From c6086d1dd97ad2d6420625de7b8009b1b0f85d06 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 18 Nov 2016 15:01:53 +0100 Subject: Static documentation rebuilt by pkgdown::build_site(run_dont_run = TRUE) Using branch 'jranke' on jranke/pkgdown, fixing issues hadley/pgkdown#178 and hadley/pkgdown#213 Remove plot=TRUE from mkinfit calls also in dontrun sections of examples to avoid a flood png files documenting the progress of the fit. --- docs/reference/mkinmod.html | 62 +++++++++++++++++++++++++++++---------------- 1 file changed, 40 insertions(+), 22 deletions(-) (limited to 'docs/reference/mkinmod.html') diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index f328c34a..9477d648 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -164,28 +164,46 @@ SFO_SFO <- mkinmod( parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"))
#> Successfully compiled differential equation model from auto-generated C code.
-## Not run: ------------------------------------ -# # The above model used to be specified like this, before the advent of mkinsub() -# SFO_SFO <- mkinmod( -# parent = list(type = "SFO", to = "m1"), -# m1 = list(type = "SFO")) -# -# # Show details of creating the C function -# SFO_SFO <- mkinmod( -# parent = mkinsub("SFO", "m1"), -# m1 = mkinsub("SFO"), verbose = TRUE) -# -# # If we have several parallel metabolites -# # (compare tests/testthat/test_synthetic_data_for_UBA_2014.R) -# m_synth_DFOP_par <- mkinmod(parent = mkinsub("DFOP", c("M1", "M2")), -# M1 = mkinsub("SFO"), -# M2 = mkinsub("SFO"), -# use_of_ff = "max", quiet = TRUE) -# -# fit_DFOP_par_c <- mkinfit(m_synth_DFOP_par, -# synthetic_data_for_UBA_2014[[12]]$data, -# quiet = TRUE) -## ---------------------------------------------
+ +# The above model used to be specified like this, before the advent of mkinsub() +SFO_SFO <- mkinmod( + parent = list(type = "SFO", to = "m1"), + m1 = list(type = "SFO"))
#> Successfully compiled differential equation model from auto-generated C code.
+# Show details of creating the C function +SFO_SFO <- mkinmod( + parent = mkinsub("SFO", "m1"), + m1 = mkinsub("SFO"), verbose = TRUE)
#> Compilation argument: +#> /usr/lib/R/bin/R CMD SHLIB file21efdcf882f.c 2> file21efdcf882f.c.err.txt +#> Program source: +#> 1: #include <R.h> +#> 2: +#> 3: +#> 4: static double parms [3]; +#> 5: #define k_parent_sink parms[0] +#> 6: #define k_parent_m1 parms[1] +#> 7: #define k_m1_sink parms[2] +#> 8: +#> 9: void initpar(void (* odeparms)(int *, double *)) { +#> 10: int N = 3; +#> 11: odeparms(&N, parms); +#> 12: } +#> 13: +#> 14: +#> 15: void func ( int * n, double * t, double * y, double * f, double * rpar, int * ipar ) { +#> 16: +#> 17: f[0] = - k_parent_sink * y[0] - k_parent_m1 * y[0]; +#> 18: f[1] = + k_parent_m1 * y[0] - k_m1_sink * y[1]; +#> 19: }
#> Successfully compiled differential equation model from auto-generated C code.
+# If we have several parallel metabolites +# (compare tests/testthat/test_synthetic_data_for_UBA_2014.R) +m_synth_DFOP_par <- mkinmod(parent = mkinsub("DFOP", c("M1", "M2")), + M1 = mkinsub("SFO"), + M2 = mkinsub("SFO"), + use_of_ff = "max", quiet = TRUE) + +fit_DFOP_par_c <- mkinfit(m_synth_DFOP_par, + synthetic_data_for_UBA_2014[[12]]$data, + quiet = TRUE)