plot.fitEmaxB {clinDR}

Plot a Emax model and dose group means.

Description

Plot an Emax model stored in an object created by function fitEmaxB.

Usage

## 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')),
      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, ...)

Arguments

x

Output of fitEmaxB with class "fitEmaxB".

int

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.

plotResid

If TRUE, a residual plot of the observed dose group means/proportions less the model-based MCMC median estimates of the means/proportions.

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 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.

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 x-axis

ylab

Label for the y-axis

ncol

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

symbol

An optional grouping variable. The values of symbol must correspond to the original data used in fitEmax.

symbolLabel

Label given to symbol in plot legend.

symbolShape

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.

symbolColor

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.

symbolSize

The size of the symbol for the dose group sample means. Set symbolSize=0 to supress plotting the means.

bwidth

Width of the cap on the predictive interval bars.

xlim

Plot limits for the x-axis

xat

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.

ylim

Plot limits for the y-axis

logScale

If TRUE, log scale is used for dose.

ngrid

The number doses evaluated when plotting the curve.

plot

Return plotting output without plotting.

...

No additional plotting options are currently used.

Details

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.

Value

A list with ggplot object, and posterior and prediction interval limits.

Author(s)

Neal Thomas

See Also

fitEmaxB

Examples

## 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$sampsize-1)*(exdat$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)

## End(Not run)