diff --git a/README.Rmd b/README.Rmd index 68d9765c..886e9b7d 100644 --- a/README.Rmd +++ b/README.Rmd @@ -131,16 +131,18 @@ Since `NMscanData` is so general and will figure out where to find input and output data on its own, let's use the `NMscanMultiple` wrapper to read multiple models and compare their predictions. -```{r} +```{r,NMscanMultiple-plot} res <- NMscanMultiple(dir=system.file("examples/nonmem", package="NMdata"), -file.pattern="xgxr.*\\.lst",as.fun="data.table",quiet=TRUE) + file.pattern="xgxr.*\\.lst",as.fun="data.table",quiet=TRUE) gmean <- function(x)exp(mean(log(x))) res.mean <- res[,.(gmeanPRED=gmean(PRED)),by=.(model,NOMTIME)] obs.all <- unique(res[,.(ID,NOMTIME,TIME,DV)]) ggplot(res.mean,aes(NOMTIME,gmeanPRED,colour=model))+geom_line()+ - geom_point(aes(TIME,DV),data=obs.all,inherit.aes=FALSE)+ + geom_point(aes(TIME,DV),data=obs.all[!is.na(DV)],inherit.aes=FALSE)+ scale_y_log10()+ - labs(x="Time",y="Concentration",subtitle="Comparison of population predictions") + labs(x="Time",y="Concentration",subtitle="Comparison of population predictions")+ + theme_bw()+ + theme(legend.position="bottom") ``` diff --git a/README.md b/README.md index 45cac84e..a4002997 100644 --- a/README.md +++ b/README.md @@ -158,22 +158,24 @@ read multiple models and compare their predictions. ``` r res <- NMscanMultiple(dir=system.file("examples/nonmem", package="NMdata"), -file.pattern="xgxr.*\\.lst",as.fun="data.table",quiet=TRUE) + file.pattern="xgxr.*\\.lst",as.fun="data.table",quiet=TRUE) #> $DATA section extracted #> Based on that, data files related to this file were expected: gmean <- function(x)exp(mean(log(x))) res.mean <- res[,.(gmeanPRED=gmean(PRED)),by=.(model,NOMTIME)] obs.all <- unique(res[,.(ID,NOMTIME,TIME,DV)]) ggplot(res.mean,aes(NOMTIME,gmeanPRED,colour=model))+geom_line()+ - geom_point(aes(TIME,DV),data=obs.all,inherit.aes=FALSE)+ + geom_point(aes(TIME,DV),data=obs.all[!is.na(DV)],inherit.aes=FALSE)+ scale_y_log10()+ - labs(x="Time",y="Concentration",subtitle="Comparison of population predictions") + labs(x="Time",y="Concentration",subtitle="Comparison of population predictions")+ + theme_bw()+ + theme(legend.position="bottom") #> Warning: Transformation introduced infinite values in continuous y-axis #> Warning: Transformation introduced infinite values in continuous y-axis ``` - + ## Get the most recent version diff --git a/man/figures/README-NMscanMultiple-plot-1.png b/man/figures/README-NMscanMultiple-plot-1.png new file mode 100644 index 00000000..292a6005 Binary files /dev/null and b/man/figures/README-NMscanMultiple-plot-1.png differ