From dfa136646cc8302158a036653f5a05566e36e118 Mon Sep 17 00:00:00 2001 From: Kyle Baron Date: Tue, 23 Mar 2021 08:52:59 -0500 Subject: [PATCH] extra vignettes --- .Rbuildignore | 7 +++---- .gitignore | 3 +++ Makefile | 6 ++++++ vignettes/events.Rmd | 14 +++++++------- vignettes/extra/global.R | 2 ++ vignettes/extra/make.R | 6 ++++++ vignettes/{ => extra}/mevent.Rmd.txt | 0 .../{mtime.Rmd => extra/modeled-event-time.Rmd} | 0 vignettes/{ => extra}/mtime-after-dose.txt | 0 vignettes/{ => extra}/mtime-model-2.txt | 0 vignettes/{ => extra}/mtime-model.txt | 0 vignettes/{ => extra}/time-after-dose.Rmd | 0 vignettes/{ => extra}/time-after-dose.txt | 0 vignettes/mrgsolve.Rmd | 2 -- vignettes/steady-state.Rmd | 4 ++-- 15 files changed, 29 insertions(+), 15 deletions(-) create mode 100644 vignettes/extra/global.R create mode 100644 vignettes/extra/make.R rename vignettes/{ => extra}/mevent.Rmd.txt (100%) rename vignettes/{mtime.Rmd => extra/modeled-event-time.Rmd} (100%) rename vignettes/{ => extra}/mtime-after-dose.txt (100%) rename vignettes/{ => extra}/mtime-model-2.txt (100%) rename vignettes/{ => extra}/mtime-model.txt (100%) rename vignettes/{ => extra}/time-after-dose.Rmd (100%) rename vignettes/{ => extra}/time-after-dose.txt (100%) diff --git a/.Rbuildignore b/.Rbuildignore index 56ff7b46..feefdc86 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -49,9 +49,8 @@ docs ^\.drone\.jsonnet$ ^doc$ ^Meta$ -vignettes/mevent\.Rmd -vignettes/mevent-0\.cpp -vignettes/mevent-1\.cpp +vignettes/extra vignettes/build -vignettes/mrgsolve_builds vignettes/mrgsolve-builds +vignettes/extra/mrgsolve-builds/ + diff --git a/.gitignore b/.gitignore index 98322c0b..f75497fe 100644 --- a/.gitignore +++ b/.gitignore @@ -17,3 +17,6 @@ Rchecks inst/maintenance/unit/tests.md doc Meta +inst/maintenance/unit/mrgsolve-so* +vignettes/mrgsolve-builds +vignettes/extra/mrgsolve-builds/ diff --git a/Makefile b/Makefile index 373bcae3..890bca8d 100644 --- a/Makefile +++ b/Makefile @@ -24,6 +24,8 @@ package: make house make doc make build-vignettes + make vignettes2 + make install check: make house @@ -35,10 +37,14 @@ check: cran: make house make doc + make vignettes2 make build-vignettes export _MRGSOLVE_SKIP_MODLIB_BUILD_=false R CMD CHECK --as-cran ${TARBALL} +vignettes2: + Rscript vignettes/extra/make.R + drone: make house R CMD build --md5 $(PKGDIR) diff --git a/vignettes/events.Rmd b/vignettes/events.Rmd index c2e2961e..ca51c83f 100755 --- a/vignettes/events.Rmd +++ b/vignettes/events.Rmd @@ -35,7 +35,7 @@ Let's illustrate event objects with a one-compartment, PK model. We read this model from the `mrgsolve` internal model library. ```{r,message=FALSE} -mod <- modlib("pk1cmt", end = 216, delta = 0.1) +mod <- house(end = 216, delta = 0.1) ``` # Events @@ -61,7 +61,7 @@ We can implement this series of doses by passing `e` in as the `events` argument to `mrgsim` ```{r} -mod %>% mrgsim(events = e) %>% plot(EV1 + CP ~ time) +mod %>% mrgsim(events = e) %>% plot(GUT + CP ~ time) ``` @@ -105,10 +105,10 @@ We can combine `e1` and `e3` with a collection operator c(e1, e4) ``` -`mrgsolve` also defines a `%then$` operator that lets you execute one event and -`%then%` a second event +`mrgsolve` also defines a `seq()` method that lets you execute one event and +then a second event ```{r} -e3 %then% e2 +seq(e3, e2) ``` Notice that `e3` has both `ii` and `addl` defined. This is required for @@ -138,10 +138,10 @@ data ``` To simulate