, stayed …
 41 labelsRCSC5                       character               TRUE   5      "No reliable change, Reliable deterioration, Reliable improvement, stayed high, Reliable improvement, high to low ('Recovered'), Reliable improvement, stayed low"  
 42 labelsRCSC5pos                    character               TRUE   5      "No reliable change, Reliable deterioration, Reliable improvement, stayed high, Reliable improvement, low to high ('Recovered'), Reliable improvement, stayed low"  
 43 labelsRCSC7                       character               TRUE   7      "No reliable change, Reliable deterioration, stayed high, Reliable deterioration, low to high, Reliable deterioration, stayed low, Reliable improvement, stayed hig…
 44 labelsRCSC7pos                    character               TRUE   7      "No reliable change, Reliable deterioration, stayed low, Reliable deterioration, high to low, Reliable deterioration, stayed high, Reliable improvement, stayed low…
 45 legendNameAreas                   character               TRUE   1      "Area mapping"                                                                                                                                                      
 46 legendNamePoints                  character               TRUE   1      "Point mapping"                                                                                                                                                     
 47 pointColourScheme                 character               TRUE   1      "RCSC5"                                                                                                                                                             
 48 pointNames                        character               TRUE   185    "1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43,…
 49 pointShapeScheme                  character               TRUE   1      "NONE"                                                                                                                                                              
 50 subtitle                          character               TRUE   185    "Showing 185 with first and last scores from 185 rows in the dataset;\n169 in help-seeking score range, 185 used., Showing 185 with first and last scores from 185 …
 51 title                             character               TRUE   1      "Jacobson plot"                                                                                                                                                     
 52 tmpVecRCSC10                      character               TRUE   12     "RelDetHSToHS, NoRelChangeHSToHS, NoRelChangeHSToHS, RelImpHSToHS, RelImpHSToNHS, RelImpNHSToNHS, NoRelChangeNHSToNHS, NoRelChangeNHSToNHS, RelDetNHSToNHS, RelDetN…
 53 tmpVecRCSC5                       character               TRUE   12     "RelDet, NoRelChange, NoRelChange, RelImpHighToHigh, RelImpHighToLow, RelImpLowToLow, NoRelChange, NoRelChange, RelDet, RelDet, NoRelChange, NoRelChange"           
 54 tmpVecRCSC7                       character               TRUE   12     "RelDetHSToHS, NoRelChange, NoRelChange, RelImpHSToHS, RelImpHSToNHS, RelImpNHSToNHS, NoRelChange, NoRelChange, RelDetNHSToNHS, RelDetNHSToHS, NoRelChange, NoRelCh…
 55 vec12colours                      character               TRUE   12     "white, white, white, white, white, white, white, white, white, white, white, white"                                                                                
 56 vecAreaColours                    character               TRUE   12     "white, white, white, white, white, white, white, white, white, white, white, white"                                                                                
 57 vecAreaLabels                     character               TRUE   12     ", , , , , , , , , , , "                                                                                                                                            
 58 vecAreas                          character               TRUE   12     "RelDetHighToHigh, NoRelChangeDetHighToHigh, NoRelChangeImpHighToHigh, RelImpHighToHigh, RelImpHighToLow, RelImpLowToLow, NoRelChangeImpLowToLow, NoRelChangeDetLow…
 59 vecPointColours                   character               TRUE   5      "grey, red, skyblue1, green, chartreuse4"                                                                                                                           
 60 vecPointLabels                    character               TRUE   5      "No reliable change, Reliable deterioration, Reliable improvement, stayed high, Reliable improvement, high to low ('Recovered'), Reliable improvement, stayed low"  
 61 vecPointsRCSC5                    character               TRUE   5      "NoRelChange, RelDet, RelImpHSToHS, RelImpHSToNHS, RelImpNHSToNHS"                                                                                                  
 62 xLab                              character               TRUE   1      "Baseline score"                                                                                                                                                    
 63 yLab                              character               TRUE   1      "Last score"                                                                                                                                                        
 64 Complete                          integer                 TRUE   1      "185"                                                                                                                                                               
 65 Incomplete                        integer                 TRUE   1      "0"                                                                                                                                                                 
 66 nAreaColours                      integer                 TRUE   1      "1"                                                                                                                                                                 
 67 nHelpSeeking                      integer                 TRUE   185    "169, 169, 169, 169, 169, 169, 169, 169, 169, 169, 169, 169, 169, 169, 169, 169, 169, 169, 169, 169, 169, 169, 169, 169, 169, 169, 169, 169, 169, 169, 169, 169, 16…
 68 nPointColours                     integer                 TRUE   1      "5"                                                                                                                                                                 
 69 nPointShapes                      integer                 TRUE   1      "1"                                                                                                                                                                 
 70 oldWarn                           integer                 TRUE   1      "0"                                                                                                                                                                 
 71 Original_n                        integer                 TRUE   1      "185"                                                                                                                                                               
 72 goodScorePos                      logical                 TRUE   1      "FALSE"                                                                                                                                                             
 73 greyScale                         logical                 TRUE   1      "FALSE"                                                                                                                                                             
 74 labelAllPolygons                  logical                 TRUE   1      "FALSE"                                                                                                                                                             
 75 labelCSClines                     logical                 TRUE   1      "FALSE"                                                                                                                                                             
 76 nameRCIDetOnly                    logical                 TRUE   1      "FALSE"                                                                                                                                                             
