xpose.panel.default: Default panel function for Xpose 4

In xpose4: Diagnostics for Nonlinear Mixed-Effect Models

Default panel function for Xpose 4

Description

This is the panel function for Xpose 4. This is not intended to be ised outside the xpose.plot.default function. Most of the arguments take their default values from xpose.data object but this can be overridden by supplying them as argument to xpose.plot.default.

Usage

xpose.panel.default(
  x,
  y,
  object,
  subscripts,
  groups = object@Prefs@Xvardef$id,
  grp.col = NULL,
  iplot = NULL,
  inclZeroWRES = FALSE,
  onlyfirst = FALSE,
  samp = NULL,
  xvarnam = NULL,
  yvarnam = NULL,
  PI = NULL,
  PI.subset = NULL,
  PI.bin.table = NULL,
  PI.real = NULL,
  PI.mirror = NULL,
  PI.ci = NULL,
  PPI = NULL,
  PI.mean = FALSE,
  PI.delta.mean = FALSE,
  PI.x.median = TRUE,
  PI.rug = "Default",
  PI.rug.col = "orange",
  PI.rug.lwd = 3,
  PI.identify.outliers = TRUE,
  PI.outliers.col = "red",
  PI.outliers.pch = 8,
  PI.outliers.cex = 1,
  PI.limits = c(0.025, 0.975),
  PI.arcol = "lightgreen",
  PI.up.lty = 2,
  PI.up.type = "l",
  PI.up.col = "black",
  PI.up.lwd = 2,
  PI.down.lty = 2,
  PI.down.type = "l",
  PI.down.col = "black",
  PI.down.lwd = 2,
  PI.med.lty = 1,
  PI.med.type = "l",
  PI.med.col = "black",
  PI.med.lwd = 2,
  PI.mean.lty = 3,
  PI.mean.type = "l",
  PI.mean.col = "black",
  PI.mean.lwd = 2,
  PI.delta.mean.lty = 3,
  PI.delta.mean.type = "l",
  PI.delta.mean.col = "black",
  PI.delta.mean.lwd = 2,
  PI.real.up.lty = 2,
  PI.real.up.type = "l",
  PI.real.up.col = "red",
  PI.real.up.lwd = 2,
  PI.real.down.lty = 2,
  PI.real.down.type = "l",
  PI.real.down.col = "red",
  PI.real.down.lwd = 2,
  PI.real.med.lty = 1,
  PI.real.med.type = "l",
  PI.real.med.col = "red",
  PI.real.med.lwd = 2,
  PI.real.mean.lty = 3,
  PI.real.mean.type = "l",
  PI.real.mean.col = "red",
  PI.real.mean.lwd = 2,
  PI.real.delta.mean.lty = 3,
  PI.real.delta.mean.type = "l",
  PI.real.delta.mean.col = "red",
  PI.real.delta.mean.lwd = 2,
  PI.mirror.up.lty = 2,
  PI.mirror.up.type = "l",
  PI.mirror.up.col = "darkgreen",
  PI.mirror.up.lwd = 1,
  PI.mirror.down.lty = 2,
  PI.mirror.down.type = "l",
  PI.mirror.down.col = "darkgreen",
  PI.mirror.down.lwd = 1,
  PI.mirror.med.lty = 1,
  PI.mirror.med.type = "l",
  PI.mirror.med.col = "darkgreen",
  PI.mirror.med.lwd = 1,
  PI.mirror.mean.lty = 3,
  PI.mirror.mean.type = "l",
  PI.mirror.mean.col = "darkgreen",
  PI.mirror.mean.lwd = 1,
  PI.mirror.delta.mean.lty = 3,
  PI.mirror.delta.mean.type = "l",
  PI.mirror.delta.mean.col = "darkgreen",
  PI.mirror.delta.mean.lwd = 1,
  PI.ci.up.arcol = "blue",
