diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2020-04-03 17:40:55 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2020-04-03 17:40:55 +0200 |
| commit | 8c19fc5261dc53dc7880b3f54f8f2adf413de996 (patch) | |
| tree | 193aad4a3b2920ad6bff1d54cd18e992ac179bdd /docs/reference | |
| parent | 312255078d2529f485a81df2a53d5928622ae81f (diff) | |
| parent | 47ba9ea512b82fb8b31da8ec5558f3c0952d86d4 (diff) | |
Merge branch 'master' into mxkin
Merge DESCRIPTION manually to combine dependencies and rerun check to
update check.log
Diffstat (limited to 'docs/reference')
24 files changed, 400 insertions, 239 deletions
diff --git a/docs/reference/CAKE_export.html b/docs/reference/CAKE_export.html index 47536237..a4161abc 100644 --- a/docs/reference/CAKE_export.html +++ b/docs/reference/CAKE_export.html @@ -70,7 +70,7 @@ specified as well." /> </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">0.9.49.6</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.9</span> </span> </div> @@ -138,12 +138,21 @@ specified as well." /> specified as well.</p> </div> - <pre class="usage"><span class='fu'>CAKE_export</span>(<span class='no'>ds</span>, <span class='kw'>map</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='st'>"Parent"</span>), <span class='kw'>links</span> <span class='kw'>=</span> <span class='fl'>NA</span>, - <span class='kw'>filename</span> <span class='kw'>=</span> <span class='st'>"CAKE_export.csf"</span>, <span class='kw'>path</span> <span class='kw'>=</span> <span class='st'>"."</span>, <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, - <span class='kw'>study</span> <span class='kw'>=</span> <span class='st'>"Codlemone aerobic soil degradation"</span>, <span class='kw'>description</span> <span class='kw'>=</span> <span class='st'>""</span>, - <span class='kw'>time_unit</span> <span class='kw'>=</span> <span class='st'>"days"</span>, <span class='kw'>res_unit</span> <span class='kw'>=</span> <span class='st'>"% AR"</span>, - <span class='kw'>comment</span> <span class='kw'>=</span> <span class='st'>"Created using mkin::CAKE_export"</span>, <span class='kw'>date</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Sys.time.html'>Sys.Date</a></span>(), - <span class='kw'>optimiser</span> <span class='kw'>=</span> <span class='st'>"IRLS"</span>)</pre> + <pre class="usage"><span class='fu'>CAKE_export</span>( + <span class='no'>ds</span>, + <span class='kw'>map</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='st'>"Parent"</span>), + <span class='kw'>links</span> <span class='kw'>=</span> <span class='fl'>NA</span>, + <span class='kw'>filename</span> <span class='kw'>=</span> <span class='st'>"CAKE_export.csf"</span>, + <span class='kw'>path</span> <span class='kw'>=</span> <span class='st'>"."</span>, + <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, + <span class='kw'>study</span> <span class='kw'>=</span> <span class='st'>"Codlemone aerobic soil degradation"</span>, + <span class='kw'>description</span> <span class='kw'>=</span> <span class='st'>""</span>, + <span class='kw'>time_unit</span> <span class='kw'>=</span> <span class='st'>"days"</span>, + <span class='kw'>res_unit</span> <span class='kw'>=</span> <span class='st'>"% AR"</span>, + <span class='kw'>comment</span> <span class='kw'>=</span> <span class='st'>"Created using mkin::CAKE_export"</span>, + <span class='kw'>date</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Sys.time.html'>Sys.Date</a></span>(), + <span class='kw'>optimiser</span> <span class='kw'>=</span> <span class='st'>"IRLS"</span> +)</pre> <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> diff --git a/docs/reference/add_err-1.png b/docs/reference/add_err-1.png Binary files differindex fb369053..3018ff7f 100644 --- a/docs/reference/add_err-1.png +++ b/docs/reference/add_err-1.png diff --git a/docs/reference/add_err.html b/docs/reference/add_err.html index 67789694..ab499a19 100644 --- a/docs/reference/add_err.html +++ b/docs/reference/add_err.html @@ -71,7 +71,7 @@ may depend on the predicted value and is specified as a standard deviation." /> </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">0.9.49.6</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.9</span> </span> </div> @@ -140,8 +140,16 @@ degradation model using <code><a href='mkinpredict.html'>mkinpredict</a></code>. may depend on the predicted value and is specified as a standard deviation.</p> </div> - <pre class="usage"><span class='fu'>add_err</span>(<span class='no'>prediction</span>, <span class='no'>sdfunc</span>, <span class='kw'>secondary</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"M1"</span>, <span class='st'>"M2"</span>), <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>1000</span>, - <span class='kw'>LOD</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>reps</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>seed</span> <span class='kw'>=</span> <span class='fl'>NA</span>)</pre> + <pre class="usage"><span class='fu'>add_err</span>( + <span class='no'>prediction</span>, + <span class='no'>sdfunc</span>, + <span class='kw'>secondary</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"M1"</span>, <span class='st'>"M2"</span>), + <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>1000</span>, + <span class='kw'>LOD</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, + <span class='kw'>reps</span> <span class='kw'>=</span> <span class='fl'>2</span>, + <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>1</span>, + <span class='kw'>seed</span> <span class='kw'>=</span> <span class='fl'>NA</span> +)</pre> <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> diff --git a/docs/reference/aw.html b/docs/reference/aw.html index 22201229..0b37847c 100644 --- a/docs/reference/aw.html +++ b/docs/reference/aw.html @@ -71,7 +71,7 @@ by Burnham and Anderson (2004)." /> </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">0.9.49.8</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.9</span> </span> </div> diff --git a/docs/reference/confint.mkinfit.html b/docs/reference/confint.mkinfit.html index ea69c3bb..1dd6288b 100644 --- a/docs/reference/confint.mkinfit.html +++ b/docs/reference/confint.mkinfit.html @@ -76,7 +76,7 @@ method of Venzon and Moolgavkar (1988)." /> </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">0.9.49.8</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.9</span> </span> </div> @@ -151,10 +151,19 @@ method of Venzon and Moolgavkar (1988).</p> </div> <pre class="usage"><span class='co'># S3 method for mkinfit</span> -<span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>object</span>, <span class='no'>parm</span>, <span class='kw'>level</span> <span class='kw'>=</span> <span class='fl'>0.95</span>, <span class='kw'>alpha</span> <span class='kw'>=</span> <span class='fl'>1</span> - - <span class='no'>level</span>, <span class='no'>cutoff</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"quadratic"</span>, <span class='st'>"profile"</span>), - <span class='kw'>transformed</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>backtransform</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, - <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Round.html'>round</a></span>(<span class='fu'>detectCores</span>()/<span class='fl'>2</span>), <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre> +<span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>( + <span class='no'>object</span>, + <span class='no'>parm</span>, + <span class='kw'>level</span> <span class='kw'>=</span> <span class='fl'>0.95</span>, + <span class='kw'>alpha</span> <span class='kw'>=</span> <span class='fl'>1</span> - <span class='no'>level</span>, + <span class='no'>cutoff</span>, + <span class='kw'>method</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"quadratic"</span>, <span class='st'>"profile"</span>), + <span class='kw'>transformed</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, + <span class='kw'>backtransform</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, + <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Round.html'>round</a></span>(<span class='fu'>detectCores</span>()/<span class='fl'>2</span>), + <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, + <span class='no'>...</span> +)</pre> <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> @@ -253,52 +262,30 @@ On Windows machines, cores > 1 is currently not supported.</p></td> <span class='no'>SFO_SFO.ff</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></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'>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'>f_d_1</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span>(<span class='no'>FOCUS_2006_D</span>, <span class='no'>value</span> <span class='kw'>!