 77 namesNotPoints                    logical                 TRUE   1      "FALSE"                                                                                                                                                             
 78 noLegend                          logical                 TRUE   1      "FALSE"                                                                                                                                                             
 79 noMessages                        logical                 TRUE   1      "FALSE"                                                                                                                                                             
 80 noWarnings                        logical                 TRUE   1      "FALSE"                                                                                                                                                             
 81 omitNHS                           logical                 TRUE   1      "FALSE"                                                                                                                                                             
 82 printVariables                    logical                 TRUE   1      "TRUE"                                                                                                                                                              
 83 warningsToErrors                  logical                 TRUE   1      "FALSE"                                                                                                                                                             
 84 areaAlpha                         numeric                 TRUE   1      "0.3"                                                                                                                                                               
 85 baselineScores                    numeric                 TRUE   185    "0.5, 0.1, 1.1, 1.44117647058824, 2.17647058823529, 1.79411764705882, 1.70588235294118, 1, 1.91176470588235, 1.38235294117647, 1.73529411764706, 2.17647058823529, …
 86 CSC                               numeric                 TRUE   1      "1.26"                                                                                                                                                              
 87 finalScores                       numeric                 TRUE   185    "2, 0.7, 0.1, 1.38235294117647, 1.52941176470588, 1.02941176470588, 1.02941176470588, 0.882352941176471, 0.878787878787879, 0.852941176470588, 1.67647058823529, 1.…
 88 lineColourCSC                     numeric                 TRUE   1      "1"                                                                                                                                                                 
 89 lineColourNoChange                numeric                 TRUE   1      "1"                                                                                                                                                                 
 90 lineColourRCI                     numeric                 TRUE   1      "1"                                                                                                                                                                 
 91 lineTypeCSC                       numeric                 TRUE   1      "1"                                                                                                                                                                 
 92 lineTypeNoChange                  numeric                 TRUE   1      "1"                                                                                                                                                                 
 93 lineTypeRCI                       numeric                 TRUE   1      "1"                                                                                                                                                                 
 94 lineWidthCSC                      numeric                 TRUE   1      "0.5"                                                                                                                                                               
 95 lineWidthNoChange                 numeric                 TRUE   1      "0.5"                                                                                                                                                               
 96 lineWidthRCI                      numeric                 TRUE   1      "0.5"                                                                                                                                                               
 97 maxPossScore                      numeric                 TRUE   1      "4"                                                                                                                                                                 
 98 minPossScore                      numeric                 TRUE   1      "0"                                                                                                                                                                 
 99 namesSize                         numeric                 TRUE   1      "2"                                                                                                                                                                 
100 pointAlpha                        numeric                 TRUE   1      "1"                                                                                                                                                                 
101 pointShape                        numeric                 TRUE   1      "16"                                                                                                                                                                
102 pointSize                         numeric                 TRUE   1      "1"                                                                                                                                                                 
103 RCI                               numeric                 TRUE   1      "0.3983001"                                                                                                                                                         
104 scoreRange                        numeric                 TRUE   1      "4"                                                                                                                                                                 
105 titleJustificn                    numeric                 TRUE   1      "0.5"                                                                                                                                                               
106 vec12alphas                       numeric                 TRUE   12     "0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3"                                                                                                        
107 vecPointShapes                    numeric                 TRUE   3      "16, 16, 16"                                                                                                                                                        
[1] " "
[1] "tmpTib has these columns:"
 [1] "pointNames"      "firstScore"      "lastScore"       "goodScorePos"    "RCIcrit"         "CSCcrit"         "firstLastChange" "direction3"      "RCIchange"       "firstCSCstatus"  "lastCSCstatus"   "CSC4"            "RCSC5"          
[14] "RCSC7"           "RCSC10"          "Shapes"          "Points"         
[1] "...and these values:"
# A tibble: 185 × 17
    pointNames firstScore lastScore goodScorePos RCIcrit CSCcrit firstLastChange direction3 RCIchange   firstCSCstatus lastCSCstatus CSC4     RCSC5          RCSC7          RCSC10              Shapes  Points        
    <chr>           <dbl>     <dbl> <lgl>          <dbl>   <dbl>           <dbl> <chr>      <chr>       <chr>          <chr>         <chr>    <chr>          <chr>          <chr>               <chr>   <chr>         
  1 1               0.5       2     FALSE          0.398    1.26          1.5    Det        RelDet      NHS            HS            NHSToHS  RelDet         RelDetNHSToHS  RelDetNHSToHS       default RelDet        
