diff options
Diffstat (limited to 'docs/dev/reference/mkinmod.html')
| -rw-r--r-- | docs/dev/reference/mkinmod.html | 91 |
1 files changed, 57 insertions, 34 deletions
diff --git a/docs/dev/reference/mkinmod.html b/docs/dev/reference/mkinmod.html index 803be90d..9e37e664 100644 --- a/docs/dev/reference/mkinmod.html +++ b/docs/dev/reference/mkinmod.html @@ -162,9 +162,13 @@ components.</p> <pre class="usage"><span class='fu'>mkinmod</span><span class='op'>(</span> <span class='va'>...</span>, use_of_ff <span class='op'>=</span> <span class='st'>"max"</span>, + name <span class='op'>=</span> <span class='cn'>NULL</span>, speclist <span class='op'>=</span> <span class='cn'>NULL</span>, quiet <span class='op'>=</span> <span class='cn'>FALSE</span>, - verbose <span class='op'>=</span> <span class='cn'>FALSE</span> + verbose <span class='op'>=</span> <span class='cn'>FALSE</span>, + dll_dir <span class='op'>=</span> <span class='cn'>NULL</span>, + unload <span class='op'>=</span> <span class='cn'>FALSE</span>, + overwrite <span class='op'>=</span> <span class='cn'>FALSE</span> <span class='op'>)</span> <span class='co'># S3 method for mkinmod</span> @@ -201,6 +205,10 @@ formation fractions is made, i.e. each pathway to a metabolite has its own rate constant.</p></td> </tr> <tr> + <th>name</th> + <td><p>A name for the model. Should be a valid R object name.</p></td> + </tr> + <tr> <th>speclist</th> <td><p>The specification of the observed variables and their submodel types and pathways can be given as a single list using this @@ -216,6 +224,23 @@ argument. Default is NULL.</p></td> applicable to give detailed information about the C function being built.</p></td> </tr> <tr> + <th>dll_dir</th> + <td><p>Directory where an DLL object, if generated internally by +<code><a href='https://rdrr.io/pkg/inline/man/cfunction.html'>inline::cfunction()</a></code>, should be saved. The DLL will only be stored in a +permanent location for use in future sessions, if 'dll_dir' and 'name' +are specified.</p></td> + </tr> + <tr> + <th>unload</th> + <td><p>If a DLL from the target location in 'dll_dir' is already +loaded, should that be unloaded first?</p></td> + </tr> + <tr> + <th>overwrite</th> + <td><p>If a file exists at the target DLL location in 'dll_dir', +should this be overwritten?</p></td> + </tr> + <tr> <th>x</th> <td><p>An <code>mkinmod</code> object.</p></td> </tr> @@ -299,18 +324,37 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p> <span class='va'>SFO_SFO</span> <span class='op'><-</span> <span class='fu'>mkinmod</span><span class='op'>(</span> parent <span class='op'>=</span> <span class='fu'>mkinsub</span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"m1"</span><span class='op'>)</span>, m1 <span class='op'>=</span> <span class='fu'>mkinsub</span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> +</div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>SFO_SFO</span><span class='op'>)</span> +</div><div class='output co'>#> <mkinmod> model generated with +#> Use of formation fractions $use_of_ff: max +#> Specification $spec: +#> $parent +#> $type: SFO; $to: m1; $sink: TRUE +#> $m1 +#> $type: SFO; $sink: TRUE +#> Coefficient matrix $coefmat available +#> Compiled model $cf available +#> Differential equations: +#> d_parent/dt = - k_parent * parent +#> d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1</div><div class='input'> <span class='co'># \dontrun{</span> -<span class='co'># Now supplying full names used for plotting</span> + <span class='va'>fit_sfo_sfo</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO</span>, <span class='va'>FOCUS_2006_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, solution_type <span class='op'>=</span> <span class='st'>"deSolve"</span><span class='op'>)</span> +</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'> + <span class='co'># Now supplying compound names used for plotting, and write to user defined location</span> + <span class='co'># We need to choose a path outside the session tempdir because this gets removed</span> + <span class='va'>DLL_dir</span> <span class='op'><-</span> <span class='st'>"~/.local/share/mkin"</span> + <span class='kw'>if</span> <span class='op'>(</span><span class='op'>!</span><span class='fu'><a href='https://rdrr.io/r/base/files2.html'>dir.exists</a></span><span class='op'>(</span><span class='va'>DLL_dir</span><span class='op'>)</span><span class='op'>)</span> <span class='fu'><a href='https://rdrr.io/r/base/files2.html'>dir.create</a></span><span class='op'>(</span><span class='va'>DLL_dir</span><span class='op'>)</span> <span class='va'>SFO_SFO.2</span> <span class='op'><-</span> <span class='fu'>mkinmod</span><span class='op'>(</span> parent <span class='op'>=</span> <span class='fu'>mkinsub</span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"m1"</span>, full_name <span class='op'>=</span> <span class='st'>"Test compound"</span><span class='op'>)</span>, - m1 <span class='op'>=</span> <span class='fu'>mkinsub</span><span class='op'>(</span><span class='st'>"SFO"</span>, full_name <span class='op'>=</span> <span class='st'>"Metabolite