=</span> <span class='fl'>0</span>), <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) -<span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span>(<span class='no'>ci_profile</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f_d_1</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"profile"</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))</div><div class='output co'>#> User System verstrichen -#> 51.058 0.000 51.088 </div><div class='input'><span class='co'># Using more cores does not save much time here, as parent_0 takes up most of the time</span> +<span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span>(<span class='no'>ci_profile</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f_d_1</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"profile"</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))</div><div class='output co'>#> <span class='error'>Error in mkinpredict.mkinmod(mkinmod, parms, odeini, outtimes, solution_type = solution_type, use_compiled = use_compiled, method.ode = method.ode, atol = atol, rtol = rtol, ...): Differential equations were not integrated for all output times because</span> +#> <span class='error'>NaN values occurred in output from ode()</span></div><div class='output co'>#> <span class='message'>Timing stopped at: 11.39 0 11.4</span></div><div class='input'><span class='co'># Using more cores does not save much time here, as parent_0 takes up most of the time</span> <span class='co'># If we additionally exclude parent_0 (the confidence of which is often of</span> <span class='co'># minor interest), we get a nice performance improvement from about 50</span> <span class='co'># seconds to about 12 seconds if we use at least four cores</span> <span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span>(<span class='no'>ci_profile_no_parent_0</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f_d_1</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"profile"</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"k_parent_sink"</span>, <span class='st'>"k_parent_m1"</span>, <span class='st'>"k_m1_sink"</span>, <span class='st'>"sigma"</span>), <span class='kw'>cores</span> <span class='kw'>=</span> <span class='no'>n_cores</span>))</div><div class='output co'>#> <span class='message'>Profiling the likelihood</span></div><div class='output co'>#> User System verstrichen -#> 0.005 0.004 11.349 </div><div class='input'><span class='no'>ci_profile</span></div><div class='output co'>#> 2.5% 97.5% -#> parent_0 96.456003650 1.027703e+02 -#> k_parent_sink 0.040762501 5.549764e-02 -#> k_parent_m1 0.046786482 5.500879e-02 -#> k_m1_sink 0.003892605 6.702778e-03 -#> sigma 2.535612399 3.985263e+00</div><div class='input'><span class='no'>ci_quadratic_transformed</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f_d_1</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"quadratic"</span>) +#> 20.058 0.122 11.784 </div><div class='input'><span class='no'>ci_profile</span></div><div class='output co'>#> <span class='error'>Error in eval(expr, envir, enclos): Objekt 'ci_profile' nicht gefunden</span></div><div class='input'><span class='no'>ci_quadratic_transformed</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f_d_1</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"quadratic"</span>) <span class='no'>ci_quadratic_transformed</span></div><div class='output co'>#> 2.5% 97.5% -#> parent_0 96.403841649 1.027931e+02 +#> parent_0 96.403841641 1.027931e+02 #> k_parent_sink 0.041033378 5.596269e-02 #> k_parent_m1 0.046777902 5.511931e-02 #> k_m1_sink 0.004012217 6.897547e-03 #> sigma 2.396089689 3.854918e+00</div><div class='input'><span class='no'>ci_quadratic_untransformed</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f_d_1</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"quadratic"</span>, <span class='kw'>transformed</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>) <span class='no'>ci_quadratic_untransformed</span></div><div class='output co'>#> 2.5% 97.5% -#> parent_0 96.403841653 102.79312450 +#> parent_0 96.403841648 102.79312450 #> k_parent_sink 0.040485331 0.05535491 -#> k_parent_m1 0.046611581 0.05494364 +#> k_parent_m1 0.046611582 0.05494364 #> k_m1_sink 0.003835483 0.00668582 #> sigma 2.396089689 3.85491806</div><div class='input'><span class='co'># Against the expectation based on Bates and Watts (1988), the confidence</span> <span class='co'># intervals based on the internal parameter transformation are less</span> <span class='co'># congruent with the likelihood based intervals. Note the superiority of the</span> <span class='co'># interval based on the untransformed fit for k_m1_sink</span> -<span class='no'>rel_diffs_transformed</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/MathFun.html'>abs</a></span>((<span class='no'>ci_quadratic_transformed</span> - <span class='no'>ci_profile</span>)/<span class='no'>ci_profile</span>) -<span class='no'>rel_diffs_untransformed</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/MathFun.html'>abs</a></span>((<span class='no'>ci_quadratic_untransformed</span> - <span class='no'>ci_profile</span>)/<span class='no'>ci_profile</span>) -<span class='no'>rel_diffs_transformed</span> <span class='kw'><</span> <span class='no'>rel_diffs_untransformed</span></div><div class='output co'>#> 2.5% 97.5% -#> parent_0 FALSE FALSE -#> k_parent_sink TRUE FALSE -#> k_parent_m1 TRUE FALSE -#> k_m1_sink FALSE FALSE -#> sigma FALSE FALSE</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/Round.html'>signif</a></span>(<span class='no'>rel_diffs_transformed</span>, <span class='fl'>3</span>)</div><div class='output co'>#> 2.5% 97.5% -#> parent_0 0.000541 0.000222 -#> k_parent_sink 0.006650 0.008380 -#> k_parent_m1 0.000183 0.002010 -#> k_m1_sink 0.030700 0.029100 -#> sigma 0.055000 0.032700</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/Round.html'>signif</a></span>(<span class='no'>rel_diffs_untransformed</span>, <span class='fl'>3</span>)</div><div class='output co'>#> 2.5% 97.5% -#> parent_0 0.000541 0.000222 -#> k_parent_sink 0.006800 0.002570 -#> k_parent_m1 0.003740 0.001180 -#> k_m1_sink 0.014700 0.002530 -#> sigma 0.055000 0.032700</div><div class='input'> +<span class='no'>rel_diffs_transformed</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/MathFun.html'>abs</a></span>((<span class='no'>ci_quadratic_transformed</span> - <span class='no'>ci_profile</span>)/<span class='no'>ci_profile</span>)</div><div class='output co'>#> <span class='error'>Error in eval(expr, envir, enclos): Objekt 'ci_profile' nicht gefunden</span></div><div class='input'><span class='no'>rel_diffs_untransformed</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/MathFun.html'>abs</a></span>((<span class='no'>ci_quadratic_untransformed</span> - <span class='no'>ci_profile</span>)/<span class='no'>ci_profile</span>)</div><div class='output co'>#> <span class='error'>Error in eval(expr, envir, enclos): Objekt 'ci_profile' nicht gefunden</span></div><div class='input'><span class='no'>rel_diffs_transformed</span> <span class='kw'><</span> <span class='no'>rel_diffs_untransformed</span></div><div class='output co'>#> <span class='error'>Error in eval(expr, envir, enclos): Objekt 'rel_diffs_transformed' nicht gefunden</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/Round.html'>signif</a></span>(<span class='no'>rel_diffs_transformed</span>, <span class='fl'>3</span>)</div><div class='output co'>#> <span class='error'>Error in eval(expr, envir, enclos): Objekt 'rel_diffs_transformed' nicht gefunden</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/Round.html'>signif</a></span>(<span class='no'>rel_diffs_untransformed</span>, <span class='fl'>3</span>)</div><div class='output co'>#> <span class='error'>Error in eval(expr, envir, enclos): Objekt 'rel_diffs_untransformed' nicht gefunden</span></div><div class='input'> <span class='co'># Investigate a case with formation fractions</span> <span class='no'>f_d_2</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO.ff</span>, <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span>(<span class='no'>FOCUS_2006_D</span>, <span class='no'>value</span> <span class='kw'>!=</span> <span class='fl'>0</span>), <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) @@ -309,16 +296,16 @@ On Windows machines, cores > 1 is currently not supported.</p></td> #> f_parent_to_m1 0.471328495 5.611550e-01 #> sigma 2.535612399 3.985263e+00</div><div class='input'><span class='no'>ci_quadratic_transformed_ff</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f_d_2</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"quadratic"</span>) <span class='no'>ci_quadratic_transformed_ff</span></div><div class='output co'>#> 2.5% 97.5% -#> parent_0 96.403840123 1.027931e+02 -#> k_parent 0.090823791 1.072543e-01 +#> parent_0 96.403839992 1.027931e+02 +#> k_parent 0.090823790 1.072543e-01 #> k_m1 0.004012216 6.897547e-03 -#> f_parent_to_m1 0.469118710 5.595960e-01 +#> f_parent_to_m1 0.469118711 5.595960e-01 #> sigma 2.396089689 3.854918e+00</div><div class='input'><span class='no'>ci_quadratic_untransformed_ff</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f_d_2</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"quadratic"</span>, <span class='kw'>transformed</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>) <span class='no'>ci_quadratic_untransformed_ff</span></div><div class='output co'>#> 2.5% 97.5% -#> parent_0 96.403840057 1.027931e+02 -#> k_parent 0.090491932 1.069035e-01 +#> parent_0 96.403839944 1.027931e+02 +#> k_parent 0.090491931 1.069035e-01 #> k_m1 0.003835483 6.685819e-03 -#> f_parent_to_m1 0.469113361 5.598386e-01 +#> f_parent_to_m1 0.469113362 5.598386e-01 #> sigma 2.396089689 3.854918e+00</div><div class='input'><span class='no'>rel_diffs_transformed_ff</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/MathFun.html'>abs</a></span>((<span class='no'>ci_quadratic_transformed_ff</span> - <span class='no'>ci_profile_ff</span>)/<span class='no'>ci_profile_ff</span>) <span class='no'>rel_diffs_untransformed_ff</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/MathFun.html'>abs</a></span>((<span class='no'>ci_quadratic_untransformed_ff</span> - <span class='no'>ci_profile_ff</span>)/<span class='no'>ci_profile_ff</span>) <span class='co'># While the confidence interval for the parent rate constant is closer to</span> @@ -330,16 +317,16 @@ On Windows machines, cores > 1 is currently not supported.</p></td> #> k_parent TRUE TRUE #> k_m1 FALSE FALSE #> f_parent_to_m1 TRUE FALSE -#> sigma FALSE TRUE</div><div class='input'><span class='no'>rel_diffs_transformed_ff</span></div><div class='output co'>#> 2.5% 97.5% -#> parent_0 0.0005408012 0.0002217857 -#> k_parent 0.0009596303 0.0009003981 -#> k_m1 0.0307277425 0.0290579163 -#> f_parent_to_m1 0.0046884178 0.0027782643 +#> sigma FALSE FALSE</div><div class='input'><span class='no'>rel_diffs_transformed_ff</span></div><div class='output co'>#> 2.5% 97.5% +#> parent_0 0.0005408026 0.0002217846 +#> k_parent 0.0009596414 0.0009003877 +#> k_m1 0.0307277403 0.0290579212 +#> f_parent_to_m1 0.0046884168 0.0027782604 #> sigma 0.0550252516 0.0327066836</div><div class='input'><span class='no'>rel_diffs_untransformed_ff</span></div><div class='output co'>#> 2.5% 97.5% -#> parent_0 0.0005408019 0.0002217863 -#> k_parent 0.0046099989 0.0023730118 -#> k_m1 0.0146746451 0.0025300990 -#> f_parent_to_m1 0.0046997668 0.0023460293 +#> parent_0 0.0005408031 0.0002217851 +#> k_parent 0.0046100089 0.0023730230 +#> k_m1 0.0146746442 0.0025300972 +#> f_parent_to_m1 0.0046997642 0.0023460268 #> sigma 0.0550252516 0.0327066836</div><div class='input'> <span class='co'># The profiling for the following fit does not finish in a reasonable time,</span> <span class='co'># therefore we use the quadratic approximation</span> @@ -351,17 +338,17 @@ On Windows machines, cores > 1 is currently not supported.