  2 2               0.1       0.7   FALSE          0.398    1.26          0.6    Det        RelDet      NHS            NHS           NHSToNHS RelDet         RelDetNHSToNHS RelDetNHSToNHS      default RelDet        
  3 3               1.1       0.1   FALSE          0.398    1.26         -1      Imp        RelImp      NHS            NHS           NHSToNHS RelImpNHSToNHS RelImpNHSToNHS RelImpNHSToNHS      default RelImpNHSToNHS
  4 4               1.44      1.38  FALSE          0.398    1.26         -0.0588 Imp        NoRelChange HS             HS            HSToHS   NoRelChange    NoRelChange    NoRelChangeHSToHS   default NoRelChange   
  5 5               2.18      1.53  FALSE          0.398    1.26         -0.647  Imp        RelImp      HS             HS            HSToHS   RelImpHSToHS   RelImpHSToHS   RelImpHSToHS        default RelImpHSToHS  
  6 6               1.79      1.03  FALSE          0.398    1.26         -0.765  Imp        RelImp      HS             NHS           HSToNHS  RelImpHSToNHS  RelImpHSToNHS  RelImpHSToNHS       default RelImpHSToNHS 
  7 7               1.71      1.03  FALSE          0.398    1.26         -0.676  Imp        RelImp      HS             NHS           HSToNHS  RelImpHSToNHS  RelImpHSToNHS  RelImpHSToNHS       default RelImpHSToNHS 
  8 8               1         0.882 FALSE          0.398    1.26         -0.118  Imp        NoRelChange NHS            NHS           NHSToNHS NoRelChange    NoRelChange    NoRelChangeNHSToNHS default NoRelChange   
  9 9               1.91      0.879 FALSE          0.398    1.26         -1.03   Imp        RelImp      HS             NHS           HSToNHS  RelImpHSToNHS  RelImpHSToNHS  RelImpHSToNHS       default RelImpHSToNHS 
 10 10              1.38      0.853 FALSE          0.398    1.26         -0.529  Imp        RelImp      HS             NHS           HSToNHS  RelImpHSToNHS  RelImpHSToNHS  RelImpHSToNHS       default RelImpHSToNHS 
 11 11              1.74      1.68  FALSE          0.398    1.26         -0.0588 Imp        NoRelChange HS             HS            HSToHS   NoRelChange    NoRelChange    NoRelChangeHSToHS   default NoRelChange   
 12 12              2.18      1.58  FALSE          0.398    1.26         -0.601  Imp        RelImp      HS             HS            HSToHS   RelImpHSToHS   RelImpHSToHS   RelImpHSToHS        default RelImpHSToHS  
 13 13              1.5       1.24  FALSE          0.398    1.26         -0.265  Imp        NoRelChange HS             NHS           HSToNHS  NoRelChange    NoRelChange    NoRelChangeHSToNHS  default NoRelChange   
 14 14              2.18      2.21  FALSE          0.398    1.26          0.0241 Det        NoRelChange HS             HS            HSToHS   NoRelChange    NoRelChange    NoRelChangeHSToHS   default NoRelChange   
 15 15              2.26      1.97  FALSE          0.398    1.26         -0.294  Imp        NoRelChange HS             HS            HSToHS   NoRelChange    NoRelChange    NoRelChangeHSToHS   default NoRelChange   
 16 16              1.68      1.06  FALSE          0.398    1.26         -0.618  Imp        RelImp      HS             NHS           HSToNHS  RelImpHSToNHS  RelImpHSToNHS  RelImpHSToNHS       default RelImpHSToNHS 
 17 17              2.06      1.94  FALSE          0.398    1.26         -0.119  Imp        NoRelChange HS             HS            HSToHS   NoRelChange    NoRelChange    NoRelChangeHSToHS   default NoRelChange   
 18 18              2.56      1.03  FALSE          0.398    1.26         -1.53   Imp        RelImp      HS             NHS           HSToNHS  RelImpHSToNHS  RelImpHSToNHS  RelImpHSToNHS       default RelImpHSToNHS 
 19 19              1.15      1.15  FALSE          0.398    1.26          0      NoChange   NoRelChange NHS            NHS           NHSToNHS NoRelChange    NoRelChange    NoRelChangeNHSToNHS default NoRelChange   
 20 20              1.62      1.38  FALSE          0.398    1.26         -0.235  Imp        NoRelChange HS             HS            HSToHS   NoRelChange    NoRelChange    NoRelChangeHSToHS   default NoRelChange   
 21 21              1.68      1.56  FALSE          0.398    1.26         -0.118  Imp        NoRelChange HS             HS            HSToHS   NoRelChange    NoRelChange    NoRelChangeHSToHS   default NoRelChange   
 22 22              3.18      2.62  FALSE          0.398    1.26         -0.559  Imp        RelImp      HS             HS            HSToHS   RelImpHSToHS   RelImpHSToHS   RelImpHSToHS        default RelImpHSToHS  
 23 23              1.59      1.03  FALSE          0.398    1.26         -0.558  Imp        RelImp      HS             NHS           HSToNHS  RelImpHSToNHS  RelImpHSToNHS  RelImpHSToNHS       default RelImpHSToNHS 
 24 24              1.59      1.03  FALSE          0.398    1.26         -0.559  Imp        RelImp      HS             NHS           HSToNHS  RelImpHSToNHS  RelImpHSToNHS  RelImpHSToNHS       default RelImpHSToNHS 
 25 25              2.71      2.59  FALSE          0.398    1.26         -0.118  Imp        NoRelChange HS             HS            HSToHS   NoRelChange    NoRelChange    NoRelChangeHSToHS   default NoRelChange   
 26 26              1.53      1.24  FALSE          0.398    1.26         -0.294  Imp        NoRelChange HS             NHS           HSToNHS  NoRelChange    NoRelChange    NoRelChangeHSToNHS  default NoRelChange   
 27 27              1.85      1.62  FALSE          0.398    1.26         -0.235  Imp        NoRelChange HS             HS            HSToHS   NoRelChange    NoRelChange    NoRelChangeHSToHS   default NoRelChange   
 28 28              2.18      1.68  FALSE          0.398    1.26         -0.5    Imp        RelImp      HS             HS            HSToHS   RelImpHSToHS   RelImpHSToHS   RelImpHSToHS        default RelImpHSToHS  
 29 29              2         0.909 FALSE          0.398    1.26         -1.09   Imp        RelImp      HS             NHS           HSToNHS  RelImpHSToNHS  RelImpHSToNHS  RelImpHSToNHS       default RelImpHSToNHS 
 30 30              2.15      1.47  FALSE          0.398    1.26         -0.681  Imp        RelImp      HS             HS            HSToHS   RelImpHSToHS   RelImpHSToHS   RelImpHSToHS        default RelImpHSToHS  
 31 31              1.68      1.26  FALSE          0.398    1.26         -0.412  Imp        RelImp      HS             HS            HSToHS   RelImpHSToHS   RelImpHSToHS   RelImpHSToHS        default RelImpHSToHS  
 32 32              1.91      1.41  FALSE          0.398    1.26         -0.5    Imp        RelImp      HS             HS            HSToHS   RelImpHSToHS   RelImpHSToHS   RelImpHSToHS        default RelImpHSToHS  
 33 33              1.47      1.26  FALSE          0.398    1.26         -0.206  Imp        NoRelChange HS             HS            HSToHS   NoRelChange    NoRelChange    NoRelChangeHSToHS   default NoRelChange   
 34 34              1.82      2.21  FALSE          0.398    1.26          0.382  Det        NoRelChange HS             HS            HSToHS   NoRelChange    NoRelChange    NoRelChangeHSToHS   default NoRelChange   
 35 35              1.76      2.15  FALSE          0.398    1.26          0.382  Det        NoRelChange HS             HS            HSToHS   NoRelChange    NoRelChange    NoRelChangeHSToHS   default NoRelChange   
 36 36              1.68      1.59  FALSE          0.398    1.26         -0.0882 Imp        NoRelChange HS             HS            HSToHS   NoRelChange    NoRelChange    NoRelChangeHSToHS   default NoRelChange   
 37 37              2.32      2.24  FALSE          0.398    1.26         -0.0882 Imp        NoRelChange HS             HS            HSToHS   NoRelChange    NoRelChange    NoRelChangeHSToHS   default NoRelChange   
 38 38              1.41      1.15  FALSE          0.398    1.26         -0.265  Imp        NoRelChange HS             NHS           HSToNHS  NoRelChange    NoRelChange    NoRelChangeHSToNHS  default NoRelChange   
 39 39              2.06      1.32  FALSE          0.398    1.26         -0.735  Imp        RelImp      HS             HS            HSToHS   RelImpHSToHS   RelImpHSToHS   RelImpHSToHS        default RelImpHSToHS  
 40 40              1.82      2.27  FALSE          0.398    1.26          0.449  Det        RelDet      HS             HS            HSToHS   RelDet         RelDetHSToHS   RelDetHSToHS        default RelDet        
