diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2021-02-15 14:08:13 +0100 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2021-02-15 15:20:53 +0100 |
| commit | a9427a09abdf7ce9aaeae7c7190f90c8f2e5ef52 (patch) | |
| tree | a9ecf25af6657e70d8f1faabd88fb6e2f6334b07 /docs/reference | |
| parent | b4582fc7d3f1d395bfd9d870137b705469d9eab2 (diff) | |
Improve README, introductory vignette and some other docsv1.0.3
Also bump version to 1.0.3.
Diffstat (limited to 'docs/reference')
111 files changed, 298 insertions, 304 deletions
diff --git a/docs/reference/AIC.mmkin.html b/docs/reference/AIC.mmkin.html index f54fd70f..fbc90802 100644 --- a/docs/reference/AIC.mmkin.html +++ b/docs/reference/AIC.mmkin.html @@ -73,7 +73,7 @@ same dataset." /> </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">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> @@ -187,8 +187,7 @@ dataframe if there are several fits in the column).</p> <span class='va'>f</span> <span class='op'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"FOMC"</span>, <span class='st'>"DFOP"</span><span class='op'>)</span>, <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='st'>"FOCUS A"</span> <span class='op'>=</span> <span class='va'>FOCUS_2006_A</span>, <span class='st'>"FOCUS C"</span> <span class='op'>=</span> <span class='va'>FOCUS_2006_C</span><span class='op'>)</span>, cores <span class='op'>=</span> <span class='fl'>1</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='warning'>Warning: Optimisation did not converge:</span> -#> <span class='warning'>false convergence (8)</span></div><div class='input'> <span class='co'># We get a warning because the FOMC model does not converge for the</span> + <span class='co'># We get a warning because the FOMC model does not converge for the</span> <span class='co'># FOCUS A dataset, as it is well described by SFO</span> <span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>[</span><span class='st'>"SFO"</span>, <span class='st'>"FOCUS A"</span><span class='op'>]</span><span class='op'>)</span> <span class='co'># We get a single number for a single fit</span> @@ -199,15 +198,15 @@ dataframe if there are several fits in the column).</p> <span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>[</span>, <span class='st'>"FOCUS A"</span><span class='op'>]</span><span class='op'>)</span> </div><div class='output co'>#> df AIC #> SFO 3 55.28197 -#> FOMC 4 57.28211 +#> FOMC 4 57.28222 #> DFOP 5 59.28197</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>[</span>, <span class='st'>"FOCUS A"</span><span class='op'>]</span>, k <span class='op'>=</span> <span class='fl'>0</span><span class='op'>)</span> <span class='co'># If we do not penalize additional parameters, we get nearly the same</span> </div><div class='output co'>#> df AIC #> SFO 3 49.28197 -#> FOMC 4 49.28211 +#> FOMC 4 49.28222 #> DFOP 5 49.28197</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>BIC</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>[</span>, <span class='st'>"FOCUS A"</span><span class='op'>]</span><span class='op'>)</span> <span class='co'># Comparing the BIC gives a very similar picture</span> </div><div class='output co'>#> df BIC #> SFO 3 55.52030 -#> FOMC 4 57.59987 +#> FOMC 4 57.59999 #> DFOP 5 59.67918</div><div class='input'> <span class='co'># For FOCUS C, the more complex models fit better</span> <span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>[</span>, <span class='st'>"FOCUS C"</span><span class='op'>]</span><span class='op'>)</span> diff --git a/docs/reference/CAKE_export.html b/docs/reference/CAKE_export.html index dcccca1b..05cd04a7 100644 --- a/docs/reference/CAKE_export.html +++ b/docs/reference/CAKE_export.html @@ -73,7 +73,7 @@ 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">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/D24_2014.html b/docs/reference/D24_2014.html index b78e73ef..e2d47f1b 100644 --- a/docs/reference/D24_2014.html +++ b/docs/reference/D24_2014.html @@ -77,7 +77,7 @@ constrained by data protection regulations." /> </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">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/DFOP.solution.html b/docs/reference/DFOP.solution.html index cff29301..d04f98cc 100644 --- a/docs/reference/DFOP.solution.html +++ b/docs/reference/DFOP.solution.html @@ -73,7 +73,7 @@ two exponential decline functions." /> </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">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index 4e3cbe64..5a99cf1b 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -72,7 +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">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> @@ -220,7 +220,7 @@ either a list of mkinfit objects or a single mkinfit object.</p></td> <span class='op'>)</span> </div><div class='output co'>#> $par #> parent_0 log_alpha log_beta sigma -#> 99.666193 2.549849 5.050586 1.890202 +#> 99.666192 2.549850 5.050586 1.890202 #> #> $objective #> [1] 28.58291 diff --git a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html index d37fa5a5..ba1cb19a 100644 --- a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html +++ b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html @@ -76,7 +76,7 @@ in this fit." /> </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">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html index d3f7894c..cfb60536 100644 --- a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html @@ -76,7 +76,7 @@ in this fit." /> </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">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html index a18abad5..c90bcdbb 100644 --- a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html @@ -76,7 +76,7 @@ in this fit." /> </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">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html