  PI.ci.up.lty = 3,
  PI.ci.up.type = "l",
  PI.ci.up.col = "darkorange",
  PI.ci.up.lwd = 2,
  PI.ci.down.arcol = "blue",
  PI.ci.down.lty = 3,
  PI.ci.down.type = "l",
  PI.ci.down.col = "darkorange",
  PI.ci.down.lwd = 2,
  PI.ci.med.arcol = "red",
  PI.ci.med.lty = 4,
  PI.ci.med.type = "l",
  PI.ci.med.col = "darkorange",
  PI.ci.med.lwd = 2,
  PI.ci.mean.arcol = "purple",
  PI.ci.mean.lty = 4,
  PI.ci.mean.type = "l",
  PI.ci.mean.col = "darkorange",
  PI.ci.mean.lwd = 2,
  PI.ci.delta.mean.arcol = "purple",
  PI.ci.delta.mean.lty = 4,
  PI.ci.delta.mean.type = "l",
  PI.ci.delta.mean.col = "darkorange",
  PI.ci.delta.mean.lwd = 2,
  PI.ci.area.smooth = FALSE,
  type = object@[e-mail]$type,
  col = object@[e-mail]$col,
  pch = object@[e-mail]$pch,
  cex = object@[e-mail]$cex,
  lty = object@[e-mail]$lty,
  lwd = object@[e-mail]$lwd,
  fill = object@[e-mail]$fill,
  ids = NULL,
  idsmode = object@[e-mail]$idsmode,
  idsext = object@[e-mail]$idsext,
  idscex = object@[e-mail]$idscex,
  idsdir = object@[e-mail]$idsdir,
  abline = object@[e-mail]$abline,
  abllwd = object@[e-mail]$abllwd,
  abllty = object@[e-mail]$abllty,
  ablcol = object@[e-mail]$ablcol,
  smooth = object@[e-mail]$smooth,
  smlwd = object@[e-mail]$smlwd,
  smlty = object@[e-mail]$smlty,
  smcol = object@[e-mail]$smcol,
  smspan = object@[e-mail]$smspan,
  smdegr = object@[e-mail]$smdegr,
  smooth.for.groups = NULL,
  lmline = object@[e-mail]$lmline,
  lmlwd = object@[e-mail]$lmlwd,
  lmlty = object@[e-mail]$lmlty,
  lmcol = object@[e-mail]$lmcol,
  suline = object@[e-mail]$suline,
  sulwd = object@[e-mail]$sulwd,
  sulty = object@[e-mail]$sulty,
  sucol = object@[e-mail]$sucol,
  suspan = object@[e-mail]$suspan,
  sudegr = object@[e-mail]$sudegr,
  grid = object@[e-mail]$grid,
  logy = FALSE,
  logx = FALSE,
  force.x.continuous = FALSE,
  bwhoriz = object@[e-mail]$bwhoriz,
  bwratio = object@[e-mail]$bwratio,
  bwvarwid = object@[e-mail]$bwvarwid,
  bwdotpch = object@[e-mail]$bwdotpch,
  bwdotcol = object@[e-mail]$bwdotcol,
  bwdotcex = object@[e-mail]$bwdotcex,
  bwreccol = object@[e-mail]$bwreccol,
  bwrecfill = object@[e-mail]$bwrecfill,
  bwreclty = object@[e-mail]$bwreclty,
  bwreclwd = object@[e-mail]$bwreclwd,
  bwumbcol = object@[e-mail]$bwumbcol,
  bwumblty = object@[e-mail]$bwumblty,
  bwumblwd = object@[e-mail]$bwumblwd,
  bwoutcol = object@[e-mail]$bwoutcol,
  bwoutcex = object@[e-mail]$bwoutcex,
  bwoutpch = object@[e-mail]$bwoutpch,
  autocorr = FALSE,
  vline = NULL,
  vllwd = 3,
  vllty = 2,
  vlcol = "grey",
  hline = NULL,
  hllwd = 3,
  hllty = 1,
  hlcol = "grey",
  pch.ip.sp = pch,
  cex.ip.sp = cex,
  ...
)