 41 41              1.88      1.79  FALSE          0.398    1.26         -0.0882 Imp        NoRelChange HS             HS            HSToHS   NoRelChange    NoRelChange    NoRelChangeHSToHS   default NoRelChange   
 42 42              1.29      1.47  FALSE          0.398    1.26          0.176  Det        NoRelChange HS             HS            HSToHS   NoRelChange    NoRelChange    NoRelChangeHSToHS   default NoRelChange   
 43 43              2.06      1.06  FALSE          0.398    1.26         -1      Imp        RelImp      HS             NHS           HSToNHS  RelImpHSToNHS  RelImpHSToNHS  RelImpHSToNHS       default RelImpHSToNHS 
 44 44              1.94      1.44  FALSE          0.398    1.26         -0.5    Imp        RelImp      HS             HS            HSToHS   RelImpHSToHS   RelImpHSToHS   RelImpHSToHS        default RelImpHSToHS  
 45 45              2.26      2.12  FALSE          0.398    1.26         -0.143  Imp        NoRelChange HS             HS            HSToHS   NoRelChange    NoRelChange    NoRelChangeHSToHS   default NoRelChange   
 46 46              2.12      1.12  FALSE          0.398    1.26         -1      Imp        RelImp      HS             NHS           HSToNHS  RelImpHSToNHS  RelImpHSToNHS  RelImpHSToNHS       default RelImpHSToNHS 
 47 47              1.56      1.15  FALSE          0.398    1.26         -0.412  Imp        RelImp      HS             NHS           HSToNHS  RelImpHSToNHS  RelImpHSToNHS  RelImpHSToNHS       default RelImpHSToNHS 
 48 48              2.09      1.79  FALSE          0.398    1.26         -0.294  Imp        NoRelChange HS             HS            HSToHS   NoRelChange    NoRelChange    NoRelChangeHSToHS   default NoRelChange   
 49 49              1.44      0.559 FALSE          0.398    1.26         -0.882  Imp        RelImp      HS             NHS           HSToNHS  RelImpHSToNHS  RelImpHSToNHS  RelImpHSToNHS       default RelImpHSToNHS 
 50 50              2.06      1.56  FALSE          0.398    1.26         -0.502  Imp        RelImp      HS             HS            HSToHS   RelImpHSToHS   RelImpHSToHS   RelImpHSToHS        default RelImpHSToHS  
 51 51              1.97      1.12  FALSE          0.398    1.26         -0.853  Imp        RelImp      HS             NHS           HSToNHS  RelImpHSToNHS  RelImpHSToNHS  RelImpHSToNHS       default RelImpHSToNHS 
 52 52              1.91      1.67  FALSE          0.398    1.26         -0.242  Imp        NoRelChange HS             HS            HSToHS   NoRelChange    NoRelChange    NoRelChangeHSToHS   default NoRelChange   
 53 53              2.35      0.853 FALSE          0.398    1.26         -1.5    Imp        RelImp      HS             NHS           HSToNHS  RelImpHSToNHS  RelImpHSToNHS  RelImpHSToNHS       default RelImpHSToNHS 
 54 54              2.24      2.24  FALSE          0.398    1.26          0      NoChange   NoRelChange HS             HS            HSToHS   NoRelChange    NoRelChange    NoRelChangeHSToHS   default NoRelChange   
 55 55              1.32      1.41  FALSE          0.398    1.26          0.0882 Det        NoRelChange HS             HS            HSToHS   NoRelChange    NoRelChange    NoRelChangeHSToHS   default NoRelChange   
 56 56              1.68      2.52  FALSE          0.398    1.26          0.839  Det        RelDet      HS             HS            HSToHS   RelDet         RelDetHSToHS   RelDetHSToHS        default RelDet        
 57 57              2.41      2.12  FALSE          0.398    1.26         -0.294  Imp        NoRelChange HS             HS            HSToHS   NoRelChange    NoRelChange    NoRelChangeHSToHS   default NoRelChange   
 58 58              1.5       0.941 FALSE          0.398    1.26         -0.559  Imp        RelImp      HS             NHS           HSToNHS  RelImpHSToNHS  RelImpHSToNHS  RelImpHSToNHS       default RelImpHSToNHS 
 59 59              1.24      0.971 FALSE          0.398    1.26         -0.265  Imp        NoRelChange NHS            NHS           NHSToNHS NoRelChange    NoRelChange    NoRelChangeNHSToNHS default NoRelChange   
 60 60              1.59      1.09  FALSE          0.398    1.26         -0.5    Imp        RelImp      HS             NHS           HSToNHS  RelImpHSToNHS  RelImpHSToNHS  RelImpHSToNHS       default RelImpHSToNHS 
 61 61              2         2.24  FALSE          0.398    1.26          0.235  Det        NoRelChange HS             HS            HSToHS   NoRelChange    NoRelChange    NoRelChangeHSToHS   default NoRelChange   
 62 62              1.64      1.65  FALSE          0.398    1.26          0.0107 Det        NoRelChange HS             HS            HSToHS   NoRelChange    NoRelChange    NoRelChangeHSToHS   default NoRelChange   
 63 63              2.06      1.55  FALSE          0.398    1.26         -0.513  Imp        RelImp      HS             HS            HSToHS   RelImpHSToHS   RelImpHSToHS   RelImpHSToHS        default RelImpHSToHS  
 64 64              1.82      0.882 FALSE          0.398    1.26         -0.941  Imp        RelImp      HS             NHS           HSToNHS  RelImpHSToNHS  RelImpHSToNHS  RelImpHSToNHS       default RelImpHSToNHS 
 65 65              2.18      0.853 FALSE          0.398    1.26         -1.32   Imp        RelImp      HS             NHS           HSToNHS  RelImpHSToNHS  RelImpHSToNHS  RelImpHSToNHS       default RelImpHSToNHS 
 66 66              2.15      1.03  FALSE          0.398    1.26         -1.12   Imp        RelImp      HS             NHS           HSToNHS  RelImpHSToNHS  RelImpHSToNHS  RelImpHSToNHS       default RelImpHSToNHS 
 67 67              3         1.79  FALSE          0.398    1.26         -1.21   Imp        RelImp      HS             HS            HSToHS   RelImpHSToHS   RelImpHSToHS   RelImpHSToHS        default RelImpHSToHS  
 68 68              1.56      0.971 FALSE          0.398    1.26         -0.588  Imp        RelImp      HS             NHS           HSToNHS  RelImpHSToNHS  RelImpHSToNHS  RelImpHSToNHS       default RelImpHSToNHS 
 69 69              1.76      1     FALSE          0.398    1.26         -0.758  Imp        RelImp      HS             NHS           HSToNHS  RelImpHSToNHS  RelImpHSToNHS  RelImpHSToNHS       default RelImpHSToNHS 
 70 70              1.85      1.24  FALSE          0.398    1.26         -0.618  Imp        RelImp      HS             NHS           HSToNHS  RelImpHSToNHS  RelImpHSToNHS  RelImpHSToNHS       default RelImpHSToNHS 
 71 71              2.09      1.58  FALSE          0.398    1.26         -0.515  Imp        RelImp      HS             HS            HSToHS   RelImpHSToHS   RelImpHSToHS   RelImpHSToHS        default RelImpHSToHS  
 72 72              2.15      0.882 FALSE          0.398    1.26         -1.26   Imp        RelImp      HS             NHS           HSToNHS  RelImpHSToNHS  RelImpHSToNHS  RelImpHSToNHS       default RelImpHSToNHS 
 73 73              2         1.18  FALSE          0.398    1.26         -0.824  Imp        RelImp      HS             NHS           HSToNHS  RelImpHSToNHS  RelImpHSToNHS  RelImpHSToNHS       default RelImpHSToNHS 
 74 74              3.03      1.56  FALSE          0.398    1.26         -1.47   Imp        RelImp      HS             HS            HSToHS   RelImpHSToHS   RelImpHSToHS   RelImpHSToHS        default RelImpHSToHS  
 75 75              2.38      1.94  FALSE          0.398    1.26         -0.441  Imp        RelImp      HS             HS            HSToHS   RelImpHSToHS   RelImpHSToHS   RelImpHSToHS        default RelImpHSToHS  
 76 76              2.47      1.91  FALSE          0.398    1.26         -0.561  Imp        RelImp      HS             HS            HSToHS   RelImpHSToHS   RelImpHSToHS   RelImpHSToHS        default RelImpHSToHS  
 77 77              1.85      1.48  FALSE          0.398    1.26         -0.368  Imp        NoRelChange HS             HS            HSToHS   NoRelChange    NoRelChange    NoRelChangeHSToHS   default NoRelChange   
 78 78              2.12      1.15  FALSE          0.398    1.26         -0.971  Imp        RelImp      HS             NHS           HSToNHS  RelImpHSToNHS  RelImpHSToNHS  RelImpHSToNHS       default RelImpHSToNHS 
 79 79              1.82      1.27  FALSE          0.398    1.26         -0.551  Imp        RelImp      HS             HS            HSToHS   RelImpHSToHS   RelImpHSToHS   RelImpHSToHS        default RelImpHSToHS  
 80 80              2.47      1.71  FALSE          0.398    1.26         -0.765  Imp        RelImp      HS             HS            HSToHS   RelImpHSToHS   RelImpHSToHS   RelImpHSToHS        default RelImpHSToHS  
