Small documenation changes

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")