Arguments

x	Name(s) of the x-variable.
y	Name(s) of the y-variable.
object	An xpose.data object.
subscripts	The standard Trellis subscripts argument (see xyplot)
groups	Name of the variable used for superpose plots.
grp.col	Logical value indicating whether or not to use colour highlighting when groups are specified. NULL means no highlighting, while TRUE will identify group members by colour.
iplot	Is this an individual plots matrix? Internal use only.
inclZeroWRES	Logical value indicating whether rows with WRES=0 is included in the plot.
onlyfirst	Logical value indicating whether only the first row per individual is included in the plot.
samp	An integer between 1 and object@Nsim (seexpose.data-class) specifying which of the simulated data sets to extract from SData.
xvarnam	Character string with the name of the x-variable.
yvarnam	Character string with the name of the y-variable.
PI	Either "lines", "area" or "both" specifying whether prediction intervals (as lines, as a shaded area or both) should be computed from the data in SData and added to the display. NULL means no prediction interval.
PI.subset	The subset to be used for the PI.
PI.bin.table	The table used to create VPC plots. Has a specific format created by read.npc.vpc.results
PI.real	Plot the percentiles of the real data in the various bins. values can be NULL or TRUE. Note that for a bin with few actual observations the percentiles will be approximate. For example, the 95th percentile of 4 data points will always be the largest of the 4 data points.
PI.mirror	Plot the percentiles of one simulated data set in each bin. values allowed are NULL, TRUE or AN.INTEGER.VALUE. TRUE takes the first mirror from PI.bin.table and AN.INTEGER.VALUE can be 1, 2, ...{} n where n is the number of mirror's output in the PI.bin.table. Used mainly by xpose.VPC.
PI.ci	Plot the prediction interval of the simulated data's percentiles for each bin. Values can be "both", "area" or "lines" This can be thought of as a prediction interval about the PI.real or a confidence interval about the PI. However, note that with increasing number of simulations the CI will not go towards zero because the interval is also dependent on the size of the data set.
PPI	The plot prediction interval. Has a specific format that must be followed. See setup.PPI.
PI.mean	Should the mean be plotted in the VPCs? TRUE or FALSE.
PI.delta.mean	Should the delta mean be plotted in the VPCs? TRUE or FALSE.
PI.x.median	Should the x-location of percentile lines in a bin be marked at the median of the x-values? (TRUE or FALSE)
PI.rug	Should there be markings on the plot showing where the binning intervals for the VPC are (or the locations of the independent variable used for each VPC calculation if binning is not used)?
PI.rug.col	Color of the PI.rug.
PI.rug.lwd	Linw width of the PI.rug.
PI.identify.outliers	Should outlying percentiles of the real data be highlighted? (TRUE of FALSE)
PI.outliers.col	Color of PI.identify.outliers points
PI.outliers.pch	pch of PI.identify.outliers points
PI.outliers.cex	cex of PI.identify.outliers points
PI.limits	A vector of two values that describe the limits of the prediction interval that should be displayed. For example c(0.025, 0.975). These limits should be found in the ‘PI.bin.table’ table. These limits are also used as the percentages for the PI.real, PI.mirror and PI.ci. However, the confidence interval in PI.ci is always the one defined in the PI.bin.table.
PI.arcol	The color of the PI area
PI.up.lty	The upper line type. can be "dotted" or "dashed", etc.
PI.up.type	The upper type used for plotting. Defaults to a line.
PI.up.col	The upper line color
PI.up.lwd	The upper line width
PI.down.lty	The lower line type. can be "dotted" or "dashed", etc.
PI.down.type	The lower type used for plotting. Defaults to a line.
PI.down.col	The lower line color
PI.down.lwd	The lower line width