index e0fbc498..7b2747dc 100644 --- a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html @@ -76,7 +76,7 @@ in this fit." /> </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">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/FOCUS_2006_datasets.html b/docs/reference/FOCUS_2006_datasets.html index 543e24ad..7a39dcd0 100644 --- a/docs/reference/FOCUS_2006_datasets.html +++ b/docs/reference/FOCUS_2006_datasets.html @@ -72,7 +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">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/FOMC.solution.html b/docs/reference/FOMC.solution.html index c376227c..9136b882 100644 --- a/docs/reference/FOMC.solution.html +++ b/docs/reference/FOMC.solution.html @@ -73,7 +73,7 @@ a decreasing rate constant." /> </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">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/HS.solution.html b/docs/reference/HS.solution.html index 8a90fec3..e3009bcc 100644 --- a/docs/reference/HS.solution.html +++ b/docs/reference/HS.solution.html @@ -73,7 +73,7 @@ between them." /> </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">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/IORE.solution.html b/docs/reference/IORE.solution.html index 8e6a2792..f1a40d44 100644 --- a/docs/reference/IORE.solution.html +++ b/docs/reference/IORE.solution.html @@ -73,7 +73,7 @@ a concentration dependent rate constant." /> </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">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/NAFTA_SOP_2015-1.png b/docs/reference/NAFTA_SOP_2015-1.png Binary files differindex 76d724f0..4f0d7833 100644 --- a/docs/reference/NAFTA_SOP_2015-1.png +++ b/docs/reference/NAFTA_SOP_2015-1.png diff --git a/docs/reference/NAFTA_SOP_2015.html b/docs/reference/NAFTA_SOP_2015.html index 301bf684..de9db9eb 100644 --- a/docs/reference/NAFTA_SOP_2015.html +++ b/docs/reference/NAFTA_SOP_2015.html @@ -72,7 +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">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/NAFTA_SOP_Attachment-1.png b/docs/reference/NAFTA_SOP_Attachment-1.png Binary files differindex eec3dd9b..9417685e 100644 --- a/docs/reference/NAFTA_SOP_Attachment-1.png +++ b/docs/reference/NAFTA_SOP_Attachment-1.png diff --git a/docs/reference/NAFTA_SOP_Attachment.html b/docs/reference/NAFTA_SOP_Attachment.html index 03a45bc3..0b063e2c 100644 --- a/docs/reference/NAFTA_SOP_Attachment.html +++ b/docs/reference/NAFTA_SOP_Attachment.html @@ -72,7 +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">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> @@ -193,7 +193,7 @@ #> Estimate Pr(>t) Lower Upper #> parent_0 9.99e+01 1.41e-26 98.8116 101.0810 #> k1 2.67e-02 5.05e-06 0.0243 0.0295 -#> k2 2.42e-12 5.00e-01 0.0000 Inf +#> k2 2.26e-12 5.00e-01 0.0000 Inf #> g 6.47e-01 3.67e-06 0.6248 0.6677 #> sigma 1.27e+00 8.91e-06 0.8395 1.6929 #> @@ -202,7 +202,7 @@ #> DT50 DT90 DT50_rep #> SFO 67.7 2.25e+02 6.77e+01 #> IORE 58.2 1.07e+03 3.22e+02 -#> DFOP 55.5 5.22e+11 2.86e+11 +#> DFOP 55.5 5.59e+11 3.07e+11 #> #> Representative half-life: #> [1] 321.51</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>nafta_att_p5a</span><span class='op'>)</span> diff --git a/docs/reference/Rplot001.png b/docs/reference/Rplot001.png Binary files differindex 762a3dd4..7f498242 100644 --- a/docs/reference/Rplot001.png +++ b/docs/reference/Rplot001.png diff --git a/docs/reference/Rplot002.png b/docs/reference/Rplot002.png Binary files differindex d24e35b4..54c31a3f 100644 --- a/docs/reference/Rplot002.png +++ b/docs/reference/Rplot002.png diff --git a/docs/reference/Rplot003.png b/docs/reference/Rplot003.png Binary files differindex e96adeb3..19198739 100644 --- a/docs/reference/Rplot003.png +++ b/docs/reference/Rplot003.png diff --git a/docs/reference/Rplot004.png b/docs/reference/Rplot004.png Binary files differindex 91058d4b..1028a9c4 100644 --- a/docs/reference/Rplot004.png +++ b/docs/reference/Rplot004.png diff --git a/docs/reference/Rplot005.png b/docs/reference/Rplot005.png Binary files differindex 91058d4b..aa844051 100644 --- a/docs/reference/Rplot005.png +++ b/docs/reference/Rplot005.png diff --git a/docs/reference/Rplot006.png b/docs/reference/Rplot006.png Binary files differindex 74f43dfa..81525882 100644 --- a/docs/reference/Rplot006.png +++ b/docs/reference/Rplot006.png diff --git a/docs/reference/Rplot007.png b/docs/reference/Rplot007.png Binary files differindex fce3b6ee..10b7455a 100644 --- a/docs/reference/Rplot007.png +++ b/docs/reference/Rplot007.png diff --git a/docs/reference/SFO.solution.html b/docs/reference/SFO.solution.html index 7e4fb237..826a0472 100644 --- a/docs/reference/SFO.solution.html +++ b/docs/reference/SFO.solution.html @@ -72,7 +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">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/SFORB.solution.html b/docs/reference/SFORB.solution.html index 7254c451..b2062e30 100644 --- a/docs/reference/SFORB.solution.html +++ b/docs/reference/SFORB.solution.html @@ -76,7 +76,7 @@ and no substance in the bound fraction." /> </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">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/add_err-1.png b/docs/reference/add_err-1.png Binary files differindex 9d333cbb..9ba106db 100644 --- a/docs/reference/add_err-1.png +++ b/docs/reference/add_err-1.png diff --git a/docs/reference/add_err-3.png b/docs/reference/add_err-3.png Binary files differindex 07cf0032..493a761a 100644 --- a/docs/reference/add_err-3.png +++ b/docs/reference/add_err-3.png diff --git a/docs/reference/add_err.html b/docs/reference/add_err.html index 2009aaf4..6fbecd14 100644 --- a/docs/reference/add_err.html +++ b/docs/reference/add_err.html @@ -74,7 +74,7 @@ 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">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/aw.html b/docs/reference/aw.html index 77ee9cef..6399b839 100644 --- a/docs/reference/aw.html +++ b/docs/reference/aw.html @@ -74,7 +74,7 @@ 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">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/confint.mkinfit.html b/docs/reference/confint.mkinfit.html index b71e039a..06e78459 100644 --- a/docs/reference/confint.mkinfit.html +++ b/docs/reference/confint.mkinfit.html @@ -79,7 +79,7 @@ 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">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> @@ -285,13 +285,13 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, <span class='va'>f_d_1</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span><span class='op'>(</span><span class='va'>FOCUS_2006_D</span>, <span class='va'>value</span> <span class='op'>!