ind.plots: Observations (DV), individual predictions (IPRED) and...

In xpose4: Diagnostics for Nonlinear Mixed-Effect Models

Observations (DV), individual predictions (IPRED) and population predictions (PRED) are plotted against the independent variable for every individual in the dataset, for Xpose 4

Description

This is a compound plot consisting of plots of observations (DV), individual predictions (IPRED) and population predictions (PRED) against the independent variable for every individual in the dataset, a specific function in Xpose 4. It is a wrapper encapsulating arguments to the xpose.plot.default function.

Usage

ind.plots(
  object,
  y.vals = c(xvardef("dv", new.obj), xvardef("ipred", new.obj), xvardef("pred", new.obj)),
  x.vals = xvardef("idv", new.obj),
  id.vals = xvardef("id", new.obj),
  key.text = y.vals,
  main = "Default",
  key = "Default",
  xlb = xlabel(xvardef("idv", object), object),
  ylb = NULL,
  layout = c(4, 4),
  inclZeroWRES = FALSE,
  subset = xsubset(object),
  type = "o",
  grid = FALSE,
  col = c(1, 2, 4),
  lty = c(0, 1, 3),
  lwd = c(1, 1, 1),
  pch = c(21, 32, 32),
  cex = c(0.7, 0.7, 0.7),
  fill = c("lightgrey", 0, 0),
  prompt = FALSE,
  mirror = NULL,
  main.cex = 0.9,
  max.plots.per.page = 1,
  pch.ip.sp = c(21, 19, 18),
  cex.ip.sp = c(0.7, 0.4, 0.4),
  y.vals.subset = NULL,
  ...
)

Arguments

object	An xpose.data object.
y.vals	The Y values to use.
x.vals	The X values to use.
id.vals	The ID values to use.
key.text	The text in the legend to use.
main	The title of the plot. If "Default" then a default title is plotted. Otherwise the value should be a string like "my title" or NULL for no plot title.
key	Create a legend.
xlb	A string giving the label for the x-axis. NULL if none.
ylb	A string giving the label for the y-axis. NULL if none.
layout	A list giving the layout of the graphs on the plot, in columns and rows. The default is 4x4.
inclZeroWRES	Logical value indicating whether rows with WRES=0 is included in the plot. The default is TRUE.
subset	A string giving the subset expression to be applied to the data before plotting. See xsubset.
type	1-character string giving the type of plot desired. The default is "o", for over-plotted points and lines. See xpose.plot.default.
grid	Should the plots have a grid in each plot?
col	A list of three elements, giving plotting characters for observations, individual predictions, and population predictions, in that order. The default is black for DV, red for individual predictions, and blue for population predictions.
lty	A list of three elements, giving line types for observations, individual predictions, and population predictions, in that order.
lwd	A list of three elements, giving line widths for observations, individual predictions, and population predictions, in that order.
pch	A list of three elements, giving plotting characters for observations, individual predictions, and population predictions, in that order.
cex	A list of three elements, giving relative point size for observations, individual predictions, and population predictions, in that order. The default is c(0.7,0.7,0.7).
fill	Fill the circles in the points?
prompt	Specifies whether or not the user should be prompted to press RETURN between plot pages. Default is TRUE.
mirror	Mirror plots are not yet implemented in this function and this argument must contain a value of NULL
main.cex	The size of the title.
max.plots.per.page	Maximum number of plots per page.
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.
y.vals.subset	Used to subset on the DV, IPRED and PRED variables separately. Either NULL or a vector of three strings, corresponding to the subset of DV, IPRED and PRED respectively. See examples below.
...	Other arguments passed to link{xpose.plot.default}.

Details

Matrices of individual plots are presented for comparison and closer inspection.

Value

Returns a stack of plots observations (DV) against individual predictions (IPRED) and population predictions (PRED).

A wide array of extra options controlling xyplots are available. See xpose.plot.default and xpose.panel.default for details.

Author(s)

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

See Also

xpose.plot.default, xpose.panel.default, xyplot, strip.default, xpose.prefs-class, xpose.data-class

Other specific functions: absval.cwres.vs.cov.bw(), absval.cwres.vs.pred(), absval.cwres.vs.pred.by.cov(), absval.iwres.cwres.vs.ipred.pred(), absval.iwres.vs.cov.bw(), absval.iwres.vs.idv(), absval.iwres.vs.ipred(), absval.iwres.vs.ipred.by.cov(), absval.iwres.vs.pred(), absval.wres.vs.cov.bw(), absval.wres.vs.idv(), absval.wres.vs.pred(), absval.wres.vs.pred.by.cov(), absval_delta_vs_cov_model_comp, addit.gof(), autocorr.cwres(), autocorr.iwres(), autocorr.wres(), basic.gof(), basic.model.comp(), cat.dv.vs.idv.sb(), cat.pc(), cov.splom(), cwres.dist.hist(), cwres.dist.qq(), cwres.vs.cov(), cwres.vs.idv(), cwres.vs.idv.bw(), cwres.vs.pred(), cwres.vs.pred.bw(), cwres.wres.vs.idv(), cwres.wres.vs.pred(), dOFV.vs.cov(), dOFV.vs.id(), dOFV1.vs.dOFV2(), data.checkout(), dv.preds.vs.idv(), dv.vs.idv(), dv.vs.ipred(), dv.vs.ipred.by.cov(), dv.vs.ipred.by.idv(), dv.vs.pred(), dv.vs.pred.by.cov(), dv.vs.pred.by.idv(), dv.vs.pred.ipred(), gof(), ind.plots.cwres.hist(), ind.plots.cwres.qq(), ipred.vs.idv(), iwres.dist.hist(), iwres.dist.qq(), iwres.vs.idv(), kaplan.plot(), par_cov_hist, par_cov_qq, parm.vs.cov(), parm.vs.parm(), pred.vs.idv(), ranpar.vs.cov(), runsum(), wres.dist.hist(), wres.dist.qq(), wres.vs.idv(), wres.vs.idv.bw(), wres.vs.pred(), wres.vs.pred.bw(), xpose.VPC(), xpose.VPC.both(), xpose.VPC.categorical(), xpose4-package

Examples

## Here we load the example xpose database 
xpdb <- simpraz.xpdb

## Monochrome, suitable for manuscript or report
ind.plots(xpdb, 
  subset="ID>40 & ID<57", 
  col=c(1,1,1), 
  lty=c(0,2,3), 
  strip=function(..., bg) 
    strip.default(..., bg="grey"))
    
## Not run:     
## IF we simulate in NONMEM using a dense grid of time points
## and all non-observed DV items are equal to zero.
ind.plots(xpdb,inclZeroWRES=TRUE,y.vals.subset=c("DV!=0","NULL","NULL"))


# to plot individual plots of multiple variables
ind.plots(xpdb,subset="FLAG==1")
ind.plots(xpdb,subset="FLAG==2")

## End(Not run)

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