Compiled models article, reduce distractions

- Added a section with platform specific notes on getting compiled
models to work to the compiled models article
- Don't return empty SFORB parameter list from endpoints() if there is no
SFORB model
- Avoid warnings when using standardized = TRUE in plot.mmkin()

1 files changed, 41 insertions, 12 deletions

diff --git a/vignettes/web_only/compiled_models.Rmd b/vignettes/web_only/compiled_models.Rmd
index 26d86811..3f4e0097 100644
--- a/vignettes/web_only/compiled_models.Rmd
+++ b/vignettes/web_only/compiled_models.Rmd
@@ -18,17 +18,46 @@ library(knitr)
 opts_chunk$set(tidy = FALSE, cache = FALSE)

 ```

 

-## Model that can also be solved with Eigenvalues

+## How to benefit from compiled models

 

-This evaluation is taken from the example section of mkinfit. When using an mkin version

-equal to or greater than 0.9-36 and a C compiler (gcc) is available, you will see

-a message that the model is being compiled from autogenerated C code when

-defining a model using mkinmod. The `mkinmod()` function checks for presence of

-the gcc compiler using

+When using an mkin version equal to or greater than 0.9-36 and a C compiler is

+available, you will see a message that the model is being compiled from

+autogenerated C code when defining a model using mkinmod. Starting from

+version 0.9.49.9, the `mkinmod()` function checks for presence of a compiler

+using

 

-```{r check_gcc}

-Sys.which("gcc")

+```{r check_gcc, eval = FALSE}

+pkgbuild::has_compiler()

 ```

+

+In previous versions, it used `Sys.which("gcc")` for this check.

+

+On Linux, you need to have the essential build tools like make and gcc or clang

+installed. On Debian based linux distributions, these will be pulled in by installing

+the build-essential package.

+

+On MacOS, which I do not use personally, I have had reports that a compiler is

+available by default.

+

+On Windows, you need to install Rtools and have the path to its bin directory

+in your PATH variable. You do not need to modify the PATH variable when

+installing Rtools. Instead, I would recommend to put the line

+

+```{r Rprofile, eval = FALSE}

+Sys.setenv(PATH = paste("C:/Rtools/bin", Sys.getenv("PATH"), sep=";"))

+```

+into your .Rprofile startup file. This is just a text file with some R

+code that is executed when your R session starts. It has to be named .Rprofile

+and has to be located in your home directory, which will generally be your

+Documents folder. You can check the location of the home directory used by R by

+issuing

+

+```{r HOME, eval = FALSE}

+Sys.getenv("HOME")

+```

+

+## Comparison with Eigenvalue based solutions

+

 First, we build a simple degradation model for a parent compound with one metabolite.

 

 ```{r create_SFO_SFO}

@@ -40,10 +69,10 @@ SFO_SFO <- mkinmod(
 

 We can compare the performance of the Eigenvalue based solution against the

 compiled version and the R implementation of the differential equations using

-the benchmark package.

-

+the benchmark package. In the output of below code, the warnings about zero

+being removed from the FOCUS D dataset are suppressed.

 

-```{r benchmark_SFO_SFO, fig.height = 3}

+```{r benchmark_SFO_SFO, fig.height = 3, message = FALSE, warning = FALSE}

 if (require(rbenchmark)) {

   b.1 <- benchmark(

     "deSolve, not compiled" = mkinfit(SFO_SFO, FOCUS_2006_D,

@@ -73,7 +102,7 @@ iterative solution of the ODEs.
 

 This evaluation is also taken from the example section of mkinfit.

 

-```{r benchmark_FOMC_SFO, fig.height = 3}

+```{r benchmark_FOMC_SFO, fig.height = 3, warning = FALSE}

 if (require(rbenchmark)) {

   FOMC_SFO <- mkinmod(

     parent = mkinsub("FOMC", "m1"),