## ----echo=FALSE,message=FALSE,warning=FALSE----------------------------------- library(nonmem2R) rm(list=ls()) ## ----echo=FALSE,fig.width=7,fig.height=5-------------------------------------- # Get path to the example files included in nonmem2R package file1 <- system.file("extdata", "vpctab004.dat", package = "nonmem2R") path1 <-gsub("vpctab004.dat","",file1) path2 <- system.file("extdata", "vpc001", package = "nonmem2R") ## ----echo=TRUE,fig.width=7,fig.height=5--------------------------------------- # Get path to the example files included in nonmem2R package file1 <- system.file("extdata", "vpctab004.dat", package = "nonmem2R") file2 <- system.file("extdata", "vpc_results.csv", package = "nonmem2R") # produce VPC with default setting, here specifying both vpctab and vpcresult vpcfig2(vpctab=file1,vpcresult=file2) ## ----echo=TRUE,fig.width=7,fig.height=5--------------------------------------- vpcfig2(path1)+ labs(x="Time after dose (hours)",y="Plasma concentration (nmol/L)")+ scale_y_log10()+ theme_bw() ## ----echo=TRUE,fig.width=7,fig.height=5--------------------------------------- fy<-function(y){log(y+1)} y.ticks<-c(0,1,10,100,1000) vpcfig2(path1,fy=fy)+ labs(x="Time after dose (hours)",y="Plasma concentration (nmol/L)")+ scale_y_continuous(breaks=fy(y.ticks),labels=y.ticks,minor_breaks=NULL)+ theme(legend.position="top") ## ----echo=TRUE,fig.width=7,fig.height=6--------------------------------------- vpcfig2(path1,strata.subset=2:1,strata.names=c("Cohort 1","Cohort 2")) ## ----echo=TRUE,fig.width=7,fig.height=6--------------------------------------- f1<-vpcfig2(path2,fy=log,strata.names=c("710mg","1000mg"),ylab="Plasma conc (umol/L)", censoring.labels=c("a","BLQ(%)"),xlab="Time after dose (hrs)") ##breaks for DV bry<-c(0.1,0.2,0.4,0.6,1,2,4,6,10,20,40,60) mbry<-c(1:10,(1:10)/10,(1:10)*10) ##breaks for BLQ, copied from the vpcfif2 console output brb<-c(5.55058263829153,6.2985767486289,7.04657085896627) lbb<-c(0,50,100) ## Get minor breaks for BLQ in between the main breaks mbrb<-(brb[-1]+brb[length(brb)])/2 f1+scale_y_continuous(breaks=c(brb,log(bry)), labels=c(lbb,bry),minor_breaks=c(mbrb,log(mbry)))