</p></td> <span class='no'>f_tc_2</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'>DFOP_par_c</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</span>, <span class='kw'>error_model_algorithm</span> <span class='kw'>=</span> <span class='st'>"direct"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f_tc_2</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"quadratic"</span>)</div><div class='output co'>#> 2.5% 97.5% -#> parent_0 94.596183241 106.19937044 -#> k_M1 0.037605436 0.04490758 -#> k_M2 0.008568746 0.01087675 -#> f_parent_to_M1 0.021464277 0.62023879 -#> f_parent_to_M2 0.015166876 0.37975352 -#> k1 0.273897622 0.33388081 -#> k2 0.018614564 0.02250380 -#> g 0.671943572 0.73583247 -#> sigma_low 0.251284138 0.83992136 -#> rsd_high 0.040410998 0.07661999</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f_tc_2</span>, <span class='st'>"parent_0"</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"quadratic"</span>)</div><div class='output co'>#> 2.5% 97.5% -#> parent_0 94.59618 106.1994</div><div class='input'># } +#> parent_0 94.596218141 106.19934683 +#> k_M1 0.037605440 0.04490756 +#> k_M2 0.008568747 0.01087674 +#> f_parent_to_M1 0.021466788 0.62023878 +#> f_parent_to_M2 0.015168650 0.37975352 +#> k1 0.273897581 0.33388066 +#> k2 0.018614556 0.02250379 +#> g 0.671943831 0.73583255 +#> sigma_low 0.251283700 0.83992071 +#> rsd_high 0.040411017 0.07662005</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f_tc_2</span>, <span class='st'>"parent_0"</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"quadratic"</span>)</div><div class='output co'>#> 2.5% 97.5% +#> parent_0 94.59622 106.1993</div><div class='input'># } </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html index e81bdbb5..f201294d 100644 --- a/docs/reference/endpoints.html +++ b/docs/reference/endpoints.html @@ -75,7 +75,7 @@ advantage that the SFORB model can also be used for metabolites." /> </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">0.9.49.6</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.9</span> </span> </div> @@ -171,9 +171,6 @@ advantage that the SFORB model can also be used for metabolites.</p> <span class='fu'>endpoints</span>(<span class='no'>fit</span>)</div><div class='output co'>#> $ff #> logical(0) #> -#> $SFORB -#> logical(0) -#> #> $distimes #> DT50 DT90 DT50back #> parent 1.785233 15.1479 4.559973 diff --git a/docs/reference/loftest-3.png b/docs/reference/loftest-3.png Binary files differindex c66c95f1..ecc4c3ee 100644 --- a/docs/reference/loftest-3.png +++ b/docs/reference/loftest-3.png diff --git a/docs/reference/loftest.html b/docs/reference/loftest.html index 757f0bbe..7d4df9f5 100644 --- a/docs/reference/loftest.html +++ b/docs/reference/loftest.html @@ -72,7 +72,7 @@ lrtest.default from the lmtest package." /> </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">0.9.49.8</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.9</span> </span> </div> diff --git a/docs/reference/lrtest.mkinfit.html b/docs/reference/lrtest.mkinfit.html index 70157db9..6861b747 100644 --- a/docs/reference/lrtest.mkinfit.html +++ b/docs/reference/lrtest.mkinfit.html @@ -73,7 +73,7 @@ and can be expressed by fixing the parameters of the other." /> </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">0.9.49.8</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.9</span> </span> </div> @@ -205,7 +205,7 @@ lower number of fitted parameters (null hypothesis).</p> <span class='co'>#lrtest(dfop_fit, error_model = "tc")</span> <span class='co'>#lrtest(dfop_fit, fixed_parms = c(k2 = 0))</span> -<span class='co'># However, this equivalent syntax works for static help pages</span> +<span class='co'># However, this equivalent syntax also works for static help pages</span> <span class='fu'><a href='https://rdrr.io/pkg/lmtest/man/lrtest.html'>lrtest</a></span>(<span class='no'>dfop_fit</span>, <span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span>(<span class='no'>dfop_fit</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</span>))</div><div class='output co'>#> Likelihood ratio test #> #> Model 1: DFOP with error model tc diff --git a/docs/reference/mkinds.html b/docs/reference/mkinds.html index 386c00d7..ef6fb35c 100644 --- a/docs/reference/mkinds.html +++ b/docs/reference/mkinds.html @@ -36,7 +36,10 @@ <meta property="og:title" content="A dataset class for mkin — mkinds" /> -<meta property="og:description" content="A dataset class for mkin" /> +<meta property="og:description" content="At the moment this dataset class is hardly used in mkin. For example, +mkinfit does not take mkinds datasets as argument, but works with dataframes +such as the on contained in the data field of mkinds objects. Some datasets +provided by this package come as mkinds objects nevertheless." /> <meta name="twitter:card" content="summary" /> @@ -69,7 +72,7 @@ </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">0.9.49.6</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.9</span> </span> </div> @@ -133,47 +136,89 @@ </div> <div class="ref-description"> - <p>A dataset class for mkin</p> + <p>At the moment this dataset class is hardly used in mkin. For example, +mkinfit does not take mkinds datasets as argument, but works with dataframes +such as the on contained in the data field of mkinds objects. Some datasets +provided by this package come as mkinds objects nevertheless.</p> </div> - <pre class="usage"><span class='no'>mkinds</span></pre> - <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> + <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> - <p>An <code>R6Class</code> generator object.</p> - <h2 class="hasAnchor" id="fields"><a class="anchor" href="#fields"></a>Fields</h2> + <div class='dont-index'><p>The S3 printing method <code><a href='print.mkinds.html'>print.mkinds</a></code></p></div> + <h2 class="hasAnchor" id="public-fields"><a class="anchor" href="#public-fields"></a>Public fields</h2> + + <p><div class="r6-fields"></p><dl class='dl-horizontal'> +<dt><code>title</code></dt><dd><p>A full title for the dataset</p></dd> + +<dt><code>sampling_times</code></dt><dd><p>The sampling times</p></dd> + +<dt><code>time_unit</code></dt><dd><p>The time unit</p></dd> + +<dt><code>observed</code></dt><dd><p>Names of the observed variables</p></dd> + +<dt><code>unit</code></dt><dd><p>The unit of the observations</p></dd> + +<dt><code>replicates</code></dt><dd><p>The maximum number of replicates per sampling time</p></dd> + +<dt><code>data</code></dt><dd><p>A data frame with at least the columns name, time +and value in order to be compatible with mkinfit</p></dd> + +</dl><p></div></p> + <h2 class="hasAnchor" id="methods"><a class="anchor" href="#methods"></a>Methods</h2> +<h3>Public methods</h3> + +<ul> +<li><p><a href='#method-new'><code>mkinds$new()</code></a></p></li> +<li><p><a href='#method-clone'><code>mkinds$clone()</code></a></p></li> +</ul> +<p><hr> +<a id="method-new"></a></p><h3>Method <code>new()</code></h3> +<p>Create a new mkinds object</p><h3>Usage</h3> +<p><div class="r"></p><pre>mkinds$new(title = "", data, time_unit = NA, unit = NA)</pre><p></div></p> +<h3>Arguments</h3> +<p><div class="arguments"></p><dl class='dl-horizontal'> +<dt><code>title</code></dt><dd><p>The dataset title</p></dd> -<dl class='dl-horizontal'> -<dt>list("title")</dt><dd><p>A full title for the dataset</p></dd> +<dt><code>data</code></dt><dd><p>The data</p></dd> -<dt>list("sampling")</dt><dd><p>times The sampling times</p></dd> +<dt><code>time_unit</code></dt><dd><p>The time unit</p></dd> -<dt>list("time_unit")</dt><dd><p>The time unit</p></dd> +<dt><code>unit</code></dt><dd><p>The unit of the observations</p></dd> -<dt>list("observed")</dt><dd><p>Names of the observed compounds</p></dd> +</dl><p></div></p> +<p><hr> +<a id="method-clone"></a></p><h3>Method <code>clone()</code></h3> +<p>The objects of this class are cloneable with this method.</p><h3>Usage</h3> +<p><div class="r"></p><pre>mkinds$clone(deep = FALSE)</pre><p></div></p> -<dt>list("unit")</dt><dd><p>The unit of the observations</p></dd> +<h3>Arguments</h3> +<p><div class="arguments"></p><dl class='dl-horizontal'> +<dt><code>deep</code></dt><dd><p>Whether to make a deep clone.</p></dd> -<dt>list("replicates")</dt><dd><p>The number of replicates</p></dd> +</dl><p></div></p> -<dt>list("data")</dt><dd><p>A dataframe with at least the columns name, time and -value in order to be compatible with mkinfit</p></dd> -</dl> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> -<span class='no'>mds</span> <span class='kw'><-</span> <span class='no'>mkinds</span>$<span class='fu'>new</span>(<span class='st'>"FOCUS A"</span>, <span class='no'>FOCUS_2006_A</span>)</div></pre> +<span class='no'>mds</span> <span class='kw'><-</span> <span class='no'>mkinds</span>$<span class='fu'>new</span>(<span class='st'>"FOCUS A"</span>, <span class='no'>FOCUS_2006_A</span>) +<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>mds</span>)</div><div class='output co'>#> <mkinds> with $title: FOCUS A +#> Observed compounds $observed: parent +#> Sampling times $sampling_times: 0, 3, 7, 14, 30, 62, 90, 118 +#> With a maximum of 1 replicates</div><div class='input'> +</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> - <li><a href="#format">Format</a></li> - <li><a href="#fields">Fields</a></li> + <li><a href="#see-also">See also</a></li> + <li><a href="#public-fields">Public fields</a></li> + <li><a href="#methods">Methods</a></li> <li><a href="#examples">Examples</a></li> </ul> diff --git a/docs/reference/mkinerrplot-1.png b/docs/reference/mkinerrplot-1.png Binary files differindex 476edc49..46a80308 100644 --- a/docs/reference/mkinerrplot-1.png +++ b/docs/reference/mkinerrplot-1.png diff --git a/docs/reference/mkinerrplot.html b/docs/reference/mkinerrplot.html index 079a6708..47f48b72 100644 --- a/docs/reference/mkinerrplot.html +++ b/docs/reference/mkinerrplot.html @@ -73,7 +73,7 @@ using the argument show_errplot = TRUE." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.6</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.9</span> </span> </div> @@ -144,11 +144,20 @@ and this error model plot can be obtained with <code><a href='plot.mkinfit.html' using the argument <code>show_errplot = TRUE</code>.</p> </div> - <pre class="usage"><span class='fu'>mkinerrplot</span>(<span class='no'>object</span>, <span class='kw'>obs_vars</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span>(<span class='no'>object</span>$<span class='no'>mkinmod</span>$<span class='no'>map</span>), <span class='kw'>xlim</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, - <span class='fl'>1.1</span> * <span class='fu'><a href='https://rdrr.io/r/base/Extremes.html'>max</a></span>(<span class='no'>object</span>$<span class='no'>data</span>$<span class='no'>predicted</span>)), <span class='kw'>xlab</span> <span class='kw'>=</span> <span class='st'>"Predicted"</span>, - <span class='kw'>ylab</span> <span class='kw'>=</span> <span class='st'>"Squared residual"</span>, <span class='kw'>maxy</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, <span class='kw'>legend</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, - <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='st'>"topright"</span>, <span class='kw'>col_obs</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, <span class='kw'>pch_obs</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, - <span class='kw'>frame</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)</pre> + <pre class="usage"><span class='fu'>mkinerrplot</span>( + <span class='no'>object</span>, + <span class='kw'>obs_vars</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span>(<span class='no'>object</span>$<span class='no'>mkinmod</span>$<span class='no'>map</span>), + <span class='kw'>xlim</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>1.1</span> * <span class='fu'><a href='https://rdrr.io/r/base/Extremes.html'>max</a></span>(<span class='no'>object</span>$<span class='no'>data</span>$<span class='no'>predicted</span>)), + <span class='kw'>xlab</span> <span class='kw'>=</span> <span class='st'>"Predicted"</span>, + <span class='kw'>ylab</span> <span class='kw'>=</span> <span class='st'>"Squared residual"</span>, + <span class='kw'>maxy</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, + <span class='kw'>legend</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, + <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='st'>"topright"</span>, + <span class='kw'>col_obs</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, + <span class='kw'>pch_obs</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, + <span class='kw'>frame</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, + <span class='no'>...</span> +)</pre> <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 7ee73f15..ffc8d52b 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -75,7 +75,7 @@ likelihood function." /> </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">0.9.49.6</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.9</span> </span> </div> @@ -148,18 +148,33 @@ degradation model parameters, as both of them are arguments of the likelihood function.</p> </div> - <pre class="usage"><span class='fu'>mkinfit</span>(<span class='no'>mkinmod</span>, <span class='no'>observed</span>, <span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, <span class='kw'>state.ini</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, - <span class='kw'>err.ini</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, <span class='kw'>fixed_parms</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, - <span class='kw'>fixed_initials</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span>(<span class='no'>mkinmod</span>$<span class='no'>diffs</span>)[-<span class='fl'>1</span>], <span class='kw'>from_max_mean</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, + <pre class="usage"><span class='fu'>mkinfit</span>( + <span class='no'>mkinmod</span>, + <span class='no'>observed</span>, + <span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, + <span class='kw'>state.ini</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, + <span class='kw'>err.ini</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, + <span class='kw'>fixed_parms</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, + <span class='kw'>fixed_initials</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span>(<span class='no'>mkinmod</span>$<span class='no'>diffs</span>)[-<span class='fl'>1</span>], + <span class='kw'>from_max_mean</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"auto"</span>, <span class='st'>"analytical"</span>, <span class='st'>"eigen"</span>, <span class='st'>"deSolve"</span>), - <span class='kw'>method.ode</span> <span class='kw'>=</span> <span class='st'>"lsoda"</span>, <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, + <span class='kw'>method.ode</span> <span class='kw'>=</span> <span class='st'>"lsoda"</span>, + <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, <span class='kw'>control</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>eval.max</span> <span class='kw'>=</span> <span class='fl'>300</span>, <span class='kw'>iter.max</span> <span class='kw'>=</span> <span class='fl'>200</span>), - <span class='kw'>transform_rates</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>transform_fractions</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, - <span class='kw'>atol</span> <span class='kw'>=</span> <span class='fl'>1e-08</span>, <span class='kw'>rtol</span> <span class='kw'>=</span> <span class='fl'>1e-10</span>, <span class='kw'>n.outtimes</span> <span class='kw'>=</span> <span class='fl'>100</span>, + <span class='kw'>transform_rates</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, + <span class='kw'>transform_fractions</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, + <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, + <span class='kw'>atol</span> <span class='kw'>=</span> <span class='fl'>1e-08</span>, + <span class='kw'>rtol</span> <span class='kw'>=</span> <span class='fl'>1e-10</span>, + <span class='kw'>n.outtimes</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"const"</span>, <span class='st'>"obs"</span>, <span class='st'>"tc"</span>), - <span class='kw'>error_model_algorithm</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"auto"</span>, <span class='st'>"d_3"</span>, <span class='st'>"direct"</span>, <span class='st'>"twostep"</span>, - <span class='st'>"threestep"</span>, <span class='st'>"fourstep"</span>, <span class='st'>"IRLS"</span>, <span class='st'>"OLS"</span>), <span class='kw'>reweight.tol</span> <span class='kw'>=</span> <span class='fl'>1e-08</span>, - <span class='kw'>reweight.max.iter</span> <span class='kw'>=</span> <span class='fl'>10</span>, <span class='kw'>trace_parms</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre> + <span class='kw'>error_model_algorithm</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"auto"</span>, <span class='st'>"d_3"</span>, <span class='st'>"direct"</span>, <span class='st'>"twostep"</span>, <span class='st'>"threestep"</span>, <span class='st'>"fourstep"</span>, + <span class='st'>"IRLS"</span>, <span class='st'>"OLS"</span>), + <span class='kw'>reweight.tol</span> <span class='kw'>=</span> <span class='fl'>1e-08</span>, + <span class='kw'>reweight.max.iter</span> <span class='kw'>=</span> <span class='fl'>10</span>, + <span class='kw'>trace_parms</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, + <span class='no'>...</span> +)</pre> <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> @@ -400,17 +415,17 @@ estimators.</p> <pre class="examples"><div class='input'> <span class='co'># Use shorthand notation for parent only degradation</span> <span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) -<span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.49.6 -#> R version used for fitting: 3.6.1 -#> Date of fit: Fri Nov 1 10:08:21 2019 -#> Date of summary: Fri Nov 1 10:08:21 2019 +<span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.49.9 +#> R version used for fitting: 3.6.3 +#> Date of fit: Mon Mar 30 21:41:20 2020 +#> Date of summary: Mon Mar 30 21:41:20 2020 #> #> Equations: #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent #> #> Model predictions using solution type analytical #> -#> Fitted using 222 model solutions performed in 0.456 s +#> Fitted using 222 model solutions performed in 0.463 s #> #> Error model: Constant variance #> @@ -440,10 +455,10 @@ estimators.</p> #> #> Parameter correlation: #> parent_0 log_alpha log_beta sigma -#> parent_0 1.000e+00 -1.565e-01 -3.142e-01 4.770e-08 -#> log_alpha -1.565e-01 1.000e+00 9.564e-01 9.974e-08 -#> log_beta -3.142e-01 9.564e-01 1.000e+00 8.468e-08 -#> sigma 4.770e-08 9.974e-08 8.468e-08 1.000e+00 +#> parent_0 1.000e+00 -1.565e-01 -3.142e-01 4.758e-08 +#> log_alpha -1.565e-01 1.000e+00 9.564e-01 1.007e-07 +#> log_beta -3.142e-01 9.564e-01 1.000e+00 8.568e-08 +#> sigma 4.758e-08 1.007e-07 8.568e-08 1.000e+00 #> #> Backtransformed parameters: #> Confidence intervals for internally transformed parameters are asymmetric. @@ -482,7 +497,7 @@ estimators.</p> <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'># Fit the model to the FOCUS example dataset D using defaults</span> <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span>(<span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)))</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#> User System verstrichen -#> 1.488 0.000 1.491 </div><div class='input'><span class='fu'><a href='https://rdrr.io/r/stats/coef.html'>coef</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> NULL</div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> $ff +#> 1.526 0.000 1.530 </div><div class='input'><span class='fu'><a href='https://rdrr.io/r/stats/coef.html'>coef</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> NULL</div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> $ff #> parent_sink parent_m1 m1_sink #> 0.485524 0.514476 1.000000 #> @@ -533,9 +548,9 @@ estimators.