From 6c62c42eb57631aa0f4ab7e008621ffb519bd7be Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 23 Jun 2015 11:21:49 +0200 Subject: Small documenation changes --- man/IORE.solution.Rd | 16 +++++++++------- man/mkinfit.Rd | 2 +- man/mkinparplot.Rd | 4 ++-- vignettes/FOCUS_D.Rmd | 5 ++--- vignettes/compiled_models.Rmd | 5 +++-- 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") -- cgit v1.2.1