 81 81              1.61      1.82  FALSE          0.398    1.26          0.217  Det        NoRelChange HS             HS            HSToHS   NoRelChange    NoRelChange    NoRelChangeHSToHS   default NoRelChange   
 82 82              2         1.35  FALSE          0.398    1.26         -0.647  Imp        RelImp      HS             HS            HSToHS   RelImpHSToHS   RelImpHSToHS   RelImpHSToHS        default RelImpHSToHS  
 83 83              1.85      1.32  FALSE          0.398    1.26         -0.529  Imp        RelImp      HS             HS            HSToHS   RelImpHSToHS   RelImpHSToHS   RelImpHSToHS        default RelImpHSToHS  
 84 84              1.79      1.79  FALSE          0.398    1.26          0      NoChange   NoRelChange HS             HS            HSToHS   NoRelChange    NoRelChange    NoRelChangeHSToHS   default NoRelChange   
 85 85              2.38      1.91  FALSE          0.398    1.26         -0.471  Imp        RelImp      HS             HS            HSToHS   RelImpHSToHS   RelImpHSToHS   RelImpHSToHS        default RelImpHSToHS  
 86 86              1.62      1.44  FALSE          0.398    1.26         -0.176  Imp        NoRelChange HS             HS            HSToHS   NoRelChange    NoRelChange    NoRelChangeHSToHS   default NoRelChange   
 87 87              1.53      0.909 FALSE          0.398    1.26         -0.620  Imp        RelImp      HS             NHS           HSToNHS  RelImpHSToNHS  RelImpHSToNHS  RelImpHSToNHS       default RelImpHSToNHS 
 88 88              2.47      1.74  FALSE          0.398    1.26         -0.735  Imp        RelImp      HS             HS            HSToHS   RelImpHSToHS   RelImpHSToHS   RelImpHSToHS        default RelImpHSToHS  
 89 89              2.74      2.38  FALSE          0.398    1.26         -0.353  Imp        NoRelChange HS             HS            HSToHS   NoRelChange    NoRelChange    NoRelChangeHSToHS   default NoRelChange   
 90 90              2.26      2.29  FALSE          0.398    1.26          0.0294 Det        NoRelChange HS             HS            HSToHS   NoRelChange    NoRelChange    NoRelChangeHSToHS   default NoRelChange   
 91 91              1.97      1.44  FALSE          0.398    1.26         -0.529  Imp        RelImp      HS             HS            HSToHS   RelImpHSToHS   RelImpHSToHS   RelImpHSToHS        default RelImpHSToHS  
 92 92              1.35      1.03  FALSE          0.398    1.26         -0.324  Imp        NoRelChange HS             NHS           HSToNHS  NoRelChange    NoRelChange    NoRelChangeHSToNHS  default NoRelChange   
 93 93              1.85      1.82  FALSE          0.398    1.26         -0.0294 Imp        NoRelChange HS             HS            HSToHS   NoRelChange    NoRelChange    NoRelChangeHSToHS   default NoRelChange   
 94 94              1.18      1.03  FALSE          0.398    1.26         -0.147  Imp        NoRelChange NHS            NHS           NHSToNHS NoRelChange    NoRelChange    NoRelChangeNHSToNHS default NoRelChange   
 95 95              2.12      1.53  FALSE          0.398    1.26         -0.588  Imp        RelImp      HS             HS            HSToHS   RelImpHSToHS   RelImpHSToHS   RelImpHSToHS        default RelImpHSToHS  
 96 96              1.52      1.35  FALSE          0.398    1.26         -0.162  Imp        NoRelChange HS             HS            HSToHS   NoRelChange    NoRelChange    NoRelChangeHSToHS   default NoRelChange   
 97 97              1.79      1.38  FALSE          0.398    1.26         -0.412  Imp        RelImp      HS             HS            HSToHS   RelImpHSToHS   RelImpHSToHS   RelImpHSToHS        default RelImpHSToHS  
 98 98              2.24      1.53  FALSE          0.398    1.26         -0.706  Imp        RelImp      HS             HS            HSToHS   RelImpHSToHS   RelImpHSToHS   RelImpHSToHS        default RelImpHSToHS  
 99 99              1.53      1.06  FALSE          0.398    1.26         -0.469  Imp        RelImp      HS             NHS           HSToNHS  RelImpHSToNHS  RelImpHSToNHS  RelImpHSToNHS       default RelImpHSToNHS 
100 100             1.59      1.36  FALSE          0.398    1.26         -0.225  Imp        NoRelChange HS             HS            HSToHS   NoRelChange    NoRelChange    NoRelChangeHSToHS   default NoRelChange   
101 101             1.70      1.76  FALSE          0.398    1.26          0.0677 Det        NoRelChange HS             HS            HSToHS   NoRelChange    NoRelChange    NoRelChangeHSToHS   default NoRelChange   
102 102             2         1.85  FALSE          0.398    1.26         -0.152  Imp        NoRelChange HS             HS            HSToHS   NoRelChange    NoRelChange    NoRelChangeHSToHS   default NoRelChange   
103 103             2.09      1.06  FALSE          0.398    1.26         -1.03   Imp        RelImp      HS             NHS           HSToNHS  RelImpHSToNHS  RelImpHSToNHS  RelImpHSToNHS       default RelImpHSToNHS 
104 104             2.03      1.76  FALSE          0.398    1.26         -0.272  Imp        NoRelChange HS             HS            HSToHS   NoRelChange    NoRelChange    NoRelChangeHSToHS   default NoRelChange   
105 105             1.62      1.15  FALSE          0.398    1.26         -0.478  Imp        RelImp      HS             NHS           HSToNHS  RelImpHSToNHS  RelImpHSToNHS  RelImpHSToNHS       default RelImpHSToNHS 
106 106             1.47      1.21  FALSE          0.398    1.26         -0.265  Imp        NoRelChange HS             NHS           HSToNHS  NoRelChange    NoRelChange    NoRelChangeHSToNHS  default NoRelChange   
107 107             1.79      0.971 FALSE          0.398    1.26         -0.824  Imp        RelImp      HS             NHS           HSToNHS  RelImpHSToNHS  RelImpHSToNHS  RelImpHSToNHS       default RelImpHSToNHS 
108 108             2.5       1.35  FALSE          0.398    1.26         -1.15   Imp        RelImp      HS             HS            HSToHS   RelImpHSToHS   RelImpHSToHS   RelImpHSToHS        default RelImpHSToHS  
109 109             2.09      1.24  FALSE          0.398    1.26         -0.856  Imp        RelImp      HS             NHS           HSToNHS  RelImpHSToNHS  RelImpHSToNHS  RelImpHSToNHS       default RelImpHSToNHS 
110 110             2.35      1.18  FALSE          0.398    1.26         -1.18   Imp        RelImp      HS             NHS           HSToNHS  RelImpHSToNHS  RelImpHSToNHS  RelImpHSToNHS       default RelImpHSToNHS 
111 111             2.82      2.30  FALSE          0.398    1.26         -0.520  Imp        RelImp      HS             HS            HSToHS   RelImpHSToHS   RelImpHSToHS   RelImpHSToHS        default RelImpHSToHS  
112 112             2.47      2.24  FALSE          0.398    1.26         -0.235  Imp        NoRelChange HS             HS            HSToHS   NoRelChange    NoRelChange    NoRelChangeHSToHS   default NoRelChange   
113 113             1.79      1.06  FALSE          0.398    1.26         -0.735  Imp        RelImp      HS             NHS           HSToNHS  RelImpHSToNHS  RelImpHSToNHS  RelImpHSToNHS       default RelImpHSToNHS 
114 114             1.85      1.24  FALSE          0.398    1.26         -0.618  Imp        RelImp      HS             NHS           HSToNHS  RelImpHSToNHS  RelImpHSToNHS  RelImpHSToNHS       default RelImpHSToNHS 
115 115             2.5       2.38  FALSE          0.398    1.26         -0.118  Imp        NoRelChange HS             HS            HSToHS   NoRelChange    NoRelChange    NoRelChangeHSToHS   default NoRelChange   
116 116             2.09      1.41  FALSE          0.398    1.26         -0.676  Imp        RelImp      HS             HS            HSToHS   RelImpHSToHS   RelImpHSToHS   RelImpHSToHS        default RelImpHSToHS  
117 117             1.97      1.79  FALSE          0.398    1.26         -0.176  Imp        NoRelChange HS             HS            HSToHS   NoRelChange    NoRelChange    NoRelChangeHSToHS   default NoRelChange   
118 118             1.97      1.38  FALSE          0.398    1.26         -0.594  Imp        RelImp      HS             HS            HSToHS   RelImpHSToHS   RelImpHSToHS   RelImpHSToHS        default RelImpHSToHS  
119 119             1.29      1.64  FALSE          0.398    1.26          0.342  Det        NoRelChange HS             HS            HSToHS   NoRelChange    NoRelChange    NoRelChangeHSToHS   default NoRelChange   
120 120             1.82      1.53  FALSE          0.398    1.26         -0.289  Imp        NoRelChange HS             HS            HSToHS   NoRelChange    NoRelChange    NoRelChangeHSToHS   default NoRelChange   