</p> #> Sum of squared residuals at call 82: 373.1711 #> Sum of squared residuals at call 84: 373.1711 #> Sum of squared residuals at call 87: 372.6445 -#> Sum of squared residuals at call 88: 372.1615 -#> Sum of squared residuals at call 90: 372.1615 -#> Sum of squared residuals at call 91: 372.1615 +#> Sum of squared residuals at call 88: 372.1614 +#> Sum of squared residuals at call 90: 372.1614 +#> Sum of squared residuals at call 91: 372.1614 #> Sum of squared residuals at call 94: 371.6464 #> Sum of squared residuals at call 99: 371.4299 #> Sum of squared residuals at call 101: 371.4299 @@ -555,7 +570,7 @@ estimators.</p> #> Sum of squared residuals at call 126: 371.2134 #> Sum of squared residuals at call 135: 371.2134 #> Negative log-likelihood at call 145: 97.22429</div><div class='output co'>#> <span class='message'>Optimisation successfully terminated.</span></div><div class='output co'>#> User System verstrichen -#> 1.058 0.000 1.059 </div><div class='input'><span class='fu'><a href='https://rdrr.io/r/stats/coef.html'>coef</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#> NULL</div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#> $ff +#> 1.083 0.000 1.084 </div><div class='input'><span class='fu'><a href='https://rdrr.io/r/stats/coef.html'>coef</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#> NULL</div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#> $ff #> parent_sink parent_m1 m1_sink #> 0.485524 0.514476 1.000000 #> @@ -589,10 +604,10 @@ estimators.</p> <span class='co'># \dontrun{</span> <span class='co'># Weighted fits, including IRLS</span> <span class='no'>SFO_SFO.ff</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></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'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</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='no'>f.noweight</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</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='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>f.noweight</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.49.6 -#> R version used for fitting: 3.6.1 -#> Date of fit: Fri Nov 1 10:08:36 2019 -#> Date of summary: Fri Nov 1 10:08:36 2019 + <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'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</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='no'>f.noweight</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</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='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>f.noweight</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.49.9 +#> R version used for fitting: 3.6.3 +#> Date of fit: Mon Mar 30 21:41:36 2020 +#> Date of summary: Mon Mar 30 21:41:36 2020 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -600,7 +615,7 @@ estimators.</p> #> #> Model predictions using solution type deSolve #> -#> Fitted using 421 model solutions performed in 1.083 s +#> Fitted using 422 model solutions performed in 1.144 s #> #> Error model: Constant variance #> @@ -634,11 +649,11 @@ estimators.</p> #> #> Parameter correlation: #> parent_0 log_k_parent log_k_m1 f_parent_ilr_1 sigma -#> parent_0 1.000e+00 5.174e-01 -1.688e-01 -5.471e-01 -2.265e-07 -#> log_k_parent 5.174e-01 1.000e+00 -3.263e-01 -5.426e-01 3.785e-07 -#> log_k_m1 -1.688e-01 -3.263e-01 1.000e+00 7.478e-01 -1.386e-07 -#> f_parent_ilr_1 -5.471e-01 -5.426e-01 7.478e-01 1.000e+00 -3.641e-08 -#> sigma -2.265e-07 3.785e-07 -1.386e-07 -3.641e-08 1.000e+00 +#> parent_0 1.000e+00 5.174e-01 -1.688e-01 -5.471e-01 -2.443e-07 +#> log_k_parent 5.174e-01 1.000e+00 -3.263e-01 -5.426e-01 3.181e-07 +#> log_k_m1 -1.688e-01 -3.263e-01 1.000e+00 7.478e-01 -1.369e-07 +#> f_parent_ilr_1 -5.471e-01 -5.426e-01 7.478e-01 1.000e+00 -2.287e-08 +#> sigma -2.443e-07 3.181e-07 -1.369e-07 -2.287e-08 1.000e+00 #> #> Backtransformed parameters: #> Confidence intervals for internally transformed parameters are asymmetric. @@ -706,10 +721,10 @@ estimators.</p> #> 100 m1 31.04 31.98163 -9.416e-01 #> 100 m1 33.13 31.98163 1.148e+00 #> 120 m1 25.15 28.78984 -3.640e+00 -#> 120 m1 33.31 28.78984 4.520e+00</div><div class='input'><span class='no'>f.obs</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"obs"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</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='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>f.obs</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.49.6 -#> R version used for fitting: 3.6.1 -#> Date of fit: Fri Nov 1 10:08:39 2019 -#> Date of summary: Fri Nov 1 10:08:39 2019 +#> 120 m1 33.31 28.78984 4.520e+00</div><div class='input'><span class='no'>f.obs</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"obs"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</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='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>f.obs</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.49.9 +#> R version used for fitting: 3.6.3 +#> Date of fit: Mon Mar 30 21:41:39 2020 +#> Date of summary: Mon Mar 30 21:41:39 2020 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -717,7 +732,7 @@ estimators.</p> #> #> Model predictions using solution type deSolve #> -#> Fitted using 978 model solutions performed in 2.553 s +#> Fitted using 979 model solutions performed in 2.576 s #> #> Error model: Variance unique to each observed variable #> @@ -838,10 +853,10 @@ estimators.</p> #> 100 m1 31.04 31.98773 -9.477e-01 #> 100 m1 33.13 31.98773 1.142e+00 #> 120 m1 25.15 28.80429 -3.654e+00 -#> 120 m1 33.31 28.80429 4.506e+00</div><div class='input'><span class='no'>f.tc</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</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='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>f.tc</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.49.6 -#> R version used for fitting: 3.6.1 -#> Date of fit: Fri Nov 1 10:08:48 2019 -#> Date of summary: Fri Nov 1 10:08:48 2019 +#> 120 m1 33.31 28.80429 4.506e+00</div><div class='input'><span class='no'>f.tc</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</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='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>f.tc</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.49.9 +#> R version used for fitting: 3.6.3 +#> Date of fit: Mon Mar 30 21:41:50 2020 +#> Date of summary: Mon Mar 30 21:41:50 2020 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -849,12 +864,12 @@ estimators.</p> #> #> Model predictions using solution type deSolve #> -#> Fitted using 2289 model solutions performed in 9.253 s +#> Fitted using 2552 model solutions performed in 10.593 s #> #> Error model: Two-component variance function #> #> Error model algorithm: d_3 -#> Direct fitting and three-step fitting yield approximately the same likelihood +#> Three-step fitting yielded a higher likelihood than direct fitting #> #> Starting values for parameters to be optimised: #> value type @@ -960,8 +975,8 @@ estimators.</p> #> 50 m1 40.01 41.34199 -1.331985 #> 75 m1 40.09 36.61471 3.475295 #> 75 m1 33.85 36.61471 -2.764705 -#> 100 m1 31.04 32.20082 -1.160823 -#> 100 m1 33.13 32.20082 0.929177 +#> 100 m1 31.04 32.20082 -1.160824 +#> 100 m1 33.13 32.20082 0.929176 #> 120 m1 25.15 29.04130 -3.891304 #> 120 m1 33.31 29.04130 4.268696</div><div class='input'># } diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index 317ffe5f..b25f2da3 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -72,7 +72,7 @@ list of lists can be given in the speclist argument." /> </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">0.9.49.6</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.9</span> </span> </div> @@ -142,8 +142,13 @@ to other observed compartments. Instead of specifying several expressions, a list of lists can be given in the speclist argument.</p> </div> - <pre class="usage"><span class='fu'>mkinmod</span>(<span class='no'>...</span>, <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"min"</span>, <span class='kw'>speclist</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, - <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre> + <pre class="usage"><span class='fu'>mkinmod</span>( + <span class='no'>...</span>, + <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"min"</span>, + <span class='kw'>speclist</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, + <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, + <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span> +)</pre> <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> @@ -239,7 +244,7 @@ in the FOCUS and NAFTA guidance documents are used.</p> <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 file12cd48616f1.c 2> file12cd48616f1.c.err.txt +#> /usr/lib/R/bin/R CMD SHLIB file414965c335f6.c 2> file414965c335f6.c.err.txt #> Program source: #> 1: #include <R.h> #> 2: diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index 0eca973c..fe5bc975 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -71,7 +71,7 @@ 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">0.9.49.6</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.9</span> </span> </div> @@ -140,24 +140,49 @@ 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='no'>x</span>, <span class='no'>odeparms</span>, <span class='no'>odeini</span>, <span class='kw'>outtimes</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>120</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>), - <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, - <span class='kw'>method.ode</span> <span class='kw'>=</span> <span class='st'>"lsoda"</span>, <span class='kw'>atol</span> <span class='kw'>=</span> <span class='fl'>1e-08</span>, <span class='kw'>rtol</span> <span class='kw'>=</span> <span class='fl'>1e-10</span>, - <span class='kw'>map_output</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>) + <pre class="usage"><span class='fu'>mkinpredict</span>( + <span class='no'>x</span>, + <span class='no'>odeparms</span>, + <span class='no'>odeini</span>, + <span class='kw'>outtimes</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>120</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>), + <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, + <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, + <span class='kw'>method.ode</span> <span class='kw'>=</span> <span class='st'>"lsoda"</span>, + <span class='kw'>atol</span> <span class='kw'>=</span> <span class='fl'>1e-08</span>, + <span class='kw'>rtol</span> <span class='kw'>=</span> <span class='fl'>1e-10</span>, + <span class='kw'>map_output</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, + <span class='no'>...