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@Prefs@Graph.prefs$type,
col = object@Prefs@Graph.prefs$col,
pch = object@Prefs@Graph.prefs$pch,
cex = object@Prefs@Graph.prefs$cex,
lty = object@Prefs@Graph.prefs$lty,
lwd = object@Prefs@Graph.prefs$lwd,
fill = object@Prefs@Graph.prefs$fill,
ids = NULL,
idsmode = object@Prefs@Graph.prefs$idsmode,
idsext = object@Prefs@Graph.prefs$idsext,
idscex = object@Prefs@Graph.prefs$idscex,
idsdir = object@Prefs@Graph.prefs$idsdir,
abline = object@Prefs@Graph.prefs$abline,
abllwd = object@Prefs@Graph.prefs$abllwd,
abllty = object@Prefs@Graph.prefs$abllty,
ablcol = object@Prefs@Graph.prefs$ablcol,
smooth = object@Prefs@Graph.prefs$smooth,
smlwd = object@Prefs@Graph.prefs$smlwd,
smlty = object@Prefs@Graph.prefs$smlty,
smcol = object@Prefs@Graph.prefs$smcol,
smspan = object@Prefs@Graph.prefs$smspan,
smdegr = object@Prefs@Graph.prefs$smdegr,
smooth.for.groups = NULL,
lmline = object@Prefs@Graph.prefs$lmline,
lmlwd = object@Prefs@Graph.prefs$lmlwd,
lmlty = object@Prefs@Graph.prefs$lmlty,
lmcol = object@Prefs@Graph.prefs$lmcol,
suline = object@Prefs@Graph.prefs$suline,
sulwd = object@Prefs@Graph.prefs$sulwd,
sulty = object@Prefs@Graph.prefs$sulty,
sucol = object@Prefs@Graph.prefs$sucol,
suspan = object@Prefs@Graph.prefs$suspan,
sudegr = object@Prefs@Graph.prefs$sudegr,
grid = object@Prefs@Graph.prefs$grid,
logy = FALSE,
logx = FALSE,
force.x.continuous = FALSE,
bwhoriz = object@Prefs@Graph.prefs$bwhoriz,
bwratio = object@Prefs@Graph.prefs$bwratio,
bwvarwid = object@Prefs@Graph.prefs$bwvarwid,
bwdotpch = object@Prefs@Graph.prefs$bwdotpch,
bwdotcol = object@Prefs@Graph.prefs$bwdotcol,
bwdotcex = object@Prefs@Graph.prefs$bwdotcex,
bwreccol = object@Prefs@Graph.prefs$bwreccol,
bwrecfill = object@Prefs@Graph.prefs$bwrecfill,
bwreclty = object@Prefs@Graph.prefs$bwreclty,
bwreclwd = object@Prefs@Graph.prefs$bwreclwd,
bwumbcol = object@Prefs@Graph.prefs$bwumbcol,
bwumblty = object@Prefs@Graph.prefs$bwumblty,
bwumblwd = object@Prefs@Graph.prefs$bwumblwd,
bwoutcol = object@Prefs@Graph.prefs$bwoutcol,
bwoutcex = object@Prefs@Graph.prefs$bwoutcex,
bwoutpch = object@Prefs@Graph.prefs$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 (see

`xpose.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.