diff options
Diffstat (limited to 'docs/reference/mkinmod.html')
| -rw-r--r-- | docs/reference/mkinmod.html | 62 |
1 files changed, 40 insertions, 22 deletions
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 @@ <span class='no'>SFO_SFO</span> <span class='kw'><-</span> <span class='fu'>mkinmod</span>( <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> -<span class='co'>## Not run: ------------------------------------</span> -<span class='co'># # The above model used to be specified like this, before the advent of mkinsub()</span> -<span class='co'># SFO_SFO <- mkinmod(</span> -<span class='co'># parent = list(type = "SFO", to = "m1"),</span> -<span class='co'># m1 = list(type = "SFO"))</span> -<span class='co'># </span> -<span class='co'># # Show details of creating the C function</span> -<span class='co'># SFO_SFO <- mkinmod(</span> -<span class='co'># parent = mkinsub("SFO", "m1"),</span> -<span class='co'># m1 = mkinsub("SFO"), verbose = TRUE)</span> -<span class='co'># </span> -<span class='co'># # If we have several parallel metabolites </span> -<span class='co'># # (compare tests/testthat/test_synthetic_data_for_UBA_2014.R)</span> -<span class='co'># m_synth_DFOP_par <- mkinmod(parent = mkinsub("DFOP", c("M1", "M2")),</span> -<span class='co'># M1 = mkinsub("SFO"),</span> -<span class='co'># M2 = mkinsub("SFO"),</span> -<span class='co'># use_of_ff = "max", quiet = TRUE)</span> -<span class='co'># </span> -<span class='co'># fit_DFOP_par_c <- mkinfit(m_synth_DFOP_par, </span> -<span class='co'># synthetic_data_for_UBA_2014[[12]]$data,</span> -<span class='co'># quiet = TRUE)</span> -<span class='co'>## ---------------------------------------------</span></div></pre> + +<span class='co'># The above model used to be specified like this, before the advent of mkinsub()</span> +<span class='no'>SFO_SFO</span> <span class='kw'><-</span> <span class='fu'>mkinmod</span>( + <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"m1"</span>), + <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> +<span class='co'># Show details of creating the C function</span> +<span class='no'>SFO_SFO</span> <span class='kw'><-</span> <span class='fu'>mkinmod</span>( + <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), + <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> 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: }</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> +<span class='co'># If we have several parallel metabolites </span> +<span class='co'># (compare tests/testthat/test_synthetic_data_for_UBA_2014.R)</span> +<span class='no'>m_synth_DFOP_par</span> <span class='kw'><-</span> <span class='fu'>mkinmod</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"DFOP"</span>, <span class='fu'>c</span>(<span class='st'>"M1"</span>, <span class='st'>"M2"</span>)), + <span class='kw'>M1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), + <span class='kw'>M2</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), + <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) + +<span class='no'>fit_DFOP_par_c</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>m_synth_DFOP_par</span>, + <span class='no'>synthetic_data_for_UBA_2014</span><span class='kw'>[[</span><span class='fl'>12</span>]]$<span class='no'>data</span>, + <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> |