</span> +) <span class='co'># S3 method for mkinmod</span> -<span class='fu'>mkinpredict</span>(<span class='no'>x</span>, <span class='kw'>odeparms</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>), - <span class='kw'>odeini</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='kw'>outtimes</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>120</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>), - <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, - <span class='kw'>method.ode</span> <span class='kw'>=</span> <span class='st'>"lsoda"</span>, <span class='kw'>atol</span> <span class='kw'>=</span> <span class='fl'>1e-08</span>, <span class='kw'>rtol</span> <span class='kw'>=</span> <span class='fl'>1e-10</span>, - <span class='kw'>map_output</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>) +<span class='fu'>mkinpredict</span>( + <span class='no'>x</span>, + <span class='kw'>odeparms</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>), + <span class='kw'>odeini</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>), + <span class='kw'>outtimes</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>120</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>), + <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, + <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, + <span class='kw'>method.ode</span> <span class='kw'>=</span> <span class='st'>"lsoda"</span>, + <span class='kw'>atol</span> <span class='kw'>=</span> <span class='fl'>1e-08</span>, + <span class='kw'>rtol</span> <span class='kw'>=</span> <span class='fl'>1e-10</span>, + <span class='kw'>map_output</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, + <span class='no'>...</span> +) <span class='co'># S3 method for mkinfit</span> -<span class='fu'>mkinpredict</span>(<span class='no'>x</span>, <span class='kw'>odeparms</span> <span class='kw'>=</span> <span class='no'>x</span>$<span class='no'>bparms.ode</span>, - <span class='kw'>odeini</span> <span class='kw'>=</span> <span class='no'>x</span>$<span class='no'>bparms.state</span>, <span class='kw'>outtimes</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>120</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>), - <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, - <span class='kw'>method.ode</span> <span class='kw'>=</span> <span class='st'>"lsoda"</span>, <span class='kw'>atol</span> <span class='kw'>=</span> <span class='fl'>1e-08</span>, <span class='kw'>rtol</span> <span class='kw'>=</span> <span class='fl'>1e-10</span>, - <span class='kw'>map_output</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)</pre> +<span class='fu'>mkinpredict</span>( + <span class='no'>x</span>, + <span class='kw'>odeparms</span> <span class='kw'>=</span> <span class='no'>x</span>$<span class='no'>bparms.ode</span>, + <span class='kw'>odeini</span> <span class='kw'>=</span> <span class='no'>x</span>$<span class='no'>bparms.state</span>, + <span class='kw'>outtimes</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>120</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>), + <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, + <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, + <span class='kw'>method.ode</span> <span class='kw'>=</span> <span class='st'>"lsoda"</span>, + <span class='kw'>atol</span> <span class='kw'>=</span> <span class='fl'>1e-08</span>, + <span class='kw'>rtol</span> <span class='kw'>=</span> <span class='fl'>1e-10</span>, + <span class='kw'>map_output</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, + <span class='no'>...</span> +)</pre> <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> @@ -350,7 +375,7 @@ solver is used.</p></td> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>), <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#> time parent m1 #> 201 20 4.978707 27.46227</div><div class='output co'>#> User System verstrichen -#> 0.004 0.000 0.003 </div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span>( +#> 0.003 0.000 0.003 </div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span>( <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_parent_m1</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>k_m1_sink</span> <span class='kw'>=</span> <span class='fl'>0.01</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>), <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#> time parent m1 @@ -360,7 +385,7 @@ solver is used.</p></td> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>), <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#> time parent m1 #> 201 20 4.978707 27.46227</div><div class='output co'>#> User System verstrichen -#> 0.021 0.000 0.022 </div><div class='input'> +#> 0.021 0.000 0.021 </div><div class='input'> <span class='co'># \dontrun{</span> <span class='co'># Predict from a fitted model</span> <span class='no'>f</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_C</span>)</div><div class='output co'>#> <span class='message'>Ordinary least squares optimisation</span></div><div class='output co'>#> Sum of squared residuals at call 1: 552.5739 @@ -372,10 +397,10 @@ solver is used.</p></td> #> Sum of squared residuals at call 9: 279.9294 #> Sum of squared residuals at call 12: 200.3629 #> Sum of squared residuals at call 13: 200.3629 -#> Sum of squared residuals at call 18: 197.9039 -#> Sum of squared residuals at call 23: 197.9039 -#> Sum of squared residuals at call 25: 196.6754 -#> Sum of squared residuals at call 27: 196.6754 +#> Sum of squared residuals at call 18: 197.904 +#> Sum of squared residuals at call 22: 197.904 +#> Sum of squared residuals at call 25: 196.6753 +#> Sum of squared residuals at call 27: 196.6753 #> Sum of squared residuals at call 32: 196.5742 #> Sum of squared residuals at call 33: 196.5742 #> Sum of squared residuals at call 34: 196.5742 @@ -390,14 +415,13 @@ solver is used.</p></td> #> Sum of squared residuals at call 58: 196.5334 #> Sum of squared residuals at call 59: 196.5334 #> Sum of squared residuals at call 65: 196.5334 -#> Sum of squared residuals at call 73: 196.5334 #> Negative log-likelihood at call 75: 26.64668</div><div class='output co'>#> <span class='message'>Optimisation successfully terminated.</span></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/utils/head.html'>head</a></span>(<span class='fu'>mkinpredict</span>(<span class='no'>f</span>))</div><div class='output co'>#> time parent m1 #> 1 0.0 82.49216 0.000000 -#> 2 0.1 80.00563 1.179955 -#> 3 0.2 77.59404 2.312580 -#> 4 0.3 75.25515 3.399419 -#> 5 0.4 72.98675 4.441969 -#> 6 0.5 70.78673 5.441679</div><div class='input'> # } +#> 2 0.1 80.00563 1.179963 +#> 3 0.2 77.59404 2.312596 +#> 4 0.3 75.25515 3.399443 +#> 5 0.4 72.98675 4.442000 +#> 6 0.5 70.78673 5.441717</div><div class='input'> # } </div></pre> </div> diff --git a/docs/reference/mkinresplot.html b/docs/reference/mkinresplot.html index 4429798b..698af302 100644 --- a/docs/reference/mkinresplot.html +++ b/docs/reference/mkinresplot.html @@ -72,7 +72,7 @@ argument show_residuals = TRUE." /> </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">0.9.49.8</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.9</span> </span> </div> @@ -142,11 +142,21 @@ the residuals can be obtained using <code><a href='plot.mkinfit.html'>plot.mkinf argument <code>show_residuals = TRUE</code>.</p> </div> - <pre class="usage"><span class='fu'>mkinresplot</span>(<span class='no'>object</span>, <span class='kw'>obs_vars</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span>(<span class='no'>object</span>$<span class='no'>mkinmod</span>$<span class='no'>map</span>), <span class='kw'>xlim</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, - <span class='fl'>1.1</span> * <span class='fu'><a href='https://rdrr.io/r/base/Extremes.html'>max</a></span>(<span class='no'>object</span>$<span class='no'>data</span>$<span class='no'>time</span>)), <span class='kw'>standardized</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>xlab</span> <span class='kw'>=</span> <span class='st'>"Time"</span>, + <pre class="usage"><span class='fu'>mkinresplot</span>( + <span class='no'>object</span>, + <span class='kw'>obs_vars</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span>(<span class='no'>object</span>$<span class='no'>mkinmod</span>$<span class='no'>map</span>), + <span class='kw'>xlim</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>1.1</span> * <span class='fu'><a href='https://rdrr.io/r/base/Extremes.html'>max</a></span>(<span class='no'>object</span>$<span class='no'>data</span>$<span class='no'>time</span>)), + <span class='kw'>standardized</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, + <span class='kw'>xlab</span> <span class='kw'>=</span> <span class='st'>"Time"</span>, <span class='kw'>ylab</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span>(<span class='no'>standardized</span>, <span class='st'>"Standardized residual"</span>, <span class='st'>"Residual"</span>), - <span class='kw'>maxabs</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, <span class='kw'>legend</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='st'>"topright"</span>, - <span class='kw'>col_obs</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, <span class='kw'>pch_obs</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, <span class='kw'>frame</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)</pre> + <span class='kw'>maxabs</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, + <span class='kw'>legend</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, + <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='st'>"topright"</span>, + <span class='kw'>col_obs</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, + <span class='kw'>pch_obs</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, + <span class='kw'>frame</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, + <span class='no'>...