from this data set, we use the `data_set` function. First, let's -load a population PK model +add an OMEGA matrix to this model: ```{r,message=FALSE} -mod <- modlib("popex") +mod <- omat(mod, as_dmat(c(0.1, 0.1, 0.1, 0.1))) ``` ```{r} mod %>% data_set(data) %>% mrgsim(end=336) %>% plot("GUT, DV") diff --git a/vignettes/extra/global.R b/vignettes/extra/global.R new file mode 100644 index 00000000..9149a205 --- /dev/null +++ b/vignettes/extra/global.R @@ -0,0 +1,2 @@ +knitr::opts_chunk$set(message = FALSE, warning = FALSE, comment='.') +options(mrgsolve.soloc = "mrgsolve-builds") diff --git a/vignettes/extra/make.R b/vignettes/extra/make.R new file mode 100644 index 00000000..0eab1c67 --- /dev/null +++ b/vignettes/extra/make.R @@ -0,0 +1,6 @@ +message("making secondary vignettes") +stopifnot(`rmarkdown is required` = require(rmarkdown)) +render("vignettes/extra/time-after-dose.Rmd", output_dir = "inst/doc", quiet = TRUE) +render("vignettes/extra/modeled-event-time.Rmd", output_dir = "inst/doc", quiet = TRUE) +res <- file.remove(list.files("inst/doc", pattern = "\\.md*", full.names=TRUE)) +res <- unlink("inst/doc/mtime_files", recursive = TRUE) diff --git a/vignettes/mevent.Rmd.txt b/vignettes/extra/mevent.Rmd.txt similarity index 100% rename from vignettes/mevent.Rmd.txt rename to vignettes/extra/mevent.Rmd.txt diff --git a/vignettes/mtime.Rmd b/vignettes/extra/modeled-event-time.Rmd similarity index 100% rename from vignettes/mtime.Rmd rename to vignettes/extra/modeled-event-time.Rmd diff --git a/vignettes/mtime-after-dose.txt b/vignettes/extra/mtime-after-dose.txt similarity index 100% rename from vignettes/mtime-after-dose.txt rename to vignettes/extra/mtime-after-dose.txt diff --git a/vignettes/mtime-model-2.txt b/vignettes/extra/mtime-model-2.txt similarity index 100% rename from vignettes/mtime-model-2.txt rename to vignettes/extra/mtime-model-2.txt diff --git a/vignettes/mtime-model.txt b/vignettes/extra/mtime-model.txt similarity index 100% rename from vignettes/mtime-model.txt rename to vignettes/extra/mtime-model.txt diff --git a/vignettes/time-after-dose.Rmd b/vignettes/extra/time-after-dose.Rmd similarity index 100% rename from vignettes/time-after-dose.Rmd rename to vignettes/extra/time-after-dose.Rmd diff --git a/vignettes/time-after-dose.txt b/vignettes/extra/time-after-dose.txt similarity index 100% rename from vignettes/time-after-dose.txt rename to vignettes/extra/time-after-dose.txt diff --git a/vignettes/mrgsolve.Rmd b/vignettes/mrgsolve.Rmd index d2ba9d03..76c59250 100644 --- a/vignettes/mrgsolve.Rmd +++ b/vignettes/mrgsolve.Rmd @@ -16,8 +16,6 @@ vignette: > --- ```{r setup, echo = FALSE, message = FALSE, warning = FALSE, code = readLines("global.R")} -mod <- mread_cache("pk1", modlib()) -mod <- mread_cache("pk2", modlib()) set.seed(20202) ``` diff --git a/vignettes/steady-state.Rmd b/vignettes/steady-state.Rmd index f7cb27e1..b89f4859 100644 --- a/vignettes/steady-state.Rmd +++ b/vignettes/steady-state.Rmd @@ -57,7 +57,7 @@ Let's load a PK model library(dplyr) library(mrgsolve) -mod <- modlib("pk2") +mod <- house(end = 24, delta = 1) ``` And let's imagine a 100 mg QD dosing regimen @@ -75,7 +75,7 @@ Let's just look at trough concentrations and see how the trough develops over the dosing period ```{r} -mod <- update(mod, delta = 24, end = 24*20, outvars = "CENT, PERIPH") +mod <- update(mod, delta = 24, end = 24*20, outvars = "CENT, RESP") ``` And simulate that out