M1"</span><span class='op'>)</span><span class='op'>)</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'># The above model used to be specified like this, before the advent of mkinsub()</span> -<span class='va'>SFO_SFO</span> <span class='op'><-</span> <span class='fu'>mkinmod</span><span class='op'>(</span> - parent <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"m1"</span><span class='op'>)</span>, - m1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> + m1 <span class='op'>=</span> <span class='fu'>mkinsub</span><span class='op'>(</span><span class='st'>"SFO"</span>, full_name <span class='op'>=</span> <span class='st'>"Metabolite M1"</span><span class='op'>)</span>, + name <span class='op'>=</span> <span class='st'>"SFO_SFO"</span>, dll_dir <span class='op'>=</span> <span class='va'>DLL_dir</span>, unload <span class='op'>=</span> <span class='cn'>TRUE</span>, overwrite <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> +</div><div class='output co'>#> <span class='message'>Copied DLL from /tmp/RtmpX9Xf3y/file6d622f3b7e08.so to /home/jranke/.local/share/mkin/SFO_SFO.so</span></div><div class='input'><span class='co'># Now we can save the model and restore it in a new session</span> +<span class='fu'><a href='https://rdrr.io/r/base/readRDS.html'>saveRDS</a></span><span class='op'>(</span><span class='va'>SFO_SFO.2</span>, file <span class='op'>=</span> <span class='st'>"~/SFO_SFO.rds"</span><span class='op'>)</span> +<span class='co'># Terminate the R session here if you would like to check, and then do</span> +<span class='kw'><a href='https://rdrr.io/r/base/library.html'>library</a></span><span class='op'>(</span><span class='va'><a href='https://pkgdown.jrwb.de/mkin/'>mkin</a></span><span class='op'>)</span> +<span class='va'>SFO_SFO.3</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/readRDS.html'>readRDS</a></span><span class='op'>(</span><span class='st'>"~/SFO_SFO.rds"</span><span class='op'>)</span> +<span class='va'>fit_sfo_sfo</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO.3</span>, <span class='va'>FOCUS_2006_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, solution_type <span class='op'>=</span> <span class='st'>"deSolve"</span><span class='op'>)</span> +</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'> <span class='co'># Show details of creating the C function</span> <span class='va'>SFO_SFO</span> <span class='op'><-</span> <span class='fu'>mkinmod</span><span class='op'>(</span> parent <span class='op'>=</span> <span class='fu'>mkinsub</span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"m1"</span><span class='op'>)</span>, @@ -330,11 +374,11 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p> #> 12: } #> 13: #> 14: -#> 15: void func ( int * n, double * t, double * y, double * f, double * rpar, int * ipar ) { +#> 15: void diffs ( int * n, double * t, double * y, double * f, double * rpar, int * ipar ) { #> 16: #> 17: f[0] = - k_parent * y[0]; #> 18: f[1] = + f_parent_to_m1 * k_parent * y[0] - k_m1 * 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'> +#> 19: }</div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'> <span class='co'># The symbolic solution which is available in this case is not</span> <span class='co'># made for human reading but for speed of computation</span> <span class='va'>SFO_SFO</span><span class='op'>$</span><span class='va'>deg_func</span> @@ -353,7 +397,7 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p> #> }) #> return(predicted) #> } -#> <environment: 0x55555c97f8d8></div><div class='input'> +#> <environment: 0x55555c5b8d68></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='va'>m_synth_DFOP_par</span> <span class='op'><-</span> <span class='fu'>mkinmod</span><span class='op'>(</span> @@ -367,27 +411,6 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p> quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> <span class='co'># }</span> - - <span class='va'>m_synth_SFO_lin</span> <span class='op'><-</span> <span class='fu'>mkinmod</span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"M1"</span><span class='op'>)</span>, - M1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"M2"</span><span class='op'>)</span>, - M2 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span>, use_of_ff <span class='op'>=</span> <span class='st'>"max"</span><span class='op'>)</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='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>m_synth_SFO_lin</span><span class='op'>)</span> -</div><div class='output co'>#> <mkinmod> model generated with -#> Use of formation fractions $use_of_ff: max -#> Specification $spec: -#> $parent -#> $type: SFO; $to: M1; $sink: TRUE -#> $M1 -#> $type: SFO; $to: M2; $sink: TRUE -#> $M2 -#> $type: SFO; $sink: TRUE -#> Coefficient matrix $coefmat available -#> Compiled model $cf available -#> Differential equations: -#> d_parent/dt = - k_parent * parent -#> d_M1/dt = + f_parent_to_M1 * k_parent * parent - k_M1 * M1 -#> d_M2/dt = + f_M1_to_M2 * k_M1 * M1 - k_M2 * M2</div><div class='input'> </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> |