</span> +)</pre> <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> diff --git a/docs/reference/mmkin-2.png b/docs/reference/mmkin-2.png Binary files differindex 5e264309..7b1d73d5 100644 --- a/docs/reference/mmkin-2.png +++ b/docs/reference/mmkin-2.png diff --git a/docs/reference/mmkin-3.png b/docs/reference/mmkin-3.png Binary files differindex 0a58a86b..4c412abc 100644 --- a/docs/reference/mmkin-3.png +++ b/docs/reference/mmkin-3.png diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index d1ea7a52..8e1ea54f 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -72,7 +72,7 @@ datasets specified in its first two arguments." /> </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">0.9.49.6</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.9</span> </span> </div> @@ -141,15 +141,20 @@ more datasets</h1> datasets specified in its first two arguments.</p> </div> - <pre class="usage"><span class='fu'>mmkin</span>(<span class='kw'>models</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"FOMC"</span>, <span class='st'>"DFOP"</span>), <span class='no'>datasets</span>, - <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Round.html'>round</a></span>(<span class='fu'>detectCores</span>()/<span class='fl'>2</span>), <span class='kw'>cluster</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>...</span>)</pre> + <pre class="usage"><span class='fu'>mmkin</span>( + <span class='kw'>models</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"FOMC"</span>, <span class='st'>"DFOP"</span>), + <span class='no'>datasets</span>, + <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Round.html'>round</a></span>(<span class='fu'>detectCores</span>()/<span class='fl'>2</span>), + <span class='kw'>cluster</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, + <span class='no'>...</span> +)</pre> <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> <colgroup><col class="name" /><col class="desc" /></colgroup> <tr> <th>models</th> - <td><p>Either a character vector of shorthand names like + <td><p>Either a character vector of shorthand names like <code><a href='https://rdrr.io/r/base/c.html'>c("SFO", "FOMC", "DFOP", "HS", "SFORB")</a></code>, or an optionally named list of <code><a href='mkinmod.html'>mkinmod</a></code> objects.</p></td> </tr> @@ -202,11 +207,11 @@ for parallel execution.</p></td> <span class='no'>time_1</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span>(<span class='no'>fits.4</span> <span class='kw'><-</span> <span class='fu'>mmkin</span>(<span class='no'>models</span>, <span class='no'>datasets</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)) <span class='no'>time_default</span></div><div class='output co'>#> User System verstrichen -#> 0.014 0.024 4.895 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#> User System verstrichen -#> 19.047 0.004 19.063 </div><div class='input'> +#> 18.739 0.379 6.198 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#> User System verstrichen +#> 19.910 0.000 19.925 </div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fits.0</span><span class='kw'>[[</span><span class='st'>"SFO_lin"</span>, <span class='fl'>2</span>]])</div><div class='output co'>#> $ff #> parent_M1 parent_sink M1_M2 M1_sink -#> 0.7340481 0.2659519 0.7505684 0.2494316 +#> 0.7340480 0.2659520 0.7505686 0.2494314 #> #> $SFORB #> logical(0) @@ -214,8 +219,8 @@ for parallel execution.</p></td> #> $distimes #> DT50 DT90 #> parent 0.8777689 2.915885 -#> M1 2.3257449 7.725957 -#> M2 33.7200958 112.015734 +#> M1 2.3257452 7.725958 +#> M2 33.7200890 112.015711 #> </div><div class='input'> <span class='co'># plot.mkinfit handles rows or columns of mmkin result objects</span> <span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>fits.0</span>[<span class='fl'>1</span>, ])</div><div class='img'><img src='mmkin-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>fits.0</span>[<span class='fl'>1</span>, ], <span class='kw'>obs_var</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"M1"</span>, <span class='st'>"M2"</span>))</div><div class='img'><img src='mmkin-2.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>fits.0</span>[, <span class='fl'>1</span>])</div><div class='img'><img src='mmkin-3.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># Use double brackets to extract a single mkinfit object, which will be plotted</span> diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html index 8dc21b06..33dc52b7 100644 --- a/docs/reference/plot.mkinfit.html +++ b/docs/reference/plot.mkinfit.html @@ -71,7 +71,7 @@ observed data together with the solution of the fitted model." /> </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">0.9.49.8</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.9</span> </span> </div> @@ -141,22 +141,47 @@ observed data together with the solution of the fitted model.</p> </div> <pre class="usage"><span class='co'># S3 method for mkinfit</span> -<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>x</span>, <span class='kw'>fit</span> <span class='kw'>=</span> <span class='no'>x</span>, <span class='kw'>obs_vars</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span>(<span class='no'>fit</span>$<span class='no'>mkinmod</span>$<span class='no'>map</span>), - <span class='kw'>xlab</span> <span class='kw'>=</span> <span class='st'>"Time"</span>, <span class='kw'>ylab</span> <span class='kw'>=</span> <span class='st'>"Observed"</span>, <span class='kw'>xlim</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/range.html'>range</a></span>(<span class='no'>fit</span>$<span class='no'>data</span>$<span class='no'>time</span>), - <span class='kw'>ylim</span> <span class='kw'>=</span> <span class='st'>"default"</span>, <span class='kw'>col_obs</span> <span class='kw'>=</span> <span class='fl'>1</span>:<span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span>(<span class='no'>obs_vars</span>), <span class='kw'>pch_obs</span> <span class='kw'>=</span> <span class='no'>col_obs</span>, - <span class='kw'>lty_obs</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>1</span>, <span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span>(<span class='no'>obs_vars</span>)), <span class='kw'>add</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>legend</span> <span class='kw'>=</span> !<span class='no'>add</span>, - <span class='kw'>show_residuals</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>show_errplot</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>maxabs</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, - <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>rel.height.middle</span> <span class='kw'>=</span> <span class='fl'>0.9</span>, <span class='kw'>row_layout</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, - <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='st'>"topright"</span>, <span class='kw'>inset</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0.05</span>, <span class='fl'>0.05</span>), <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, - <span class='kw'>errmin_digits</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='kw'>frame</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>) - -<span class='fu'>plot_sep</span>(<span class='no'>fit</span>, <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, - <span class='kw'>show_residuals</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/identical.html'>identical</a></span>(<span class='no'>fit</span>$<span class='no'>err_mod</span>, <span class='st'>"const"</span>), <span class='fl'>TRUE</span>, - <span class='st'>"standardized"</span>), <span class='no'>...</span>) - -<span class='fu'>plot_res</span>(<span class='no'>fit</span>, <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='no'>sep_obs</span>, +<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>( + <span class='no'>x</span>, + <span class='kw'>fit</span> <span class='kw'>=</span> <span class='no'>x</span>, + <span class='kw'>obs_vars</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span>(<span class='no'>fit</span>$<span class='no'>mkinmod</span>$<span class='no'>map</span>), + <span class='kw'>xlab</span> <span class='kw'>=</span> <span class='st'>"Time"</span>, + <span class='kw'>ylab</span> <span class='kw'>=</span> <span class='st'>"Observed"</span>, + <span class='kw'>xlim</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/range.html'>range</a></span>(<span class='no'>fit</span>$<span class='no'>data</span>$<span class='no'>time</span>), + <span class='kw'>ylim</span> <span class='kw'>=</span> <span class='st'>"default"</span>, + <span class='kw'>col_obs</span> <span class='kw'>=</span> <span class='fl'>1</span>:<span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span>(<span class='no'>obs_vars</span>), + <span class='kw'>pch_obs</span> <span class='kw'>=</span> <span class='no'>col_obs</span>, + <span class='kw'>lty_obs</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>1</span>, <span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span>(<span class='no'>obs_vars</span>)), + <span class='kw'>add</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, + <span class='kw'>legend</span> <span class='kw'>=</span> !<span class='no'>add</span>, + <span class='kw'>show_residuals</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, + <span class='kw'>show_errplot</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, + <span class='kw'>maxabs</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, + <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, + <span class='kw'>rel.height.middle</span> <span class='kw'>=</span> <span class='fl'>0.9</span>, + <span class='kw'>row_layout</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, + <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='st'>"topright"</span>, + <span class='kw'>inset</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0.05</span>, <span class='fl'>0.05</span>), + <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, + <span class='kw'>errmin_digits</span> <span class='kw'>=</span> <span class='fl'>3</span>, + <span class='kw'>frame</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, + <span class='no'>...