Description Usage Arguments Author(s) See Also
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
.
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 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93  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, ...)

x 
Name(s) of the xvariable. 
y 
Name(s) of the yvariable. 
object 
An xpose.data object. 
subscripts 
The standard Trellis subscripts argument (see

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 [email protected]
(see 
xvarnam 
Character string with the name of the xvariable. 
yvarnam 
Character string with the name of the yvariable. 
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 
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 
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 
PI.ci 
Plot the prediction interval of the simulated data's
percentiles for each bin. Values can be 
PPI 
The plot prediction interval. Has a specific format that must be
followed. See 
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 xlocation of percentile lines in a bin be
marked at the median of the xvalues? ( 
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 
PI.arcol 
The color of the 
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.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.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.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.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.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 
type 
1character string giving the type of plot desired. The following values are possible, for details, see 'plot': '"p"' for points, '"l"' for lines, '"o"' for overplotted points and lines, '"b"', '"c"') for (empty if '"c"') points joined by lines, '"s"' and '"S"' for stair steps and '"h"' for histogramlike 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 
pch 
The plotting character, or symbol, to use. Specified as an
integer. See R help on 
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.

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 
abllwd 
Line width of any abline. 
abllty 
Line type of any abline. 
ablcol 
Line colour of any abline. 
smooth 
A 
smlwd 
Line width of the xy smooth. 
smlty 
Line type of the xy smooth. 
smcol 
Line color of the xy smooth. 
smspan 
The smoothness parameter for the xy smooth. The default is
0.667. An argument to 
smdegr 
The degree of the polynomials to be used for the xy smooth,
up to 2. The default is 1. An argument to

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 
lmlwd 
Line width of the lmline. 
lmlty 
Line type of the lmline. 
lmcol 
Line colour of the lmline. 
suline 
A 
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

sudegr 
The degree of the polynomials to be used, up to 2. The default
is 1. An argument to 
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 yaxis should be logarithmic. 
logx 
Logical value indicating whether the yaxis should be logarithmic. 
force.x.continuous 
Logical value indicating whether xvalues 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 interbox space. The default is 1.5.
An argument for 
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

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

bwdotcol 
Graphical parameter controlling the dot colour in boxplots 
an integer or string. See 'col'. The default is black. An argument for

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 
bwreccol 
The colour to use for the box rectangle in boxplots  an
integer or string. The default is blue. See

bwrecfill 
The colour to use for filling the box rectangle in boxplots
 an integer or string. The default is transparent (none). See

bwreclty 
The line type for the box rectangle in boxplots  an integer
or string. The default is solid. See 
bwreclwd 
The width of the lines for the box rectangle in boxplots 
an integer. The default is 1. See 
bwumbcol 
The colour to use for the umbrellas in boxplots  an integer
or string. The default is blue. See 
bwumblty 
The line type for the umbrellas in boxplots  an integer or
string. The default is solid.See 
bwumblwd 
the width of the lines for the umbrellas in boxplots  an
integer. The default is 1. See 
bwoutcol 
The colour to use for the outliers in boxplots  an integer
or string. The default is blue. See 
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 
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 
autocorr 
Is this an autocorrelation plot? Values can be

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. 
E. Niclas Jonsson, Mats Karlsson, Justin Wilkins and Andrew Hooker
xpose.dataclass
, Crossreferences above.
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