Plot an Emax model stored in an object
created by function fitEmaxB.
# S3 method for fitEmaxB
plot(
x,int=0,plotResid=FALSE,clev=0.9,
predict=TRUE,plotci=TRUE,plotDif=FALSE,
xlab='Dose',
ylab=ifelse(plotResid,'Residuals',ifelse(plotDif,
'Difference With Placebo','Response')),
ncol=NULL,
symbol=NULL,symbolLabel='Group',symbolShape=8,
symbolColor='red',symbolSize=4,
bwidth=NULL,
xlim=NULL,
xat=NULL,
ylim=NULL,
logScale=FALSE,
ngrid=200,
plot=TRUE, ...)A list with ggplot object, and posterior and prediction interval limits.
Output of fitEmaxB with class
"fitEmaxB".
The index for the protocol (intercept) to use for the predictions
and computation of dose group means/proportions. The default
value is 0, which displays all protocols in a grid layout.
If TRUE, a residual plot of the observed
dose group means/proportions
less the model-based MCMC median estimates of the means/proportions.
Level for posterior probability intervals about the mean/proportion for each dose.
When predict=TRUE, predictive intervals for sample dose group
means/proportions are plotted. They are gray-shaded bars. If there is >1 symbol group
mean/proportion for a protocol/dose combination, then the smaller sample size is used when computing
the prediction interval.
When plotCI=TRUE, posterior intervals for the population dose group means/proportions are plotted. They are black bars.
Plot difference between doses and placebo. It is assumed the lowest dose in each protocol is placebo.
Label for the x-axis
Label for the y-axis
When more than one protocol is plotted, ncol specifies
the number of side by side plots in the plot grid. The default is 3 or
5 depending on the plot type
An optional grouping variable.
The values of symbol must correspond to the original data used in
fitEmax.
Label given to symbol in plot legend.
A character vector with named elements giving
the shapes assigned
to different levels of variable symbol. If a single shape is
specified, it is replicated for all dose group means/proportions. See package
ggplot2 for symbol mappings.
A character vector with named elements
giving the colors assigned
to different levels of variable symbol. If a single color is
specified, it is replicated for all dose group means/proportions. See package
ggplot2 for color mappings.
The size of the symbol for the dose group sample means.
Set symbolSize=0 to supress plotting the means.
Width of the cap on the predictive interval bars.
Plot limits for the x-axis
The points at which tick-marks are to be drawn. Errors occur if the points are outside the range of xlim. By default (when NULL) tickmark locations are computed.
Plot limits for the y-axis
If TRUE, log scale is used for dose.
The number doses evaluated when plotting the curve.
Return plotting output without plotting.
No additional plotting options are currently used.
Neal Thomas
Model-based medians, standard deviations, and interval bounds for the dose groups means/proportions based on the MCMC parameters evaluated in the Emax function.
The function generates random numbers when predict=TRUE, so the random number generator/seed must
be set before the function is called for exact reproducibility.
If baseline covaraties were included in the fit, then the mean of the predictions for
the protocol given by int is plotted. This can be computationally intensive
when the dosing grid is dense, the MCMC sample size is large, and the input sample
size is large. Consider reducing ngrid in this situation.
Note that the protocol must be specified, or the prediction defaults to patients
from the first protocol.
fitEmaxB
if (FALSE) {
data("metaData")
exdat<-metaData[metaData$taid==1,]
prior<-emaxPrior.control(epmu=0,epsca=4,difTargetmu=0,difTargetsca=4,dTarget=20,
p50=(2+5)/2,
sigmalow=0.01,sigmaup=3)
mcmc<-mcmc.control(chains=3)
msSat<-sum((exdat$sampsize-1)*(exdat$sd)^2)/(sum(exdat$sampsize)-length(exdat$sampsize))
fitout<-fitEmaxB(exdat$rslt,exdat$dose,prior,modType=4,prot=exdat$protid,
count=exdat$sampsize,msSat=msSat,mcmc=mcmc)
plot(fitout)
}
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