=</span> <span class='fl'>0</span><span class='op'>)</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> <span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span><span class='op'>(</span><span class='va'>ci_profile</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span><span class='va'>f_d_1</span>, method <span class='op'>=</span> <span class='st'>"profile"</span>, cores <span class='op'>=</span> <span class='fl'>1</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span><span class='op'>)</span> </div><div class='output co'>#> user system elapsed -#> 4.324 0.980 3.960 </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> +#> 4.255 1.029 3.937 </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 if we use at least 4 cores</span> <span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span><span class='op'>(</span><span class='va'>ci_profile_no_parent_0</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span><span class='va'>f_d_1</span>, method <span class='op'>=</span> <span class='st'>"profile"</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</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='op'>)</span>, cores <span class='op'>=</span> <span class='va'>n_cores</span><span class='op'>)</span><span class='op'>)</span> </div><div class='output co'>#> <span class='message'>Profiling the likelihood</span></div><div class='output co'>#> user system elapsed -#> 1.480 0.109 0.905 </div><div class='input'><span class='va'>ci_profile</span> +#> 1.469 0.092 0.911 </div><div class='input'><span class='va'>ci_profile</span> </div><div class='output co'>#> 2.5% 97.5% #> parent_0 96.456003640 1.027703e+02 #> k_parent_sink 0.040762501 5.549764e-02 @@ -349,14 +349,14 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, #> sigma 2.535612399 3.985263e+00</div><div class='input'><span class='va'>ci_quadratic_transformed_ff</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span><span class='va'>f_d_2</span>, method <span class='op'>=</span> <span class='st'>"quadratic"</span><span class='op'>)</span> <span class='va'>ci_quadratic_transformed_ff</span> </div><div class='output co'>#> 2.5% 97.5% -#> parent_0 96.403833585 102.79311650 +#> parent_0 96.403833578 102.79311649 #> k_parent 0.090823771 0.10725430 #> k_m1 0.004012219 0.00689755 #> f_parent_to_m1 0.469118824 0.55959615 #> sigma 2.396089689 3.85491806</div><div class='input'><span class='va'>ci_quadratic_untransformed_ff</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span><span class='va'>f_d_2</span>, method <span class='op'>=</span> <span class='st'>"quadratic"</span>, transformed <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span> <span class='va'>ci_quadratic_untransformed_ff</span> </div><div class='output co'>#> 2.5% 97.5% -#> parent_0 96.403833589 1.027931e+02 +#> parent_0 96.403833583 1.027931e+02 #> k_parent 0.090491913 1.069035e-01 #> k_m1 0.003835485 6.685823e-03 #> f_parent_to_m1 0.469113477 5.598387e-01 @@ -374,15 +374,15 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, #> f_parent_to_m1 TRUE FALSE #> sigma TRUE FALSE</div><div class='input'><span class='va'>rel_diffs_transformed_ff</span> </div><div class='output co'>#> 2.5% 97.5% -#> parent_0 0.0005408689 0.0002217234 +#> parent_0 0.0005408690 0.0002217233 #> k_parent 0.0009598532 0.0009001864 -#> k_m1 0.0307283044 0.0290588365 -#> f_parent_to_m1 0.0046881768 0.0027780063 +#> k_m1 0.0307283041 0.0290588361 +#> f_parent_to_m1 0.0046881769 0.0027780063 #> sigma 0.0550252516 0.0327066836</div><div class='input'><span class='va'>rel_diffs_untransformed_ff</span> </div><div class='output co'>#> 2.5% 97.5% -#> parent_0 0.0005408689 0.0002217233 -#> k_parent 0.0046102155 0.0023732281 -#> k_m1 0.0146740688 0.0025291817 +#> parent_0 0.0005408689 0.0002217232 +#> k_parent 0.0046102156 0.0023732281 +#> k_m1 0.0146740690 0.0025291820 #> f_parent_to_m1 0.0046995211 0.0023457712 #> 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> @@ -396,18 +396,18 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, error_model_algorithm <span class='op'>=</span> <span class='st'>"direct"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span><span class='va'>f_tc_2</span>, method <span class='op'>=</span> <span class='st'>"quadratic"</span><span class='op'>)</span> </div><div class='output co'>#> 2.5% 97.5% -#> parent_0 94.596126334 106.19944007 -#> k_M1 0.037605408 0.04490759 -#> k_M2 0.008568739 0.01087675 -#> f_parent_to_M1 0.021463787 0.62023881 -#> f_parent_to_M2 0.015166531 0.37975349 -#> k1 0.273897467 0.33388084 -#> k2 0.018614555 0.02250379 -#> g 0.671943606 0.73583278 -#> sigma_low 0.251283766 0.83992113 -#> rsd_high 0.040411014 0.07662005</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span><span class='va'>f_tc_2</span>, <span class='st'>"parent_0"</span>, method <span class='op'>=</span> <span class='st'>"quadratic"</span><span class='op'>)</span> +#> parent_0 94.596039609 106.19954892 +#> k_M1 0.037605368 0.04490762 +#> k_M2 