121 121             2.09      1.5   FALSE          0.398    1.26         -0.588  Imp        RelImp      HS             HS            HSToHS   RelImpHSToHS   RelImpHSToHS   RelImpHSToHS        default RelImpHSToHS  
122 122             1.12      1.32  FALSE          0.398    1.26          0.199  Det        NoRelChange NHS            HS            NHSToHS  NoRelChange    NoRelChange    NoRelChangeNHSToHS  default NoRelChange   
123 123             1.65      1.69  FALSE          0.398    1.26          0.0404 Det        NoRelChange HS             HS            HSToHS   NoRelChange    NoRelChange    NoRelChangeHSToHS   default NoRelChange   
124 124             1.21      1.12  FALSE          0.398    1.26         -0.0945 Imp        NoRelChange NHS            NHS           NHSToNHS NoRelChange    NoRelChange    NoRelChangeNHSToNHS default NoRelChange   
125 125             1.71      0.941 FALSE          0.398    1.26         -0.765  Imp        RelImp      HS             NHS           HSToNHS  RelImpHSToNHS  RelImpHSToNHS  RelImpHSToNHS       default RelImpHSToNHS 
126 126             2.5       1.94  FALSE          0.398    1.26         -0.559  Imp        RelImp      HS             HS            HSToHS   RelImpHSToHS   RelImpHSToHS   RelImpHSToHS        default RelImpHSToHS  
127 127             1.38      0.971 FALSE          0.398    1.26         -0.412  Imp        RelImp      HS             NHS           HSToNHS  RelImpHSToNHS  RelImpHSToNHS  RelImpHSToNHS       default RelImpHSToNHS 
128 128             2.09      1.03  FALSE          0.398    1.26         -1.06   Imp        RelImp      HS             NHS           HSToNHS  RelImpHSToNHS  RelImpHSToNHS  RelImpHSToNHS       default RelImpHSToNHS 
129 129             1.59      1.35  FALSE          0.398    1.26         -0.235  Imp        NoRelChange HS             HS            HSToHS   NoRelChange    NoRelChange    NoRelChangeHSToHS   default NoRelChange   
130 130             1.64      1.24  FALSE          0.398    1.26         -0.401  Imp        RelImp      HS             NHS           HSToNHS  RelImpHSToNHS  RelImpHSToNHS  RelImpHSToNHS       default RelImpHSToNHS 
131 131             1.85      1.85  FALSE          0.398    1.26          0      NoChange   NoRelChange HS             HS            HSToHS   NoRelChange    NoRelChange    NoRelChangeHSToHS   default NoRelChange   
132 132             1.79      1.65  FALSE          0.398    1.26         -0.147  Imp        NoRelChange HS             HS            HSToHS   NoRelChange    NoRelChange    NoRelChangeHSToHS   default NoRelChange   
133 133             1.97      1.85  FALSE          0.398    1.26         -0.118  Imp        NoRelChange HS             HS            HSToHS   NoRelChange    NoRelChange    NoRelChangeHSToHS   default NoRelChange   
134 134             2         1.59  FALSE          0.398    1.26         -0.412  Imp        RelImp      HS             HS            HSToHS   RelImpHSToHS   RelImpHSToHS   RelImpHSToHS        default RelImpHSToHS  
135 135             1.85      1.06  FALSE          0.398    1.26         -0.794  Imp        RelImp      HS             NHS           HSToNHS  RelImpHSToNHS  RelImpHSToNHS  RelImpHSToNHS       default RelImpHSToNHS 
136 136             3.03      2.97  FALSE          0.398    1.26         -0.0588 Imp        NoRelChange HS             HS            HSToHS   NoRelChange    NoRelChange    NoRelChangeHSToHS   default NoRelChange   
137 137             2.79      1.29  FALSE          0.398    1.26         -1.5    Imp        RelImp      HS             HS            HSToHS   RelImpHSToHS   RelImpHSToHS   RelImpHSToHS        default RelImpHSToHS  
138 138             2.68      1.26  FALSE          0.398    1.26         -1.41   Imp        RelImp      HS             HS            HSToHS   RelImpHSToHS   RelImpHSToHS   RelImpHSToHS        default RelImpHSToHS  
139 139             2.29      1.52  FALSE          0.398    1.26         -0.779  Imp        RelImp      HS             HS            HSToHS   RelImpHSToHS   RelImpHSToHS   RelImpHSToHS        default RelImpHSToHS  
140 140             2.21      1.41  FALSE          0.398    1.26         -0.800  Imp        RelImp      HS             HS            HSToHS   RelImpHSToHS   RelImpHSToHS   RelImpHSToHS        default RelImpHSToHS  
141 141             2.47      1.56  FALSE          0.398    1.26         -0.912  Imp        RelImp      HS             HS            HSToHS   RelImpHSToHS   RelImpHSToHS   RelImpHSToHS        default RelImpHSToHS  
142 142             1.68      1.47  FALSE          0.398    1.26         -0.206  Imp        NoRelChange HS             HS            HSToHS   NoRelChange    NoRelChange    NoRelChangeHSToHS   default NoRelChange   
143 143             1.79      1.35  FALSE          0.398    1.26         -0.441  Imp        RelImp      HS             HS            HSToHS   RelImpHSToHS   RelImpHSToHS   RelImpHSToHS        default RelImpHSToHS  
144 144             2.29      2     FALSE          0.398    1.26         -0.294  Imp        NoRelChange HS             HS            HSToHS   NoRelChange    NoRelChange    NoRelChangeHSToHS   default NoRelChange   
145 145             2.97      1.18  FALSE          0.398    1.26         -1.79   Imp        RelImp      HS             NHS           HSToNHS  RelImpHSToNHS  RelImpHSToNHS  RelImpHSToNHS       default RelImpHSToNHS 
146 146             1.97      1.21  FALSE          0.398    1.26         -0.765  Imp        RelImp      HS             NHS           HSToNHS  RelImpHSToNHS  RelImpHSToNHS  RelImpHSToNHS       default RelImpHSToNHS 
147 147             1.85      0.971 FALSE          0.398    1.26         -0.882  Imp        RelImp      HS             NHS           HSToNHS  RelImpHSToNHS  RelImpHSToNHS  RelImpHSToNHS       default RelImpHSToNHS 
148 148             2.88      2.09  FALSE          0.398    1.26         -0.794  Imp        RelImp      HS             HS            HSToHS   RelImpHSToHS   RelImpHSToHS   RelImpHSToHS        default RelImpHSToHS  
149 149             1.74      1.32  FALSE          0.398    1.26         -0.412  Imp        RelImp      HS             HS            HSToHS   RelImpHSToHS   RelImpHSToHS   RelImpHSToHS        default RelImpHSToHS  
150 150             2.47      1.97  FALSE          0.398    1.26         -0.5    Imp        RelImp      HS             HS            HSToHS   RelImpHSToHS   RelImpHSToHS   RelImpHSToHS        default RelImpHSToHS  
151 151             2.24      2.29  FALSE          0.398    1.26          0.0588 Det        NoRelChange HS             HS            HSToHS   NoRelChange    NoRelChange    NoRelChangeHSToHS   default NoRelChange   
152 152             2.41      2.24  FALSE          0.398    1.26         -0.169  Imp        NoRelChange HS             HS            HSToHS   NoRelChange    NoRelChange    NoRelChangeHSToHS   default NoRelChange   
153 153             2.03      1.26  FALSE          0.398    1.26         -0.765  Imp        RelImp      HS             HS            HSToHS   RelImpHSToHS   RelImpHSToHS   RelImpHSToHS        default RelImpHSToHS  
154 154             1.38      0.853 FALSE          0.398    1.26         -0.522  Imp        RelImp      HS             NHS           HSToNHS  RelImpHSToNHS  RelImpHSToNHS  RelImpHSToNHS       default RelImpHSToNHS 
155 155             1.35      0.971 FALSE          0.398    1.26         -0.382  Imp        NoRelChange HS             NHS           HSToNHS  NoRelChange    NoRelChange    NoRelChangeHSToNHS  default NoRelChange   
156 156             1.91      1.64  FALSE          0.398    1.26         -0.275  Imp        NoRelChange HS             HS            HSToHS   NoRelChange    NoRelChange    NoRelChangeHSToHS   default NoRelChange   
157 157             2.88      2.41  FALSE          0.398    1.26         -0.471  Imp        RelImp      HS             HS            HSToHS   RelImpHSToHS   RelImpHSToHS   RelImpHSToHS        default RelImpHSToHS  
158 158             1.44      1.03  FALSE          0.398    1.26         -0.412  Imp        RelImp      HS             NHS           HSToNHS  RelImpHSToNHS  RelImpHSToNHS  RelImpHSToNHS       default RelImpHSToNHS 
159 159             2.38      0.971 FALSE          0.398    1.26         -1.40   Imp        RelImp      HS             NHS           HSToNHS  RelImpHSToNHS  RelImpHSToNHS  RelImpHSToNHS       default RelImpHSToNHS 