</span> +) + +<span class='fu'>plot_sep</span>( + <span class='no'>fit</span>, + <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, + <span class='kw'>show_residuals</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/identical.html'>identical</a></span>(<span class='no'>fit</span>$<span class='no'>err_mod</span>, <span class='st'>"const"</span>), <span class='fl'>TRUE</span>, <span class='st'>"standardized"</span>), + <span class='no'>...</span> +) + +<span class='fu'>plot_res</span>( + <span class='no'>fit</span>, + <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, + <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='no'>sep_obs</span>, <span class='kw'>standardized</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/identical.html'>identical</a></span>(<span class='no'>fit</span>$<span class='no'>err_mod</span>, <span class='st'>"const"</span>), <span class='fl'>FALSE</span>, <span class='fl'>TRUE</span>), - <span class='no'>...</span>) + <span class='no'>...</span> +) <span class='fu'>plot_err</span>(<span class='no'>fit</span>, <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='no'>sep_obs</span>, <span class='no'>...</span>)</pre> diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html index 18907aa2..be60f228 100644 --- a/docs/reference/plot.mmkin.html +++ b/docs/reference/plot.mmkin.html @@ -73,7 +73,7 @@ the fit of at least one model to the same dataset is shown." /> </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">0.9.49.8</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.9</span> </span> </div> @@ -144,10 +144,20 @@ the fit of at least one model to the same dataset is shown.</p> </div> <pre class="usage"><span class='co'># S3 method for mmkin</span> -<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>x</span>, <span class='kw'>main</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, <span class='kw'>legends</span> <span class='kw'>=</span> <span class='fl'>1</span>, - <span class='kw'>resplot</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"time"</span>, <span class='st'>"errmod"</span>), <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, - <span class='kw'>errmin_var</span> <span class='kw'>=</span> <span class='st'>"All data"</span>, <span class='kw'>errmin_digits</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='kw'>cex</span> <span class='kw'>=</span> <span class='fl'>0.7</span>, - <span class='kw'>rel.height.middle</span> <span class='kw'>=</span> <span class='fl'>0.9</span>, <span class='kw'>ymax</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, <span class='no'>...</span>)</pre> +<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>( + <span class='no'>x</span>, + <span class='kw'>main</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, + <span class='kw'>legends</span> <span class='kw'>=</span> <span class='fl'>1</span>, + <span class='kw'>resplot</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"time"</span>, <span class='st'>"errmod"</span>), + <span class='kw'>standardized</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, + <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, + <span class='kw'>errmin_var</span> <span class='kw'>=</span> <span class='st'>"All data"</span>, + <span class='kw'>errmin_digits</span> <span class='kw'>=</span> <span class='fl'>3</span>, + <span class='kw'>cex</span> <span class='kw'>=</span> <span class='fl'>0.7</span>, + <span class='kw'>rel.height.middle</span> <span class='kw'>=</span> <span class='fl'>0.9</span>, + <span class='kw'>ymax</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, + <span class='no'>...</span> +)</pre> <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> @@ -172,6 +182,12 @@ column.</p></td> values, with the error model, using <code><a href='mkinerrplot.html'>mkinerrplot</a></code>.</p></td> </tr> <tr> + <th>standardized</th> + <td><p>Should the residuals be standardized? This option +is passed to <code><a href='mkinresplot.html'>mkinresplot</a></code>, it only takes effect if +`resplot = "time"`.</p></td> + </tr> + <tr> <th>show_errmin</th> <td><p>Should the chi2 error level be shown on top of the plots to the left?</p></td> diff --git a/docs/reference/print.mkinds.html b/docs/reference/print.mkinds.html index d7ba94e1..de1a2410 100644 --- a/docs/reference/print.mkinds.html +++ b/docs/reference/print.mkinds.html @@ -36,7 +36,7 @@ <meta property="og:title" content="Print mkinds objects — print.mkinds" /> -<meta property="og:description" content="Print mkinds objects." /> +<meta property="og:description" content="Print mkinds objects" /> <meta name="twitter:card" content="summary" /> @@ -69,7 +69,7 @@ </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">0.9.49.6</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.9</span> </span> </div> @@ -133,7 +133,7 @@ </div> <div class="ref-description"> - <p>Print mkinds objects.</p> + <p>Print mkinds objects</p> </div> <pre class="usage"><span class='co'># S3 method for mkinds</span> diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index fb3c43ef..ec79c37d 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -73,7 +73,7 @@ values." /> </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">0.9.49.6</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.9</span> </span> </div> @@ -145,12 +145,10 @@ values.</p> </div> <pre class="usage"><span class='co'># S3 method for mkinfit</span> -<span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>object</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>distimes</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, - <span class='kw'>alpha</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='no'>...</span>) +<span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>object</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>distimes</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>alpha</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='no'>...</span>) <span class='co'># S3 method for summary.mkinfit</span> -<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>x</span>, <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Extremes.html'>max</a></span>(<span class='fl'>3</span>, <span class='fu'><a href='https://rdrr.io/r/base/options.html'>getOption</a></span>(<span class='st'>"digits"</span>) - - <span class='fl'>3</span>), <span class='no'>...</span>)</pre> +<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>x</span>, <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Extremes.html'>max</a></span>(<span class='fl'>3</span>, <span class='fu'><a href='https://rdrr.io/r/base/options.html'>getOption</a></span>(<span class='st'>"digits"</span>) - <span class='fl'>3</span>), <span class='no'>...</span>)</pre> <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> @@ -223,17 +221,17 @@ distribution</p></td> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> - <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='fu'><a href='mkinmod.html'>mkinmod</a></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='no'>FOCUS_2006_A</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))</div><div class='output co'>#> mkin version used for fitting: 0.9.49.6 -#> R version used for fitting: 3.6.1 -#> Date of fit: Fri Nov 1 10:10:07 2019 -#> Date of summary: Fri Nov 1 10:10:07 2019 + <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='fu'><a href='mkinmod.html'>mkinmod</a></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='no'>FOCUS_2006_A</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))</div><div class='output co'>#> mkin version used for fitting: 0.9.49.9 +#> R version used for fitting: 3.6.3 +#> Date of fit: Mon Mar 30 21:43:00 2020 +#> Date of summary: Mon Mar 30 21:43:00 2020 #> #> Equations: #> d_parent/dt = - k_parent_sink * parent #> #> Model predictions using solution type analytical #> -#> Fitted using 131 model solutions performed in 0.265 s +#> Fitted using 131 model solutions performed in 0.306 s #> #> Error model: Constant variance #> @@ -260,9 +258,9 @@ distribution</p></td> #> #> Parameter correlation: #> parent_0 log_k_parent_sink sigma -#> parent_0 1.000e+00 5.428e-01 1.648e-07 -#> log_k_parent_sink 5.428e-01 1.000e+00 2.513e-07 -#> sigma 1.648e-07 2.513e-07 1.000e+00 +#> parent_0 1.000e+00 5.428e-01 1.642e-07 +#> log_k_parent_sink 5.428e-01 1.000e+00 2.507e-07 +#> sigma 1.642e-07 2.507e-07 1.000e+00 #> #> Backtransformed parameters: #> Confidence intervals for internally transformed parameters are asymmetric. diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index 4d88a03e..2a08228d 100644 --- a/docs/reference/transform_odeparms.html +++ b/docs/reference/transform_odeparms.html @@ -74,7 +74,7 @@ the ilr transformation is used." /> </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">0.9.49.6</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.9</span> </span> </div> @@ -146,11 +146,19 @@ formations fractions that should always sum up to 1 and can not be negative, the <code><a href='ilr.html'>ilr</a></code> transformation is used.</p> </div> - <pre class="usage"><span class='fu'>transform_odeparms</span>(<span class='no'>parms</span>, <span class='no'>mkinmod</span>, <span class='kw'>transform_rates</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, - <span class='kw'>transform_fractions</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) - -<span class='fu'>backtransform_odeparms</span>(<span class='no'>transparms</span>, <span class='no'>mkinmod</span>, <span class='kw'>transform_rates</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, - <span class='kw'>transform_fractions</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre> + <pre class="usage"><span class='fu'>transform_odeparms</span>( + <span class='no'>parms</span>, + <span class='no'>mkinmod</span>, + <span class='kw'>transform_rates</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, + <span class='kw'>transform_fractions</span> <span class='kw'>=</span> <span class='fl'>TRUE</span> +) + +<span class='fu'>backtransform_odeparms</span>( + <span class='no'>transparms</span>, + <span class='no'>mkinmod</span>, + <span class='kw'>transform_rates</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, + <span class='kw'>transform_fractions</span> <span class='kw'>=</span> <span class='fl'>TRUE</span> +)</pre> <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> |