0.008568731 0.01087676 +#> f_parent_to_M1 0.021462489 0.62023882 +#> f_parent_to_M2 0.015165617 0.37975348 +#> k1 0.273897348 0.33388101 +#> k2 0.018614554 0.02250378 +#> g 0.671943411 0.73583305 +#> sigma_low 0.251283495 0.83992077 +#> rsd_high 0.040411024 0.07662008</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span><span class='va'>f_tc_2</span>, <span class='st'>"parent_0"</span>, method <span class='op'>=</span> <span class='st'>"quadratic"</span><span class='op'>)</span> </div><div class='output co'>#> 2.5% 97.5% -#> parent_0 94.59613 106.1994</div><div class='input'><span class='co'># }</span> +#> parent_0 94.59604 106.1995</div><div class='input'><span class='co'># }</span> </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> diff --git a/docs/reference/create_deg_func.html b/docs/reference/create_deg_func.html index ed49e37e..82583f1a 100644 --- a/docs/reference/create_deg_func.html +++ b/docs/reference/create_deg_func.html @@ -72,7 +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">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> @@ -182,7 +182,7 @@ replications <span class='op'>=</span> <span class='fl'>2</span><span class='op'>)</span> </div><div class='output co'>#> <span class='message'>Loading required package: rbenchmark</span></div><div class='output co'>#> test replications elapsed relative user.self sys.self user.child #> 1 analytical 2 0.389 1.000 0.389 0 0 -#> 2 deSolve 2 0.689 1.771 0.688 0 0 +#> 2 deSolve 2 0.690 1.774 0.690 0 0 #> sys.child #> 1 0 #> 2 0</div><div class='input'> <span class='va'>DFOP_SFO</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span> @@ -193,8 +193,8 @@ deSolve <span class='op'>=</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>DFOP_SFO</span>, <span class='va'>FOCUS_D</span>, solution_type <span class='op'>=</span> <span class='st'>"deSolve"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>, replications <span class='op'>=</span> <span class='fl'>2</span><span class='op'>)</span> </div><div class='output co'>#> test replications elapsed relative user.self sys.self user.child -#> 1 analytical 2 0.825 1.000 0.825 0 0 -#> 2 deSolve 2 1.574 1.908 1.573 0 0 +#> 1 analytical 2 0.817 1.000 0.818 0 0 +#> 2 deSolve 2 1.591 1.947 1.591 0 0 #> sys.child #> 1 0 #> 2 0</div><div class='input'><span class='co'># }</span> diff --git a/docs/reference/dimethenamid_2018.html b/docs/reference/dimethenamid_2018.html index 435848c2..6845f74f 100644 --- a/docs/reference/dimethenamid_2018.html +++ b/docs/reference/dimethenamid_2018.html @@ -77,7 +77,7 @@ constrained by data protection regulations." /> </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">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html index e42ca9fe..584079d2 100644 --- a/docs/reference/endpoints.html +++ b/docs/reference/endpoints.html @@ -78,7 +78,7 @@ 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">1.0.2</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/experimental_data_for_UBA-1.png b/docs/reference/experimental_data_for_UBA-1.png Binary files differindex 22f38cc2..33946ded 100644 --- a/docs/reference/experimental_data_for_UBA-1.png +++ b/docs/reference/experimental_data_for_UBA-1.png diff --git a/docs/reference/experimental_data_for_UBA.html b/docs/reference/experimental_data_for_UBA.html index 9333a34f..77f75678 100644 --- a/docs/reference/experimental_data_for_UBA.html +++ b/docs/reference/experimental_data_for_UBA.html @@ -100,7 +100,7 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl </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">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/f_time_norm_focus.html b/docs/reference/f_time_norm_focus.html index 6917b4b3..aa494b27 100644 --- a/docs/reference/f_time_norm_focus.html +++ b/docs/reference/f_time_norm_focus.html @@ -73,7 +73,7 @@ in Appendix 8 to the FOCUS kinetics guidance (FOCUS 2014, p. 369)." /> </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">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/focus_soil_moisture.html b/docs/reference/focus_soil_moisture.html index f0c766da..61f235db 100644 --- a/docs/reference/focus_soil_moisture.html +++ b/docs/reference/focus_soil_moisture.html @@ -73,7 +73,7 @@ corresponds to pF2, MWHC to pF 1 and 1/3 bar to pF 2.5." /> </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">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/get_deg_func.html b/docs/reference/get_deg_func.html index a0e341c9..44703806 100644 --- a/docs/reference/get_deg_func.html +++ b/docs/reference/get_deg_func.html @@ -72,7 +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">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/ilr.html b/docs/reference/ilr.html index b91ef055..671faf5d 100644 --- a/docs/reference/ilr.html +++ b/docs/reference/ilr.html @@ -73,7 +73,7 @@ transformations." /> </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">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/index.html b/docs/reference/index.html index 7b1bc4f1..e21304b9 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -71,7 +71,7 @@ </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">1.0.2</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/loftest-3.png b/docs/reference/loftest-3.png Binary files differindex 43e6a00f..6afd084b 100644 --- a/docs/reference/loftest-3.png +++ b/docs/reference/loftest-3.png diff --git a/docs/reference/loftest-5.png b/docs/reference/loftest-5.png Binary files differindex cf7e5862..43460a65 100644 --- a/docs/reference/loftest-5.png +++ b/docs/reference/loftest-5.png diff --git a/docs/reference/loftest.html b/docs/reference/loftest.html index 614b8eea..6e72774e 100644 --- a/docs/reference/loftest.html +++ b/docs/reference/loftest.html @@ -75,7 +75,7 @@ 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">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/logLik.mkinfit.html