# Plot a Emax model and dose group means. Plot an Emax model stored in an object created by function `fitEmax`. ```r ## S3 method for class 'fitEmax' 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 `fitEmax` with class "fitEmax". - `int`: The index for the protocol (intercept) to use for the predictions and computation of dose group means and standard errors. 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 is produced instead of a dose response curve plot. - `clev`: Confidence level for intervals about the estimated mean for each dose. - `predict`: When predict=TRUE, predictive intervals for sample dose group means are plotted. They are gray-shaded bars. If there is `>1` symbol group mean for a protocol/dose combination, then the smaller sample size is used when computing the prediction interval. - `plotci`: When plotCI=TRUE, confidence intervals for the population dose group means 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. 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. 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. ## Returns A list with ggplot object, and a matrix with the confidence and prediction interval limits. ## Details Model estimates, standard errors, and confidence bounds are computed using function `SeEmax`. 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. ## Author(s) Neal Thomas ## See Also `nls` ## Examples ```r ### example changes the random number seed doselev<-c(0,5,25,50,100,350) n<-c(78,81,81,81,77,80) ### population parameters for simulation e0<-2.465375 ed50<-67.481113 dtarget<-100 diftarget<-9.032497 emax<-solveEmax(diftarget,dtarget,log(ed50),1,e0) sdy<-8.0 pop.parm<-c(log(ed50),emax,e0) dose<-rep(doselev,n) meanlev<-emaxfun(dose,pop.parm) y<-rnorm(sum(n),meanlev,sdy) testout<-fitEmax(y,dose,modType=4) plot(testout) ```

plot.fitEmax function