PI.med.lty	The median line type. can be "dotted" or "dashed", etc.
PI.med.type	The median type used for plotting. Defaults to a line.
PI.med.col	The median line color
PI.med.lwd	The median line width
PI.mean.lty	The mean line type. can be "dotted" or "dashed", etc.
PI.mean.type	The mean type used for plotting. Defaults to a line.
PI.mean.col	The mean line color
PI.mean.lwd	The mean line width
PI.delta.mean.lty	The delta.mean line type. can be "dotted" or "dashed", etc.
PI.delta.mean.type	The delta.mean type used for plotting. Defaults to a line.
PI.delta.mean.col	The delta.mean line color
PI.delta.mean.lwd	The delta.mean line width
PI.real.up.lty	The upper line type. can be "dotted" or "dashed", etc.
PI.real.up.type	The upper type used for plotting. Defaults to a line.
PI.real.up.col	The upper line color
PI.real.up.lwd	The upper line width
PI.real.down.lty	The lower line type. can be "dotted" or "dashed", etc.
PI.real.down.type	The lower type used for plotting. Defaults to a line.
PI.real.down.col	The lower line color
PI.real.down.lwd	The lower line width
PI.real.med.lty	The median line type. can be "dotted" or "dashed", etc.
PI.real.med.type	The median type used for plotting. Defaults to a line.
PI.real.med.col	The median line color
PI.real.med.lwd	The median line width
PI.real.mean.lty	The mean line type. can be "dotted" or "dashed", etc.
PI.real.mean.type	The mean type used for plotting. Defaults to a line.
PI.real.mean.col	The mean line color
PI.real.mean.lwd	The mean line width
PI.real.delta.mean.lty	The delta.mean line type. can be "dotted" or "dashed", etc.
PI.real.delta.mean.type	The delta.mean type used for plotting. Defaults to a line.
PI.real.delta.mean.col	The delta.mean line color
PI.real.delta.mean.lwd	The delta.mean line width
PI.mirror.up.lty	The upper line type. can be "dotted" or "dashed", etc.
PI.mirror.up.type	The upper type used for plotting. Defaults to a line.
PI.mirror.up.col	The upper line color
PI.mirror.up.lwd	The upper line width
PI.mirror.down.lty	The lower line type. can be "dotted" or "dashed", etc.
PI.mirror.down.type	The lower type used for plotting. Defaults to a line.
PI.mirror.down.col	The lower line color
PI.mirror.down.lwd	The lower line width
PI.mirror.med.lty	The median line type. can be "dotted" or "dashed", etc.
PI.mirror.med.type	The median type used for plotting. Defaults to a line.
PI.mirror.med.col	The median line color
PI.mirror.med.lwd	The median line width
PI.mirror.mean.lty	The mean line type. can be "dotted" or "dashed", etc.
PI.mirror.mean.type	The mean type used for plotting. Defaults to a line.
PI.mirror.mean.col	The mean line color
PI.mirror.mean.lwd	The mean line width
PI.mirror.delta.mean.lty	The delta.mean line type. can be "dotted" or "dashed", etc.
PI.mirror.delta.mean.type	The delta.mean type used for plotting. Defaults to a line.
PI.mirror.delta.mean.col	The delta.mean line color
PI.mirror.delta.mean.lwd	The delta.mean line width
PI.ci.up.arcol	The color of the upper PI.ci.
PI.ci.up.lty	The upper line type. can be "dotted" or "dashed", etc.
PI.ci.up.type	The upper type used for plotting. Defaults to a line.
PI.ci.up.col	The upper line color
PI.ci.up.lwd	The upper line width
PI.ci.down.arcol	The color of the lower PI.ci.
PI.ci.down.lty	The lower line type. can be "dotted" or "dashed", etc.
PI.ci.down.type	The lower type used for plotting. Defaults to a line.
PI.ci.down.col	The lower line color
PI.ci.down.lwd	The lower line width
PI.ci.med.arcol	The color of the median PI.ci.
PI.ci.med.lty	The median line type. can be "dotted" or "dashed", etc.
PI.ci.med.type	The median type used for plotting. Defaults to a line.
PI.ci.med.col	The median line color
PI.ci.med.lwd	The median line width
PI.ci.mean.arcol	The color of the mean PI.ci.
PI.ci.mean.lty	The mean line type. can be "dotted" or "dashed", etc.
PI.ci.mean.type	The mean type used for plotting. Defaults to a line.