b/docs/reference/logLik.mkinfit.html index 8d984e55..9e5b4069 100644 --- a/docs/reference/logLik.mkinfit.html +++ b/docs/reference/logLik.mkinfit.html @@ -76,7 +76,7 @@ the error 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">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/logistic.solution-2.png b/docs/reference/logistic.solution-2.png Binary files differindex 79bf3453..73e6436d 100644 --- a/docs/reference/logistic.solution-2.png +++ b/docs/reference/logistic.solution-2.png diff --git a/docs/reference/logistic.solution.html b/docs/reference/logistic.solution.html index 404344a3..d11e1b3c 100644 --- a/docs/reference/logistic.solution.html +++ b/docs/reference/logistic.solution.html @@ -73,7 +73,7 @@ an increasing rate constant, supposedly caused by microbial growth" /> </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">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> @@ -240,10 +240,10 @@ Version 1.1, 18 December 2014 <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span><span class='op'>(</span><span class='va'>m</span><span class='op'>)</span> </div><div class='img'><img src='logistic.solution-2.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>m</span><span class='op'>)</span><span class='op'>$</span><span class='va'>bpar</span> </div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower -#> parent_0 1.057896e+02 1.9023449703 55.610119 3.768361e-16 1.016451e+02 -#> kmax 6.398190e-02 0.0143201031 4.467978 3.841829e-04 3.929235e-02 +#> parent_0 1.057896e+02 1.9023449590 55.610120 3.768360e-16 1.016451e+02 +#> kmax 6.398190e-02 0.0143201029 4.467978 3.841828e-04 3.929235e-02 #> k0 1.612775e-04 0.0005866813 0.274898 3.940351e-01 5.846688e-08 -#> r 2.263946e-01 0.1718110715 1.317695 1.061044e-01 4.335843e-02 +#> r 2.263946e-01 0.1718110662 1.317695 1.061043e-01 4.335843e-02 #> sigma 5.332935e+00 0.9145907310 5.830952 4.036926e-05 3.340213e+00 #> Upper #> parent_0 109.9341588 diff --git a/docs/reference/lrtest.mkinfit.html b/docs/reference/lrtest.mkinfit.html index e39314d9..d670fb0c 100644 --- a/docs/reference/lrtest.mkinfit.html +++ b/docs/reference/lrtest.mkinfit.html @@ -76,7 +76,7 @@ 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">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/max_twa_parent.html b/docs/reference/max_twa_parent.html index 2aa5d5f1..4d473893 100644 --- a/docs/reference/max_twa_parent.html +++ b/docs/reference/max_twa_parent.html @@ -78,7 +78,7 @@ soil section of the FOCUS guidance." /> </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">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/mccall81_245T-1.png b/docs/reference/mccall81_245T-1.png Binary files differindex 58ae716a..91fe060e 100644 --- a/docs/reference/mccall81_245T-1.png +++ b/docs/reference/mccall81_245T-1.png diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index b99138a0..b7dca4a7 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -74,7 +74,7 @@ </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">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> @@ -181,30 +181,30 @@ <span class='va'>fit.1</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO_SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span><span class='op'>(</span><span class='va'>mccall81_245T</span>, <span class='va'>soil</span> <span class='op'>==</span> <span class='st'>"Commerce"</span><span class='op'>)</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> </div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>fit.1</span><span class='op'>)</span><span class='op'>$</span><span class='va'>bpar</span> </div><div class='output co'>#> Estimate se_notrans t value Pr(>t) -#> T245_0 1.038550e+02 2.1847074888 47.537272 4.472189e-18 +#> T245_0 1.038550e+02 2.1847074945 47.537272 4.472189e-18 #> k_T245 4.337042e-02 0.0018983965 22.845818 2.276911e-13 -#> k_phenol 4.050581e-01 0.2986993400 1.356073 9.756988e-02 -#> k_anisole 6.678742e-03 0.0008021439 8.326114 2.623176e-07 -#> f_T245_to_phenol 6.227599e-01 0.3985340295 1.562627 6.949412e-02 -#> f_phenol_to_anisole 1.000000e+00 0.6718439378 1.488441 7.867787e-02 -#> sigma 2.514628e+00 0.4907558750 5.123989 6.233156e-05 +#> k_phenol 4.050581e-01 0.2986993563 1.356073 9.756989e-02 +#> k_anisole 6.678742e-03 0.0008021439 8.326114 2.623177e-07 +#> f_T245_to_phenol 6.227599e-01 0.3985340558 1.562627 6.949413e-02 +#> f_phenol_to_anisole 1.000000e+00 0.6718439825 1.488441 7.867789e-02 +#> sigma 2.514628e+00 0.4907558883 5.123989 6.233157e-05 #> Lower Upper -#> T245_0 99.246061370 1.084640e+02 +#> T245_0 99.246061385 1.084640e+02 #> k_T245 0.039631621 4.746194e-02 -#> k_phenol 0.218013878 7.525762e-01 +#> k_phenol 0.218013879 7.525762e-01 #> k_anisole 0.005370739 8.305299e-03 -#> f_T245_to_phenol 0.547559083 6.924813e-01 +#> f_T245_to_phenol 0.547559081 6.924813e-01 #> f_phenol_to_anisole 0.000000000 1.000000e+00 #> sigma 1.706607296 3.322649e+00</div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>fit.1</span><span class='op'>)</span> </div><div class='output co'>#> $ff #> T245_phenol T245_sink phenol_anisole phenol_sink -#> 6.227599e-01 3.772401e-01 1.000000e+00 6.894640e-11 +#> 6.227599e-01 3.772401e-01 1.000000e+00 3.773626e-10 #> #> $distimes #> DT50 DT90 #> T245 15.982025 53.09114 #> phenol 1.711229 5.68458 -#> anisole 103.784092 344.76329 +#> anisole 103.784093 344.76329 #> </div><div class='input'> <span class='co'># formation fraction from phenol to anisol is practically 1. As we cannot</span> <span class='co'># fix formation fractions when using the ilr transformation, we can turn of</span> <span class='co'># the sink in the model generation</span> @@ -215,28 +215,28 @@ quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> </div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>fit.2</span><span class='op'>)</span><span