160 160             2.52      2.81  FALSE          0.398    1.26          0.297  Det        NoRelChange HS             HS            HSToHS   NoRelChange    NoRelChange    NoRelChangeHSToHS   default NoRelChange   
161 161             1.53      1.39  FALSE          0.398    1.26         -0.135  Imp        NoRelChange HS             HS            HSToHS   NoRelChange    NoRelChange    NoRelChangeHSToHS   default NoRelChange   
162 162             3         2.73  FALSE          0.398    1.26         -0.273  Imp        NoRelChange HS             HS            HSToHS   NoRelChange    NoRelChange    NoRelChangeHSToHS   default NoRelChange   
163 163             1.82      1.59  FALSE          0.398    1.26         -0.235  Imp        NoRelChange HS             HS            HSToHS   NoRelChange    NoRelChange    NoRelChangeHSToHS   default NoRelChange   
164 164             1.59      1.06  FALSE          0.398    1.26         -0.529  Imp        RelImp      HS             NHS           HSToNHS  RelImpHSToNHS  RelImpHSToNHS  RelImpHSToNHS       default RelImpHSToNHS 
165 165             1.45      1.18  FALSE          0.398    1.26         -0.278  Imp        NoRelChange HS             NHS           HSToNHS  NoRelChange    NoRelChange    NoRelChangeHSToNHS  default NoRelChange   
166 166             2.66      2.36  FALSE          0.398    1.26         -0.293  Imp        NoRelChange HS             HS            HSToHS   NoRelChange    NoRelChange    NoRelChangeHSToHS   default NoRelChange   
167 167             2.53      1.53  FALSE          0.398    1.26         -1      Imp        RelImp      HS             HS            HSToHS   RelImpHSToHS   RelImpHSToHS   RelImpHSToHS        default RelImpHSToHS  
168 168             1.09      1.03  FALSE          0.398    1.26         -0.0588 Imp        NoRelChange NHS            NHS           NHSToNHS NoRelChange    NoRelChange    NoRelChangeNHSToNHS default NoRelChange   
169 169             2.41      2.32  FALSE          0.398    1.26         -0.0882 Imp        NoRelChange HS             HS            HSToHS   NoRelChange    NoRelChange    NoRelChangeHSToHS   default NoRelChange   
170 170             1         1     FALSE          0.398    1.26          0      NoChange   NoRelChange NHS            NHS           NHSToNHS NoRelChange    NoRelChange    NoRelChangeNHSToNHS default NoRelChange   
171 171             1.29      1.44  FALSE          0.398    1.26          0.147  Det        NoRelChange HS             HS            HSToHS   NoRelChange    NoRelChange    NoRelChangeHSToHS   default NoRelChange   
172 172             1.03      1.09  FALSE          0.398    1.26          0.0588 Det        NoRelChange NHS            NHS           NHSToNHS NoRelChange    NoRelChange    NoRelChangeNHSToNHS default NoRelChange   
173 173             1.91      1.18  FALSE          0.398    1.26         -0.730  Imp        RelImp      HS             NHS           HSToNHS  RelImpHSToNHS  RelImpHSToNHS  RelImpHSToNHS       default RelImpHSToNHS 
174 174             0.879     1.15  FALSE          0.398    1.26          0.273  Det        NoRelChange NHS            NHS           NHSToNHS NoRelChange    NoRelChange    NoRelChangeNHSToNHS default NoRelChange   
175 175             1.03      0.941 FALSE          0.398    1.26         -0.0882 Imp        NoRelChange NHS            NHS           NHSToNHS NoRelChange    NoRelChange    NoRelChangeNHSToNHS default NoRelChange   
176 176             1.94      1.33  FALSE          0.398    1.26         -0.608  Imp        RelImp      HS             HS            HSToHS   RelImpHSToHS   RelImpHSToHS   RelImpHSToHS        default RelImpHSToHS  
177 177             1.35      1.24  FALSE          0.398    1.26         -0.118  Imp        NoRelChange HS             NHS           HSToNHS  NoRelChange    NoRelChange    NoRelChangeHSToNHS  default NoRelChange   
178 178             1.65      1.29  FALSE          0.398    1.26         -0.353  Imp        NoRelChange HS             HS            HSToHS   NoRelChange    NoRelChange    NoRelChangeHSToHS   default NoRelChange   
179 179             3.03      1.68  FALSE          0.398    1.26         -1.35   Imp        RelImp      HS             HS            HSToHS   RelImpHSToHS   RelImpHSToHS   RelImpHSToHS        default RelImpHSToHS  
180 180             1.47      1.26  FALSE          0.398    1.26         -0.206  Imp        NoRelChange HS             HS            HSToHS   NoRelChange    NoRelChange    NoRelChangeHSToHS   default NoRelChange   
181 181             1.79      1.26  FALSE          0.398    1.26         -0.529  Imp        RelImp      HS             HS            HSToHS   RelImpHSToHS   RelImpHSToHS   RelImpHSToHS        default RelImpHSToHS  
182 182             1.88      1.41  FALSE          0.398    1.26         -0.471  Imp        RelImp      HS             HS            HSToHS   RelImpHSToHS   RelImpHSToHS   RelImpHSToHS        default RelImpHSToHS  
183 183             1.85      1.74  FALSE          0.398    1.26         -0.118  Imp        NoRelChange HS             HS            HSToHS   NoRelChange    NoRelChange    NoRelChangeHSToHS   default NoRelChange   
184 184             1.06      0.941 FALSE          0.398    1.26         -0.118  Imp        NoRelChange NHS            NHS           NHSToNHS NoRelChange    NoRelChange    NoRelChangeNHSToNHS default NoRelChange   
185 185             1         0.912 FALSE          0.398    1.26         -0.0882 Imp        NoRelChange NHS            NHS           NHSToNHS NoRelChange    NoRelChange    NoRelChangeNHSToNHS default NoRelChange   
[1] " "
[1] "tibAreas has these columns:"
 [1] "iPolygon"    "namePolygon" "RCI"         "direction"   "start"       "end"         "CSC4"        "areaAlpha"   "RCSC5"       "RCSC7"       "RCSC10"      "x"           "y"           "xCentre"     "yCentre"     "Areas"      
[1] "... and these values:"
# A tibble: 44 × 16
   iPolygon namePolygon              RCI         direction start end   CSC4       areaAlpha RCSC5            RCSC7          RCSC10                  x     y xCentre yCentre Areas
      <dbl> <ord>                    <chr>       <chr>     <chr> <chr> <chr>          <dbl> <chr>            <chr>          <chr>               <dbl> <dbl>   <dbl>   <dbl> <chr>
 1        1 RelDetHighToHigh         RelDet      Det       High  High  StayedHigh       0.3 RelDet           RelDetHSToHS   RelDetHSToHS        1.26  1.66    2.04    3.22  ""   
 2        1 RelDetHighToHigh         RelDet      Det       High  High  StayedHigh       0.3 RelDet           RelDetHSToHS   RelDetHSToHS        3.60  4       2.04    3.22  ""   
 3        1 RelDetHighToHigh         RelDet      Det       High  High  StayedHigh       0.3 RelDet           RelDetHSToHS   RelDetHSToHS        1.26  4       2.04    3.22  ""   
 4        2 NoRelChangeDetHighToHigh NoRelChange Det       High  High  StayedHigh       0.3 NoRelChange      NoRelChange    NoRelChangeHSToHS   1.26  1.26    2.53    2.73  ""   
 5        2 NoRelChangeDetHighToHigh NoRelChange Det       High  High  StayedHigh       0.3 NoRelChange      NoRelChange    NoRelChangeHSToHS   4     4       2.53    2.73  ""   
 6        2 NoRelChangeDetHighToHigh NoRelChange Det       High  High  StayedHigh       0.3 NoRelChange      NoRelChange    NoRelChangeHSToHS   3.60  4       2.53    2.73  ""   
 7        2 NoRelChangeDetHighToHigh NoRelChange Det       High  High  StayedHigh       0.3 NoRelChange      NoRelChange    NoRelChangeHSToHS   1.26  1.66    2.53    2.73  ""   
 8        3 NoRelChangeImpHighToHigh NoRelChange Imp       High  High  StayedHigh       0.3 NoRelChange      NoRelChange    NoRelChangeHSToHS   1.26  1.26    2.73    2.53  ""   
 9        3 NoRelChangeImpHighToHigh NoRelChange Imp       High  High  StayedHigh       0.3 NoRelChange      NoRelChange    NoRelChangeHSToHS   1.66  1.26    2.73    2.53  ""   
10        3 NoRelChangeImpHighToHigh NoRelChange Imp       High  High  StayedHigh       0.3 NoRelChange      NoRelChange    NoRelChangeHSToHS   4     3.60    2.73    2.53  ""   
11        3 NoRelChangeImpHighToHigh NoRelChange Imp       High  High  StayedHigh       0.3 NoRelChange      NoRelChange    NoRelChangeHSToHS   4     4       2.73    2.53  ""   
12        4 RelImpHighToHigh         RelImp      Imp       High  High  StayedHigh       0.3 RelImpHighToHigh RelImpHSToHS   RelImpHSToHS        1.66  1.26    3.22    2.04  ""   
13        4 RelImpHighToHigh         RelImp      Imp       High  High  StayedHigh       0.3 RelImpHighToHigh RelImpHSToHS   RelImpHSToHS        4     1.26    3.22    2.04  ""   
