From 3eefecf0adfbb30b8fb895c244dea6903bcb3e9c Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 31 Jan 2019 16:55:20 +0100 Subject: Restore NAMESPACE which was accidentally overwritten by pkgdown -> roxygen --- docs/reference/mkinmod.html | 35 +++++++++++++++++++++++++++++------ 1 file changed, 29 insertions(+), 6 deletions(-) (limited to 'docs/reference/mkinmod.html') diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index d8114300..84b335f7 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -217,28 +217,51 @@ For the definition of model types and their parameters, the equations given

Examples

# Specify the SFO model (this is not needed any more, as we can now mkinfit("SFO", ...)
-SFO <- mkinmod(parent = list(type = "SFO"))
#> Error in mkinmod(parent = list(type = "SFO")): konnte Funktion "mkinmod" nicht finden

+SFO <- mkinmod(parent = list(type = "SFO"))
+
 # One parent compound, one metabolite, both single first order
 SFO_SFO <- mkinmod(
   parent = mkinsub("SFO", "m1"),
-  m1 = mkinsub("SFO"))
#> Error in mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO")): konnte Funktion "mkinmod" nicht finden

+  m1 = mkinsub("SFO"))
#> Successfully compiled differential equation model from auto-generated C code.

 
# 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"))
#> Error in mkinmod(parent = list(type = "SFO", to = "m1"), m1 = list(type = "SFO")): konnte Funktion "mkinmod" nicht finden

+  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)
#> Error in mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"), verbose = TRUE): konnte Funktion "mkinmod" nicht finden

+  m1 = mkinsub("SFO"), verbose = TRUE)
#> Compilation argument:
+#>  /usr/lib/R/bin/R CMD SHLIB file165a4bc987b7.c 2> file165a4bc987b7.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)
#> Error in mkinmod(parent = mkinsub("DFOP", c("M1", "M2")), M1 = mkinsub("SFO"),     M2 = mkinsub("SFO"), use_of_ff = "max", quiet = TRUE): konnte Funktion "mkinmod" nicht finden

+                           use_of_ff = "max", quiet = TRUE)
+
 fit_DFOP_par_c <- mkinfit(m_synth_DFOP_par,
                           synthetic_data_for_UBA_2014[[12]]$data,
-                          quiet = TRUE)
#> Error in mkinfit(m_synth_DFOP_par, synthetic_data_for_UBA_2014[[12]]$data,     quiet = TRUE): konnte Funktion "mkinfit" nicht finden
+ quiet = TRUE)