PI.ci.mean.col	The mean line color
PI.ci.mean.lwd	The mean line width
PI.ci.delta.mean.arcol	The color of the delta.mean PI.ci.
PI.ci.delta.mean.lty	The delta.mean line type. can be "dotted" or "dashed", etc.
PI.ci.delta.mean.type	The delta.mean type used for plotting. Defaults to a line.
PI.ci.delta.mean.col	The delta.mean line color
PI.ci.delta.mean.lwd	The delta.mean line width
PI.ci.area.smooth	Should the "area" for PI.ci be smoothed to match the "lines" argument? Allowed values are TRUE/FALSE. The "area" is set by default to show the bins used in the PI.ci computation. By smoothing, information is lost and, in general, the confidence intervals will be smaller than they are in reality.
type	1-character string giving the type of plot desired. The following values are possible, for details, see 'plot': '"p"' for points, '"l"' for lines, '"o"' for over-plotted points and lines, '"b"', '"c"') for (empty if '"c"') points joined by lines, '"s"' and '"S"' for stair steps and '"h"' for histogram-like vertical lines. Finally, '"n"' does not produce any points or lines.
col	The color for lines and points. Specified as an integer or a text string. A full list is obtained by the R command colours(). The default is blue (col=4).
pch	The plotting character, or symbol, to use. Specified as an integer. See R help on points. The default is an open circle.
cex	The amount by which plotting text and symbols should be scaled relative to the default. 'NULL' and 'NA' are equivalent to '1.0'.
lty	The line type. Line types can either be specified as an integer (0=blank, 1=solid, 2=dashed, 3=dotted, 4=dotdash, 5=longdash, 6=twodash) or as one of the character strings '"blank"', '"solid"', '"dashed"', '"dotted"', '"dotdash"', '"longdash"', or '"twodash"', where '"blank"' uses 'invisible lines' (i.e., doesn't draw them).
lwd	the width for lines. Specified as an integer. The default is 1.
fill	fill for areas in plot
ids	Logical value specifying whether to label data points.
idsmode	Determines the way text labels are added to plots. NULL means that only extreme points are labelled. Non-NULL means all data points are labelled. (See link{xpose.plot.default})
idsext	specifies the extent of the extremes to be used in labelling points. The default is 0.05 (only the most extreme 5% of points are labelled).
idscex	the amount by which labels should be scaled relative to the default. 'NULL' and 'NA' are equivalent to '1.0'.
idsdir	a string indicating the directions of the extremes to include in labelling. Possible values are "up", "down" and "both".
abline	Vector of arguments to the panel.abline function. No abline is drawn if NULL.
abllwd	Line width of any abline.
abllty	Line type of any abline.
ablcol	Line colour of any abline.
smooth	A NULL value indicates that no superposed line should be added to the graph. If TRUE then a smooth of the data will be superimposed.
smlwd	Line width of the x-y smooth.
smlty	Line type of the x-y smooth.
smcol	Line color of the x-y smooth.
smspan	The smoothness parameter for the x-y smooth. The default is 0.667. An argument to panel.loess.
smdegr	The degree of the polynomials to be used for the x-y smooth, up to 2. The default is 1. An argument to panel.loess.
smooth.for.groups	Should a smooth for each group be drawn?
lmline	logical variable specifying whether a linear regression line should be superimposed over an xyplot. NULL ~ FALSE. (y~x)
lmlwd	Line width of the lmline.
lmlty	Line type of the lmline.
lmcol	Line colour of the lmline.
suline	A NULL value indicates that no superposed line should be added to the graph. If non-NULL then this should be the vector (the same length as y) of data points to be used for the smoothed superposed line.
sulwd	Line width of the superposed smooth.
sulty	Line type of the superposed smooth.
sucol	Line color of the superposed smooth.
suspan	The smoothness parameter. The default is 0.667. An argument to panel.loess.