class='op'>$</span><span class='va'>bpar</span> </div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower -#> T245_0 1.038550e+02 2.1623653027 48.028439 4.993108e-19 99.271020526 -#> k_T245 4.337042e-02 0.0018343666 23.643268 3.573555e-14 0.039650977 -#> k_phenol 4.050582e-01 0.1177237248 3.440752 1.679252e-03 0.218746585 -#> k_anisole 6.678741e-03 0.0006829745 9.778903 1.872894e-08 0.005377083 -#> f_T245_to_phenol 6.227599e-01 0.0342197865 18.198825 2.039410e-12 0.547975628 +#> T245_0 1.038550e+02 2.1623653066 48.028439 4.993108e-19 99.271020284 +#> k_T245 4.337042e-02 0.0018343666 23.643268 3.573556e-14 0.039650976 +#> k_phenol 4.050582e-01 0.1177237473 3.440752 1.679254e-03 0.218746587 +#> k_anisole 6.678742e-03 0.0006829745 9.778903 1.872894e-08 0.005377083 +#> f_T245_to_phenol 6.227599e-01 0.0342197875 18.198824 2.039411e-12 0.547975637 #> sigma 2.514628e+00 0.3790944250 6.633250 2.875782e-06 1.710983655 #> Upper -#> T245_0 108.43904097 +#> T245_0 108.43904074 #> k_T245 0.04743877 -#> k_phenol 0.75005577 +#> k_phenol 0.75005585 #> k_anisole 0.00829550 -#> f_T245_to_phenol 0.69212306 +#> f_T245_to_phenol 0.69212308 #> sigma 3.31827222</div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>fit.1</span><span class='op'>)</span> </div><div class='output co'>#> $ff #> T245_phenol T245_sink phenol_anisole phenol_sink -#> 6.227599e-01 3.772401e-01 1.000000e+00 6.894640e-11 +#> 6.227599e-01 3.772401e-01 1.000000e+00 3.773626e-10 #> #> $distimes #> DT50 DT90 #> T245 15.982025 53.09114 #> phenol 1.711229 5.68458 -#> anisole 103.784092 344.76329 +#> anisole 103.784093 344.76329 #> </div><div class='input'> <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span><span class='op'>(</span><span class='va'>fit.2</span><span class='op'>)</span> </div><div class='img'><img src='mccall81_245T-1.png' alt='' width='700' height='433' /></div><div class='input'> <span class='co'># }</span> </div></pre> diff --git a/docs/reference/mixed-1.png b/docs/reference/mixed-1.png Binary files differindex 05beffc9..28a376f4 100644 --- a/docs/reference/mixed-1.png +++ b/docs/reference/mixed-1.png diff --git a/docs/reference/mixed.html b/docs/reference/mixed.html index f5429f8b..23d955e3 100644 --- a/docs/reference/mixed.html +++ b/docs/reference/mixed.html @@ -72,7 +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">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> @@ -235,18 +235,16 @@ #> Status of individual fits: #> #> dataset -#> model 1 2 3 4 5 6 7 8 -#> DFOP-SFO OK OK OK OK OK C OK OK +#> model 1 2 3 4 5 6 7 8 +#> DFOP-SFO OK OK OK OK OK OK OK OK #> #> OK: No warnings -#> C: Optimisation did not converge: -#> iteration limit reached without convergence (10) #> #> Mean fitted parameters: #> parent_0 log_k_m1 f_parent_qlogis log_k1 log_k2 -#> 100.606304 -8.759216 -0.002001 -3.350539 -3.989549 +#> 100.674757 -8.761916 -0.004347 -3.348812 -3.986853 #> g_qlogis -#> -0.090353 </div><div class='input'><span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_mixed</span><span class='op'>)</span> +#> -0.087392 </div><div class='input'><span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_mixed</span><span class='op'>)</span> </div><div class='img'><img src='mixed-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># }</span> </div></pre> </div> diff --git a/docs/reference/mkin_long_to_wide.html b/docs/reference/mkin_long_to_wide.html index 7eca35de..c82da5dd 100644 --- a/docs/reference/mkin_long_to_wide.html +++ b/docs/reference/mkin_long_to_wide.html @@ -74,7 +74,7 @@ variable and several dependent variables as columns." /> </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">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/mkin_wide_to_long.html b/docs/reference/mkin_wide_to_long.html index 5df8972f..15619fba 100644 --- a/docs/reference/mkin_wide_to_long.html +++ b/docs/reference/mkin_wide_to_long.html @@ -74,7 +74,7 @@ mkinfit." /> </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">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/mkinds.html b/docs/reference/mkinds.html index 543ea68d..5111a9e0 100644 --- a/docs/reference/mkinds.html +++ b/docs/reference/mkinds.html @@ -75,7 +75,7 @@ provided by this package come as mkinds objects nevertheless." /> </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">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/mkindsg.html b/docs/reference/mkindsg.html index 74d3a26c..003e5e8f 100644 --- a/docs/reference/mkindsg.html +++ b/docs/reference/mkindsg.html @@ -75,7 +75,7 @@ dataset if no data are supplied." /> </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">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/mkinerrmin.html b/docs/reference/mkinerrmin.html index 161eadca..f22b4350 100644 --- a/docs/reference/mkinerrmin.html +++ b/docs/reference/mkinerrmin.html @@ -73,7 +73,7 @@ the chi-squared test as defined in the FOCUS kinetics report from 2006." /> </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">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/mkinerrplot.html b/docs/reference/mkinerrplot.html index 2509e4c1..361ce79a 100644 --- a/docs/reference/mkinerrplot.html +++ b/docs/reference/mkinerrplot.html @@ -76,7 +76,7 @@ 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">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/mkinfit-1.png b/docs/reference/mkinfit-1.png Binary files differindex bbc0ccb6..de2a90a9 100644 --- a/docs/reference/mkinfit-1.png +++ b/docs/reference/mkinfit-1.png diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 4d8aeb40..180f2ee7 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -80,7 +80,7 @@ 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">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> @@ -431,10 +431,10 @@ doi: <a href='https://doi.org/10.3390/environments6120124'>10.3390/environments6 <span class='co'># Use shorthand notation for parent only degradation</span> <span class='va'>fit</span> <span class='op'><-</span> <span class='fu'>mkinfit</span><span class='op'>(</span><span class='st'>"FOMC"</span>, <span class='va'>FOCUS_2006_C</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span> -</div><div class='output co'>#> mkin version used for fitting: 1.0.0 +</div><div class='output co'>#> mkin version used for fitting: 1.0.3 #> R version used for fitting: 4.0.3 -#> Date of fit: Wed Feb 3 17:28:58 2021 -#> Date of summary: Wed Feb 3 17:28:58 2021 +#> Date of fit: Mon Feb 15 13:43:26 2021 +#> Date of summary: Mon Feb 15 13:43:26 2021 #> #> Equations: #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent @@ -476,10 +476,10 @@ doi: <a href='https://doi.org/10.3390/environments6120124'>10.3390/environments6 #> #> Parameter correlation: #> parent_0 log_alpha log_beta sigma -#> 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 +#> parent_0 1.000e+00 -1.565e-01 -3.142e-01 4.772e-08 +#> log_alpha -1.565e-01 1.000e+00 9.564e-01 1.005e-07 +#> log_beta -3.142e-01 9.564e-01 1.000e+00 8.541e-08 +#> sigma 4.772e-08 1.005e-07 8.541e-08 1.000e+00 #> #> Backtransformed parameters: #> Confidence intervals for internally transformed parameters are asymmetric. @@ -548,7 +548,7 @@ doi: <a href='https://doi.org/10.3390/environments6120124'>10.3390/environments6 #> --- #> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1</div><div class='input'><span class='fu'><a href='parms.html'>parms</a></span><span class='op'>(</span><span class='va'>fit.tc</span><span class='op'>)</span> </div><div class='output co'>#> parent_0 k_parent k_m1 f_parent_to_m1 sigma_low -#> 1.007343e+02 1.005562e-01 5.166712e-03 5.083933e-01 3.049884e-03 +#> 1.007343e+02 1.005562e-01 5.166712e-03 5.083933e-01 3.049883e-03 #> rsd_high #> 7.928118e-02 </div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>fit.tc</span><span class='op'>)</span> </div><div class='output co'>#> $ff @@ -575,9 +575,9 @@ doi: <a href='https://doi.org/10.3390/environments6120124'>10.3390/environments6 solution_type <span class='op'>=</span> <span class='st'>"analytical"</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>}</span> </div><div class='output co'>#> test relative elapsed -#> 3 analytical 1.000 0.542 -#> 1 deSolve_compiled 1.812 0.982 -#> 2 eigen 2.234 1.211</div><div class='input'><span class='co'># }</span> +#> 3 analytical 1.000 0.550 +#> 1 deSolve_compiled 1.731 0.952 +#> 2 eigen 2.662 1.464</div><div class='input'><span class='co'># }</span> <span class='co'># Use stepwise fitting, using optimised parameters from parent only fit, FOMC-SFO</span> <span class='co'># \dontrun{</span> @@ -587,22 +587,21 @@ doi: <a href='https://doi.org/10.3390/environments6120124'>10.3390/environments6 </div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'><span class='va'>fit.FOMC_SFO</span> <span class='op'><-</span> <span class='fu'>mkinfit</span><span class='op'>(</span><span class='va'>FOMC_SFO</span>, <span class='va'>FOCUS_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> <span class='co'># Again, we get a warning and try a more sophisticated error model</span> <span class='va'>fit.FOMC_SFO.tc</span> <span class='op'><-</span> <span class='fu'>mkinfit</span><span class='op'>(</span><span class='va'>FOMC_SFO</span>, <span class='va'>FOCUS_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='warning'>Warning: Optimisation did not converge:</span> -#> <span class='warning'>iteration limit reached without convergence (10)</span></div><div class='input'><span class='co'># This model has a higher likelihood, but not significantly so</span> +<span class='co'># This model has a higher likelihood, but not significantly so</span> <span class='fu'><a href='https://rdrr.io/pkg/lmtest/man/lrtest.html'>lrtest</a></span><span class='op'>(</span><span class='va'>fit.tc</span>, <span class='va'>fit.FOMC_SFO.tc</span><span class='op'>)</span> </div><div class='output co'>#> Likelihood ratio test #> #> Model 1: FOMC_SFO with error model tc and fixed parameter(s) m1_0 #> Model 2: SFO_SFO with error model tc and fixed parameter(s) m1_0 #> #Df LogLik Df Chisq Pr(>Chisq) -#> 1 7 -64.870 -#> 2 6 -64.983 -1 0.2259 0.6346</div><div class='input'><span class='co'># Also, the missing standard error for log_beta and the t-tests for alpha</span> +#> 1 7 -64.829 +#> 2 6 -64.983 -1 0.3075 0.5792</div><div class='input'><span class='co'># Also, the missing standard error for log_beta and the t-tests for alpha</span> <span class='co'># and beta indicate overparameterisation</span> <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>fit.FOMC_SFO.tc</span>, data <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='warning'>Warning: NaNs produced</span></div><div class='output co'>#> <span class='warning'>Warning: NaNs produced</span></div><div class='output co'>#> <span class='warning'>Warning: NaNs produced</span></div><div class='output co'>#> <span class='warning'>Warning: diag(.) had 0 or NA entries; non-finite result is doubtful</span></div><div class='output co'>#> mkin version used for fitting: 1.0.0 +</div><div class='output co'>#> <span class='warning'>Warning: NaNs produced</span></div><div class='output co'>#> <span class='warning'>Warning: NaNs produced</span></div><div class='output co'>#> <span class='warning'>Warning: diag(.) had 0 or NA entries; non-finite result is doubtful</span></div><div class='output co'>#> mkin version used for fitting: 1.0.3 #> R version used for fitting: 4.0.3 -#> Date of fit: Wed Feb 3 17:29:09 2021 -#> Date of summary: Wed Feb 3 17:29:09 2021 +#> Date of fit: Mon Feb 15 13:43:38 2021 +#> Date of summary: Mon Feb 15 13:43:38 2021 #> #> Equations: #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent @@ -611,12 +610,12 @@ doi: <a