From a11db44b5483b8c28752173bf31d2f51cfeb15b5 Mon Sep 17 00:00:00 2001 From: Philip Delff Date: Sun, 10 Sep 2023 22:20:26 -0400 Subject: [PATCH] vignette fix --- DESCRIPTION | 2 +- vignettes/NMsim-simulate.Rmd | 25 ++++++++++++-------- vignettes/simulate-results/simres_varka.fst | Bin 10564 -> 21940 bytes 3 files changed, 16 insertions(+), 11 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 1993cf6b..c3c45502 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: NMsim Type: Package Title: Nonmem simulation seamlessly integrated in R -Version: 0.0.1.946 +Version: 0.0.1.947 Authors@R: c(person("Philip", "Delff", email = "philip@delff.dk",role = c("aut","cre")), person("Matthew","Fidler", role = c("ctb"), email = "matt.fidler@novartis.com", comment="Co-author on NMreadCov")) Maintainer: Philip Delff diff --git a/vignettes/NMsim-simulate.Rmd b/vignettes/NMsim-simulate.Rmd index e672e0c4..99f7beb7 100644 --- a/vignettes/NMsim-simulate.Rmd +++ b/vignettes/NMsim-simulate.Rmd @@ -721,7 +721,7 @@ Sometimes we want to simulate with some modification to the estimated model. NMs The SAD study was run with a fast solution formulation. We want to see how a slower absorption rate would affect the PK prediction for the multiple dose regimen. In the model estimate, `TVKA=2.17`. We now try with a four times slower absorption: -```{r} +```{r,eval=FALSE} ## NMscanData(file.mod) |> findCovs() simres.slowabs <- NMsim(file.mod=file.mod, data=dat.sim @@ -731,11 +731,6 @@ simres.slowabs <- NMsim(file.mod=file.mod, ,list.sections=list(PK=function(x)c(x,"TVKA=TVKA/4","KA=KA/4")) ) -simres.slowabs |> findCovs() - -rbind(simres,simres.slowabs) |> - ggplot(aes(TIME,PRED,colour=model))+ - geom_line() ``` ```{r,include=FALSE,eval=TRUE} file.fst <- "simulate-results/simres_slowabs.fst" @@ -746,6 +741,14 @@ if(run.simuls){ } ``` +```{r,eval=TRUE} +simres.slowabs |> findCovs() + +rbind(simres,simres.slowabs) |> + ggplot(aes(TIME,PRED,colour=model))+ + geom_line() + +``` We used `list.sections` to modify the `$PK` section. We used it to append two lines. We could use it to modify any section in the model, @@ -768,10 +771,6 @@ simres.varka <- NMsim(file.mod=file.mod, ,list.sections=list(PK=function(x)c(x,"TVKA=TVKA/KASCALE","KA=KA/KASCALE")) ) -simres.varka |> findCovs(by="KASCALE") -simres.varka - -ggplot(simres.varka[EVID==2],aes(TIME,PRED,colour=factor(KASCALE)))+geom_line()+labs(colour="Fold absorption prolongation") ``` ```{r,include=FALSE,eval=TRUE} file.fst <- "simulate-results/simres_varka.fst" @@ -782,4 +781,10 @@ if(run.simuls){ } ``` +```{r,eval=TRUE} +simres.varka |> findCovs(by="KASCALE") + +ggplot(simres.varka[simres.varka$EVID==2,],aes(TIME,PRED,colour=factor(KASCALE)))+geom_line()+labs(colour="Fold absorption prolongation") +``` + diff --git a/vignettes/simulate-results/simres_varka.fst b/vignettes/simulate-results/simres_varka.fst index 39e9fb1cffa5b60ecf0ddf63ba66ae04a641fb4a..6f5be8a9706e8c34a1465c477ddd130aeb88adf0 100644 GIT binary patch literal 21940 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