plot.fitEmaxB {clinDR}  R Documentation 
Plot an Emax model stored in an object
created by function fitEmaxB
.
## S3 method for class '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')),
symbol=NULL,symbolLabel='Group',symbolShape=8,
symbolColor='red',symbolSize=4,
bwidth=NULL,
xlim=NULL,
xat=NULL,
ylim=NULL,
logScale=FALSE,
ngrid=200,
plot=TRUE, ...)
x 
Output of 
int 
The index for the protocol (intercept) to use for the predictions
and computation of dose group means/proportions. The default
value is 
plotResid 
If 
clev 
Level for posterior probability intervals about the mean/proportion for each dose. 
predict 
When predict=TRUE, predictive intervals for sample dose group
means/proportions are plotted. They are grayshaded bars. If there is 
plotci 
When plotCI=TRUE, posterior intervals for the population dose group means/proportions are plotted. They are black bars. 
plotDif 
Plot difference between doses and placebo. It is assumed the lowest dose in each protocol is placebo. 
xlab 
Label for the xaxis 
ylab 
Label for the yaxis 
symbol 
An optional grouping variable.
The values of symbol must correspond to the original data used in

symbolLabel 
Label given to symbol in plot legend. 
symbolShape 
A character vector with named elements giving
the shapes assigned
to different levels of variable 
symbolColor 
A character vector with named elements
giving the colors assigned
to different levels of variable 
symbolSize 
The size of the symbol for the dose group sample means.
Set 
bwidth 
Width of the cap on the predictive interval bars. 
xlim 
Plot limits for the xaxis 
xat 
The points at which tickmarks are to be drawn. Errors occur if the points are outside the range of xlim. By default (when NULL) tickmark locations are computed. 
ylim 
Plot limits for the yaxis 
logScale 
If 
ngrid 
The number doses evaluated when plotting the curve. 
plot 
Return plotting output without plotting. 
... 
No additional plotting options are currently used. 
Modelbased 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.
A list with ggplot object, and posterior and prediction interval limits.
Neal Thomas
## Not run:
data("metaData")
exdat<metaData[metaData$taid==1,]
prior<emaxPrior.control(epmu=0,epsca=4,difTargetmu=0,difTargetsca=4,dTarget=20,
p50=(2+5)/2,
sigmalow=0.01,sigmaup=3)
mcmc<mcmc.control(chains=3)
msSat<sum((exdat$sampsize1)*(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)
## End(Not run)