sudegr	The degree of the polynomials to be used, up to 2. The default is 1. An argument to panel.loess.
grid	logical value indicating whether a visual reference grid should be added to the graph. (Could use arguments for line type, color etc).
logy	Logical value indicating whether the y-axis should be logarithmic.
logx	Logical value indicating whether the y-axis should be logarithmic.
force.x.continuous	Logical value indicating whether x-values should be taken as continuous, even if categorical.
bwhoriz	logical value indicating whether box and whiskers should be horizontal or not. The default is FALSE.
bwratio	Ratio of box height to inter-box space. The default is 1.5. An argument for panel.bwplot.
bwvarwid	Logical. If TRUE, widths of boxplots are proportional to the number of points used in creating it. The default is FALSE. An argument for panel.bwplot.
bwdotpch	Graphical parameter controlling the dot plotting character in boxplots. 'bwdotpch="|"' is treated specially, by replacing the dot with a line. The default is 16. An argument for panel.bwplot.
bwdotcol	Graphical parameter controlling the dot colour in boxplots - an integer or string. See 'col'. The default is black. An argument for panel.bwplot.
bwdotcex	The amount by which plotting text and symbols should be scaled relative to the default in boxplots. 'NULL' and 'NA' are equivalent to '1.0'. An argument for panel.bwplot.
bwreccol	The colour to use for the box rectangle in boxplots - an integer or string. The default is blue. See trellis.par.get and "box.rectangle".
bwrecfill	The colour to use for filling the box rectangle in boxplots - an integer or string. The default is transparent (none). See trellis.par.get and "box.rectangle".
bwreclty	The line type for the box rectangle in boxplots - an integer or string. The default is solid. See trellis.par.get and "box.rectangle".
bwreclwd	The width of the lines for the box rectangle in boxplots - an integer. The default is 1. See trellis.par.get and "box.rectangle".
bwumbcol	The colour to use for the umbrellas in boxplots - an integer or string. The default is blue. See trellis.par.get and "box.umbrella".
bwumblty	The line type for the umbrellas in boxplots - an integer or string. The default is solid.See trellis.par.get and "box.umbrella".
bwumblwd	the width of the lines for the umbrellas in boxplots - an integer. The default is 1. See trellis.par.get and "box.umbrella".
bwoutcol	The colour to use for the outliers in boxplots - an integer or string. The default is blue. See trellis.par.get and "box.symbol".
bwoutcex	The amount by which outlier points should be scaled relative to the default in boxplots. 'NULL' and 'NA' are equivalent to '1.0'. The default is 0.8. See trellis.par.get and "box.symbol".
bwoutpch	The plotting character, or symbol, to use for outlier points in boxplots. Specified as an integer. See R help on 'points'. The default is an open circle. See trellis.par.get and "box.symbol".
autocorr	Is this an autocorrelation plot? Values can be TRUE/FALSE.
vline	Add a vertical line to the plot at the values specified.
vllwd	Width (lwd) of vertical line
vllty	Line type (lty) for vertical line
vlcol	Color (col) of vertical line
hline	Add a horizontal line to the plot at the values specified.
hllwd	Width (lwd) of horizontal line
hllty	Line type (lty) for horizontal line
hlcol	Color (col) of horizontal line
pch.ip.sp	If there is a panel with just one observation then this specifies the type of points for the DV, IPRED and PRED respectively.
cex.ip.sp	If there is a panel with just one observation then this specifies the size of the points for the DV, IPRED and PRED respectively.
...	Other arguments that may be needed in the function.

Author(s)

E. Niclas Jonsson, Mats Karlsson, Justin Wilkins and Andrew Hooker

See Also

xpose.data-class, Cross-references above.

xpose4 documentation built on May 29, 2024, 7:56 a.m.