14        4 RelImpHighToHigh         RelImp      Imp       High  High  StayedHigh       0.3 RelImpHighToHigh RelImpHSToHS   RelImpHSToHS        4     3.60    3.22    2.04  ""   
15        5 RelImpHighToLow          RelImp      Imp       High  Low   HighToLow        0.3 RelImpHighToLow  RelImpHSToNHS  RelImpHSToNHS       1.26  0       2.44    0.676 ""   
16        5 RelImpHighToLow          RelImp      Imp       High  Low   HighToLow        0.3 RelImpHighToLow  RelImpHSToNHS  RelImpHSToNHS       1.26  0.862   2.44    0.676 ""   
17        5 RelImpHighToLow          RelImp      Imp       High  Low   HighToLow        0.3 RelImpHighToLow  RelImpHSToNHS  RelImpHSToNHS       1.66  1.26    2.44    0.676 ""   
18        5 RelImpHighToLow          RelImp      Imp       High  Low   HighToLow        0.3 RelImpHighToLow  RelImpHSToNHS  RelImpHSToNHS       4     1.26    2.44    0.676 ""   
19        5 RelImpHighToLow          RelImp      Imp       High  Low   HighToLow        0.3 RelImpHighToLow  RelImpHSToNHS  RelImpHSToNHS       4     0       2.44    0.676 ""   
20        6 RelImpLowToLow           RelImp      Imp       Low   Low   StayedLow        0.3 RelImpLowToLow   RelImpNHSToNHS RelImpNHSToNHS      0.398 0       0.973   0.287 ""   
21        6 RelImpLowToLow           RelImp      Imp       Low   Low   StayedLow        0.3 RelImpLowToLow   RelImpNHSToNHS RelImpNHSToNHS      1.26  0       0.973   0.287 ""   
22        6 RelImpLowToLow           RelImp      Imp       Low   Low   StayedLow        0.3 RelImpLowToLow   RelImpNHSToNHS RelImpNHSToNHS      1.26  0.862   0.973   0.287 ""   
23        7 NoRelChangeImpLowToLow   NoRelChange Imp       Low   Low   StayedLow        0.3 NoRelChange      NoRelChange    NoRelChangeNHSToNHS 0     0       0.730   0.530 ""   
24        7 NoRelChangeImpLowToLow   NoRelChange Imp       Low   Low   StayedLow        0.3 NoRelChange      NoRelChange    NoRelChangeNHSToNHS 0.398 0       0.730   0.530 ""   
25        7 NoRelChangeImpLowToLow   NoRelChange Imp       Low   Low   StayedLow        0.3 NoRelChange      NoRelChange    NoRelChangeNHSToNHS 1.26  0.862   0.730   0.530 ""   
26        7 NoRelChangeImpLowToLow   NoRelChange Imp       Low   Low   StayedLow        0.3 NoRelChange      NoRelChange    NoRelChangeNHSToNHS 1.26  1.26    0.730   0.530 ""   
27        8 NoRelChangeDetLowToLow   NoRelChange Det       Low   Low   StayedLow        0.3 NoRelChange      NoRelChange    NoRelChangeNHSToNHS 0     0       0.530   0.730 ""   
28        8 NoRelChangeDetLowToLow   NoRelChange Det       Low   Low   StayedLow        0.3 NoRelChange      NoRelChange    NoRelChangeNHSToNHS 1.26  1.26    0.530   0.730 ""   
29        8 NoRelChangeDetLowToLow   NoRelChange Det       Low   Low   StayedLow        0.3 NoRelChange      NoRelChange    NoRelChangeNHSToNHS 0.862 1.26    0.530   0.730 ""   
30        8 NoRelChangeDetLowToLow   NoRelChange Det       Low   Low   StayedLow        0.3 NoRelChange      NoRelChange    NoRelChangeNHSToNHS 0     0.398   0.530   0.730 ""   
31        9 RelDetLowToLow           RelDet      Det       Low   Low   StayedLow        0.3 RelDet           RelDetNHSToNHS RelDetNHSToNHS      0     0.398   0.287   0.973 ""   
32        9 RelDetLowToLow           RelDet      Det       Low   Low   StayedLow        0.3 RelDet           RelDetNHSToNHS RelDetNHSToNHS      0.862 1.26    0.287   0.973 ""   
33        9 RelDetLowToLow           RelDet      Det       Low   Low   StayedLow        0.3 RelDet           RelDetNHSToNHS RelDetNHSToNHS      0     1.26    0.287   0.973 ""   
34       10 RelDetLowToHigh          RelDet      Det       Low   High  LowToHigh        0.3 RelDet           RelDetNHSToHS  RelDetNHSToHS       0     1.26    0.676   2.44  ""   
35       10 RelDetLowToHigh          RelDet      Det       Low   High  LowToHigh        0.3 RelDet           RelDetNHSToHS  RelDetNHSToHS       0.862 1.26    0.676   2.44  ""   
36       10 RelDetLowToHigh          RelDet      Det       Low   High  LowToHigh        0.3 RelDet           RelDetNHSToHS  RelDetNHSToHS       1.26  1.66    0.676   2.44  ""   
37       10 RelDetLowToHigh          RelDet      Det       Low   High  LowToHigh        0.3 RelDet           RelDetNHSToHS  RelDetNHSToHS       1.26  4       0.676   2.44  ""   
38       10 RelDetLowToHigh          RelDet      Det       Low   High  LowToHigh        0.3 RelDet           RelDetNHSToHS  RelDetNHSToHS       0     4       0.676   2.44  ""   
39       11 NoRelChangeDetLowToHigh  NoRelChange Det       Low   High  LowToHigh        0.3 NoRelChange      NoRelChange    NoRelChangeNHSToHS  0.862 1.26    1.13    1.39  ""   
40       11 NoRelChangeDetLowToHigh  NoRelChange Det       Low   High  LowToHigh        0.3 NoRelChange      NoRelChange    NoRelChangeNHSToHS  1.26  1.26    1.13    1.39  ""   
41       11 NoRelChangeDetLowToHigh  NoRelChange Det       Low   High  LowToHigh        0.3 NoRelChange      NoRelChange    NoRelChangeNHSToHS  1.26  1.66    1.13    1.39  ""   
42       12 NoRelChangeImpHighToLow  NoRelChange Imp       High  Low   HighToLow        0.3 NoRelChange      NoRelChange    NoRelChangeHSToNHS  1.26  0.862   1.39    1.13  ""   
43       12 NoRelChangeImpHighToLow  NoRelChange Imp       High  Low   HighToLow        0.3 NoRelChange      NoRelChange    NoRelChangeHSToNHS  1.26  1.26    1.39    1.13  ""   
44       12 NoRelChangeImpHighToLow  NoRelChange Imp       High  Low   HighToLow        0.3 NoRelChange      NoRelChange    NoRelChangeHSToNHS  1.66  1.26    1.39    1.13  ""   

The plot areas

The plotting by area works by breaking up the plot area into the 12 areas/polygons that cover the entire RCSC plot. These are as follows, spiralling in clockwise from top to the right of the CSC (tdc: to dead centre?!)

  1. relDetHighToHigh,
  2. noRelChangeDetHighToHigh
  3. noRelChangeImpHighToHigh
  4. relImpHighToHigh
  5. relImpHighToLow (“recovered”)
  6. relImpLowToLow
  7. noRelChangeImpLowToLow
  8. noRelChangeDetLowToLow
  9. relDetLowToLow
  10. relDetLowToHigh … and now back into the two litle triangles in the middle
  11. noRelChangeDetLowToLow
  12. noRelChangeImpHighToLow

You can see these using the labelAllPolygons = TRUE argument to getJacobsonPlot()

Show code
### just to restart the plot area
# ggplot(data = tibble(x = 1:10, y = 1:10), aes(x = x, y = y)) + geom_point() + geom_line()
getJacobsonPlot(baselineScores = tibDat$firstScore, finalScores = tibDat$lastScore, 
             pointNames = as.character(tibDat$id),
             namesNotPoints = FALSE,
             namesSize = 2,
             nameRCIDetOnly = FALSE,
             CSC = 1.26,
             RCI = 0.3123851,
             minPossScore = 0, 
             maxPossScore = 4, 
             goodScorePos = FALSE,
             omitNHS = FALSE, # use to omit scores starting in non-help-seeking range
             title = "Jacobson plot, Quito clinic data",
             subtitle = NULL, #"All completions were of full CORE-OM",
             xLab = "Initial score",
             yLab = "Final score",
             noLegend = FALSE,
             labelCSClines = FALSE,
             areaColourScheme = "RCSC5",
             legendNameArea = "Area mapping: RCSC5",
             pointColourScheme = "RCI3",
             legendNamePoints = "Point mapping: RCI3",
             pointSize = 1,
             pointAlpha = 1,
             areaAlpha = .1,
             pointShapeScheme = "NONE",
             lineTypeCSC = 1,
             lineWidthCSC = .5,
             lineColourCSC = 1,
             lineTypeNoChange = 1,
             lineWidthNoChange = .5,
             lineColourNoChange = 1,
             lineTypeRCI = 1,
             lineWidthRCI = .5,
             lineColourRCI = 1,
             labelAllPolygons = TRUE,
             noMessages = FALSE, # suppress messages
             noWarnings = FALSE, # suppress my warnings (not other R ones)
             warningsToErrors = FALSE,
             greyScale = FALSE)

Improvements/todo list

Rejected options

Things still to do for getJacobsonPlot()

Reuse

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Citation

For attribution, please cite this work as

Evans (2023, Nov. 1). Chris (Evans) R SAFAQ: Background on plotJacobson() function. Retrieved from https://www.psyctc.org/R_blog/posts/2023-11-01-plotjacobson/

BibTeX citation

@misc{evans2023background,
  author = {Evans, Chris},
  title = {Chris (Evans) R SAFAQ: Background on plotJacobson() function},
  url = {https://www.psyctc.org/R_blog/posts/2023-11-01-plotjacobson/},
  year = {2023}
}