In metrumresearchgroup/mrgsolve: Simulate from ODE-Based Models

library(mrgsolve)
library(dplyr)
library(knitr)
options(width=120)
opts_chunk$set(comment='',echo=FALSE,message=FALSE)

prep_chunk <- function(x) {
  paste(capture.output(print(x)),collapse="\n")
}

mod <- mread(model = params$model, project = params$project, compile=params$compile, quiet=TRUE)

blocks <- modelparse(mod@code, drop_blank=FALSE, comment_re="//")
prob <- blocks[["PROB"]]
if(is.null(prob)) prob <- paste0("# Model: `", mrgsolve:::model(mod),"`")

par <-  capture.output(param(mod))
init <- capture.output(init(mod))
rmbl <- function(x) x[x!=""]

r knit(text=prob)

Details

d <- mrgsolve:::details(mod,values=FALSE)
if(nrow(d) > 0) {

  om <- omat(mod)
  dfom <- data.frame(name=unlist(labels(om)),
                     value=diag(as.matrix(om)))

  sg <- smat(mod)
  dfsg <- data.frame(name=unlist(labels(sg)),
                     value=diag(as.matrix(sg)))

  dfp <- 
    as.data.frame(t(as.data.frame(allparam(mod)))) %>% 
    setNames(.,"value") %>%
    mutate(name=rownames(.))

  dfi <- as.data.frame(t(as.data.frame(init(mod)))) %>%
    setNames(.,"value") %>%
    mutate(name=rownames(.))

  dfj <- bind_rows(dfp,dfi,dfom,dfsg)

  d <- left_join(d,dfj,by="name")

  x <- paste(capture.output(print(d,row.names=FALSE)),collapse="\n")

} else {
  x <- "No annotations were found in the model file."
}

```{c,echo=TRUE,eval=FALSE,code=x}

# Parameter and fixed values
```r
x <- prep_chunk(allparam(mod))

```{c,code=x,eval=FALSE,echo=TRUE}

# Compartments and initial values
```r
x <- prep_chunk(init(mod))

```{bash,code=x,eval=FALSE,echo=TRUE}

# Model code

```r
x <- paste(capture.output(blocks(mod,GLOBAL,MAIN,ODE,TABLE,SET,PKMODEL)),collapse="\n")

```{Rcpp,code=x,eval=FALSE,echo=TRUE}

# Environment
```r
x <- env_ls(mod)
if(nrow(x) > 0) {
  x <- capture.output(print(x,row.names=FALSE))
  x <- paste(x,collapse="\n")
} else {
  x <- capture.output(cat("No objects in $ENV"))
}

```{c,echo=TRUE,eval=FALSE,code=x}

# Rendered
```r
x <- capture.output(cat(date()))

{c,code=x,eval=FALSE,echo=TRUE}

metrumresearchgroup/mrgsolve documentation built on Feb. 13, 2024, 10:27 p.m.