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Diffstat (limited to 'docs/reference/mkinpredict.html')
| -rw-r--r-- | docs/reference/mkinpredict.html | 47 |
1 files changed, 20 insertions, 27 deletions
diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index 17f38938..035a21f9 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -74,7 +74,7 @@ kinetic parameters and initial values for the state variables." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.0</span> </span> </div> @@ -123,7 +123,7 @@ kinetic parameters and initial values for the state variables." /> <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin/"> - <span class="fab fa fab fa-github fa-lg"></span> + <span class="fab fa-github fa-lg"></span> </a> </li> @@ -151,19 +151,7 @@ kinetic model as specified by <code><a href='mkinmod.html'>mkinmod</a></code>, u kinetic parameters and initial values for the state variables.</p> </div> - <pre class="usage"><span class='fu'>mkinpredict</span><span class='op'>(</span> - <span class='va'>x</span>, - <span class='va'>odeparms</span>, - <span class='va'>odeini</span>, - outtimes <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span><span class='op'>(</span><span class='fl'>0</span>, <span class='fl'>120</span>, by <span class='op'>=</span> <span class='fl'>0.1</span><span class='op'>)</span>, - solution_type <span class='op'>=</span> <span class='st'>"deSolve"</span>, - use_compiled <span class='op'>=</span> <span class='st'>"auto"</span>, - method.ode <span class='op'>=</span> <span class='st'>"lsoda"</span>, - atol <span class='op'>=</span> <span class='fl'>1e-08</span>, - rtol <span class='op'>=</span> <span class='fl'>1e-10</span>, - map_output <span class='op'>=</span> <span class='cn'>TRUE</span>, - <span class='va'>...</span> -<span class='op'>)</span> + <pre class="usage"><span class='fu'>mkinpredict</span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>odeparms</span>, <span class='va'>odeini</span>, <span class='va'>outtimes</span>, <span class='va'>...</span><span class='op'>)</span> <span class='co'># S3 method for mkinmod</span> <span class='fu'>mkinpredict</span><span class='op'>(</span> @@ -177,6 +165,7 @@ kinetic parameters and initial values for the state variables.</p> atol <span class='op'>=</span> <span class='fl'>1e-08</span>, rtol <span class='op'>=</span> <span class='fl'>1e-10</span>, map_output <span class='op'>=</span> <span class='cn'>TRUE</span>, + na_stop <span class='op'>=</span> <span class='cn'>TRUE</span>, <span class='va'>...</span> <span class='op'>)</span> @@ -222,6 +211,11 @@ observed variables, for example in the case of the SFORB model.</p></td> predictions should be generated.</p></td> </tr> <tr> + <th>...</th> + <td><p>Further arguments passed to the ode solver in case such a +solver is used.</p></td> + </tr> + <tr> <th>solution_type</th> <td><p>The method that should be used for producing the predictions. This should generally be "analytical" if there is only one @@ -258,9 +252,8 @@ FALSE). Setting this to FALSE has no effect for analytical solutions, as these always return mapped output.</p></td> </tr> <tr> - <th>...</th> - <td><p>Further arguments passed to the ode solver in case such a -solver is used.</p></td> + <th>na_stop</th> + <td><p>Should it be an error if deSolve::ode returns NaN values</p></td> </tr> </table> @@ -273,7 +266,7 @@ solver is used.</p></td> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> -<span class='va'>SFO</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>degradinol <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span><span class='op'>)</span> +<span class='va'>SFO</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>degradinol <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span><span class='op'>)</span> <span class='co'># Compare solution types</span> <span class='fu'>mkinpredict</span><span class='op'>(</span><span class='va'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>k_degradinol <span class='op'>=</span> <span class='fl'>0.3</span><span class='op'>)</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>degradinol <span class='op'>=</span> <span class='fl'>100</span><span class='op'>)</span>, <span class='fl'>0</span><span class='op'>:</span><span class='fl'>20</span>, solution_type <span class='op'>=</span> <span class='st'>"analytical"</span><span class='op'>)</span> @@ -395,7 +388,7 @@ solver is used.</p></td> <span class='co'># Comparison of the performance of solution types</span> <span class='va'>SFO_SFO</span> <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></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>, 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='kw'>if</span><span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='va'><a href='http://rbenchmark.googlecode.com'>rbenchmark</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span> +</div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'><span class='kw'>if</span><span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='va'><a href='http://rbenchmark.googlecode.com'>rbenchmark</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span> <span class='fu'><a href='https://rdrr.io/pkg/rbenchmark/man/benchmark.html'>benchmark</a></span><span class='op'>(</span>replications <span class='op'>=</span> <span class='fl'>10</span>, order <span class='op'>=</span> <span class='st'>"relative"</span>, columns <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"test"</span>, <span class='st'>"relative"</span>, <span class='st'>"elapsed"</span><span class='op'>)</span>, eigen <span class='op'>=</span> <span class='fu'>mkinpredict</span><span class='op'>(</span><span class='va'>SFO_SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>k_parent <span class='op'>=</span> <span class='fl'>0.15</span>, f_parent_to_m1 <span class='op'>=</span> <span class='fl'>0.5</span>, k_m1 <span class='op'>=</span> <span class='fl'>0.01</span><span class='op'>)</span>, @@ -415,10 +408,10 @@ solver is used.</p></td> solution_type <span class='op'>=</span> <span class='st'>"analytical"</span>, use_compiled <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span><span class='op'>[</span><span class='fl'>201</span>,<span class='op'>]</span><span class='op'>)</span> <span class='op'>}</span> </div><div class='output co'>#> test relative elapsed +#> 2 deSolve_compiled 1.0 0.005 #> 4 analytical 1.0 0.005 -#> 2 deSolve_compiled 1.2 0.006 #> 1 eigen 4.0 0.020 -#> 3 deSolve 45.6 0.228</div><div class='input'> +#> 3 deSolve 44.6 0.223</div><div class='input'> <span class='co'># \dontrun{</span> <span class='co'># Predict from a fitted model</span> <span class='va'>f</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_C</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> @@ -426,11 +419,11 @@ solver is used.</p></td> <span class='fu'><a href='https://rdrr.io/r/utils/head.html'>head</a></span><span class='op'>(</span><span class='fu'>mkinpredict</span><span class='op'>(</span><span class='va'>f</span><span class='op'>)</span><span class='op'>)</span> </div><div class='output co'>#> time parent m1 #> 0 0.0 82.49216 0.000000 -#> 0.1 0.1 80.00562 1.236198 -#> 0.2 0.2 77.59404 2.422818 -#> 0.3 0.3 75.25514 3.561476 -#> 0.4 0.4 72.98675 4.653740 -#> 0.5 0.5 70.78673 5.701130</div><div class='input'><span class='co'># }</span> +#> 0.1 0.1 80.00562 1.236394 +#> 0.2 0.2 77.59404 2.423201 +#> 0.3 0.3 75.25514 3.562040 +#> 0.4 0.4 72.98675 4.654478 +#> 0.5 0.5 70.78673 5.702033</div><div class='input'><span class='co'># }</span> </div></pre> </div> |