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-rw-r--r--man/IORE.solution.Rd16
-rw-r--r--man/mkinfit.Rd2
-rw-r--r--man/mkinparplot.Rd4
-rw-r--r--vignettes/FOCUS_D.Rmd5
-rw-r--r--vignettes/compiled_models.Rmd5
5 files changed, 17 insertions, 15 deletions
diff --git a/man/IORE.solution.Rd b/man/IORE.solution.Rd
index bb377d3f..bad7c1fa 100644
--- a/man/IORE.solution.Rd
+++ b/man/IORE.solution.Rd
@@ -30,12 +30,14 @@
Media
}
\examples{
- \dontrun{plot(function(x) IORE.solution(x, 100, 0.2, 1.3), 0, 2,
- ylim = c(0, 100))}
- m.fomc <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
- m.iore <- mkinfit("IORE", FOCUS_2006_C, quiet = TRUE)
- m.iore.deS <- mkinfit("IORE", FOCUS_2006_C, solution_type = "deSolve", quiet = TRUE)
- data.frame(coef(m.fomc), coef(m.iore), coef(m.iore.deS), row.names = paste("par", 1:3))
- rbind(endpoints(m.fomc)$distimes, endpoints(m.iore)$distimes, endpoints(m.iore)$distimes)
+ plot(function(x) IORE.solution(x, 100, 0.2, 1.3), 0, 2,
+ ylim = c(0, 100))
+ fit.fomc <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
+ fit.iore <- mkinfit("IORE", FOCUS_2006_C, quiet = TRUE)
+ fit.iore.deS <- mkinfit("IORE", FOCUS_2006_C, solution_type = "deSolve", quiet = TRUE)
+
+ data.frame(coef(fit.fomc), coef(fit.iore), coef(fit.iore.deS), row.names = paste("model par", 1:3))
+ print(rbind(fomc = endpoints(m.fomc)$distimes, iore = endpoints(m.iore)$distimes,
+ iore.deS = endpoints(m.iore)$distimes))
}
\keyword{ manip }
diff --git a/man/mkinfit.Rd b/man/mkinfit.Rd
index bf47879c..c6b6d601 100644
--- a/man/mkinfit.Rd
+++ b/man/mkinfit.Rd
@@ -247,7 +247,7 @@ print(system.time(fit <- mkinfit(SFO_SFO, FOCUS_2006_D,
coef(fit)
endpoints(fit)
\dontrun{
-# deSolve is slower when the gcc compiler is not available
+# deSolve is slower when no C compiler (gcc) was available during model generation
print(system.time(fit.deSolve <- mkinfit(SFO_SFO, FOCUS_2006_D,
solution_type = "deSolve")))
coef(fit.deSolve)
diff --git a/man/mkinparplot.Rd b/man/mkinparplot.Rd
index f40a96d1..3eda08d2 100644
--- a/man/mkinparplot.Rd
+++ b/man/mkinparplot.Rd
@@ -28,7 +28,7 @@ model <- mkinmod(
T245 = list(type = "SFO", to = c("phenol"), sink = FALSE),
phenol = list(type = "SFO", to = c("anisole")),
anisole = list(type = "SFO"), use_of_ff = "max")
-fit <- mkinfit(model, subset(mccall81_245T, soil == "Commerce"))
-\dontrun{mkinparplot(fit)}
+fit <- mkinfit(model, subset(mccall81_245T, soil == "Commerce"), quiet = TRUE)
+mkinparplot(fit)
}
\keyword{ hplot }
diff --git a/vignettes/FOCUS_D.Rmd b/vignettes/FOCUS_D.Rmd
index 38613082..4c65b80a 100644
--- a/vignettes/FOCUS_D.Rmd
+++ b/vignettes/FOCUS_D.Rmd
@@ -34,9 +34,8 @@ kinetics (SFO) to one metabolite named m1, which also degrades with SFO kinetics
The call to mkinmod returns a degradation model. The differential equations represented in
R code can be found in the character vector `$diffs` of the `mkinmod` object. If
-the gcc compiler is installed and functional, the differential equation model
-will be compiled from auto-generated C code.
-
+a C compiler (gcc) is installed and functional, the differential equation model will
+be compiled from auto-generated C code.
```{r}
SFO_SFO <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"))
diff --git a/vignettes/compiled_models.Rmd b/vignettes/compiled_models.Rmd
index 5ee3f7bc..8dc74692 100644
--- a/vignettes/compiled_models.Rmd
+++ b/vignettes/compiled_models.Rmd
@@ -22,9 +22,10 @@ opts_chunk$set(tidy = FALSE, cache = TRUE)
## Benchmark for a model that can also be solved with Eigenvalues
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 compiler (gcc) is installed, you will see
+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 package tests for presence of the gcc compiler using
+defining a model using mkinmod. The `mkinmod()` function checks for presence of
+the gcc compiler using
```{r check_gcc}
Sys.which("gcc")

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