href='https://doi.org/10.3390/environments6120124'>10.3390/environments6 #> #> Model predictions using solution type deSolve #> -#> Fitted using 4273 model solutions performed in 3.195 s +#> Fitted using 3729 model solutions performed in 2.802 s #> #> Error model: Two-component variance function #> #> Error model algorithm: d_3 -#> Three-step fitting yielded a higher likelihood than direct fitting +#> Direct fitting and three-step fitting yield approximately the same likelihood #> #> Starting values for parameters to be optimised: #> value type @@ -642,72 +641,67 @@ doi: <a href='https://doi.org/10.3390/environments6120124'>10.3390/environments6 #> value type #> m1_0 0 state #> -#> -#> Warning(s): -#> Optimisation did not converge: -#> iteration limit reached without convergence (10) -#> #> Results: #> -#> AIC BIC logLik -#> 143.7396 155.2027 -64.86982 +#> AIC BIC logLik +#> 143.658 155.1211 -64.82902 #> #> Optimised, transformed parameters with symmetric confidence intervals: -#> Estimate Std. Error Lower Upper -#> parent_0 1.016e+02 1.90600 97.7400 105.5000 -#> log_k_m1 -5.285e+00 0.09286 -5.4740 -5.0950 -#> f_parent_qlogis 6.482e-04 0.06164 -0.1251 0.1264 -#> log_alpha 5.467e+00 NaN NaN NaN -#> log_beta 7.750e+00 NaN NaN NaN -#> sigma_low 0.000e+00 NaN NaN NaN -#> rsd_high 7.989e-02 NaN NaN NaN +#> Estimate Std. Error Lower Upper +#> parent_0 101.600000 2.6400000 96.240000 107.000000 +#> log_k_m1 -5.284000 0.0929100 -5.474000 -5.095000 +#> f_parent_qlogis 0.001426 0.0767000 -0.155000 0.157800 +#> log_alpha 5.522000 0.0077320 5.506000 5.538000 +#> log_beta 7.806000 NaN NaN NaN +#> sigma_low 0.002488 0.0002431 0.001992 0.002984 +#> rsd_high 0.079210 0.0093280 0.060180 0.098230 #> #> Parameter correlation: -#> parent_0 log_k_m1 f_parent_qlogis log_alpha log_beta -#> parent_0 1.0000000 -0.0002167 -0.6060 NaN NaN -#> log_k_m1 -0.0002167 1.0000000 0.5474 NaN NaN -#> f_parent_qlogis -0.6060320 0.5474423 1.0000 NaN NaN -#> log_alpha NaN NaN NaN 1 NaN -#> log_beta NaN NaN NaN NaN 1 -#> sigma_low NaN NaN NaN NaN NaN -#> rsd_high NaN NaN NaN NaN NaN -#> sigma_low rsd_high -#> parent_0 NaN NaN -#> log_k_m1 NaN NaN -#> f_parent_qlogis NaN NaN -#> log_alpha NaN NaN -#> log_beta NaN NaN -#> sigma_low 1 NaN -#> rsd_high NaN 1 +#> parent_0 log_k_m1 f_parent_qlogis log_alpha log_beta +#> parent_0 1.000000 -0.095226 -0.76678 0.70544 NaN +#> log_k_m1 -0.095226 1.000000 0.51432 -0.14387 NaN +#> f_parent_qlogis -0.766780 0.514321 1.00000 -0.61396 NaN +#> log_alpha 0.705444 -0.143872 -0.61396 1.00000 NaN +#> log_beta NaN NaN NaN NaN 1 +#> sigma_low 0.016073 0.001586 0.01548 5.87007 NaN +#> rsd_high 0.006626 -0.011700 -0.05357 0.04849 NaN +#> sigma_low rsd_high +#> parent_0 0.016073 0.006626 +#> log_k_m1 0.001586 -0.011700 +#> f_parent_qlogis 0.015476 -0.053566 +#> log_alpha 5.870075 0.048487 +#> log_beta NaN NaN +#> sigma_low 1.000000 -0.652558 +#> rsd_high -0.652558 1.000000 #> #> Backtransformed parameters: #> Confidence intervals for internally transformed parameters are asymmetric. #> t-test (unrealistically) based on the assumption of normal distribution #> for estimators of untransformed parameters. #> Estimate t value Pr(>t) Lower Upper -#> parent_0 1.016e+02 32.5400 7.812e-26 97.740000 1.055e+02 -#> k_m1 5.069e-03 10.0400 1.448e-11 0.004194 6.126e-03 -#> f_parent_to_m1 5.002e-01 20.7300 5.001e-20 0.468800 5.315e-01 -#> alpha 2.367e+02 0.6205 2.697e-01 NA NA -#> beta 2.322e+03 0.6114 2.727e-01 NA NA -#> sigma_low 0.000e+00 NaN NaN NaN NaN -#> rsd_high 7.989e-02 8.6630 4.393e-10 NaN NaN +#> parent_0 1.016e+02 32.7800 6.311e-26 9.624e+01 1.070e+02 +#> k_m1 5.072e-03 10.1200 1.216e-11 4.196e-03 6.130e-03 +#> f_parent_to_m1 5.004e-01 20.8300 4.317e-20 4.613e-01 5.394e-01 +#> alpha 2.502e+02 0.5624 2.889e-01 2.463e+02 2.542e+02 +#> beta 2.455e+03 0.5549 2.915e-01 NA NA +#> sigma_low 2.488e-03 0.4843 3.158e-01 1.992e-03 2.984e-03 +#> rsd_high 7.921e-02 8.4300 8.001e-10 6.018e-02 9.823e-02 #> #> FOCUS Chi2 error levels in percent: #> err.min n.optim df -#> All data 6.782 5 14 -#> parent 7.142 3 6 -#> m1 4.639 2 8 +#> All data 6.781 5 14 +#> parent 7.141 3 6 +#> m1 4.640 2 8 #> #> Resulting formation fractions: #> ff -#> parent_m1 0.5002 -#> parent_sink 0.4998 +#> parent_m1 0.5004 +#> parent_sink 0.4996 #> #> Estimated disappearance times: -#> DT50 DT90 DT50back -#> parent 6.81 22.7 6.833 -#> m1 136.74 454.2 NA</div><div class='input'> +#> DT50 DT90 DT50back +#> parent 6.812 22.7 6.834 +#> m1 136.661 454.0 NA</div><div class='input'> <span class='co'># We can easily use starting parameters from the parent only fit (only for illustration)</span> <span class='va'>fit.FOMC</span> <span class='op'>=</span> <span class='fu'>mkinfit</span><span class='op'>(</span><span class='st'>"FOMC"</span>, <span class='va'>FOCUS_2006_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span><span class='op'>)</span> <span class='va'>fit.FOMC_SFO</span> <span class='op'><-</span> <span class='fu'>mkinfit</span><span class='op'>(</span><span class='va'>FOMC_SFO</span>, <span class='va'>FOCUS_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index 43e5cc23..4ce9468a 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -78,7 +78,7 @@ mkinmod." /> </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">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> @@ -348,7 +348,7 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p> parent <span class='op'>=</span> <span class='fu'>mkinsub</span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"m1"</span>, full_name <span class='op'>=</span> <span class='st'>"Test compound"</span><span class='op'>)</span>, m1 <span class='op'>=</span> <span class='fu'>mkinsub</span><span class='op'>(</span><span class='st'>"SFO"</span>, full_name <span class='op'>=</span> <span class='st'>"Metabolite M1"</span><span class='op'>)</span>, name <span class='op'>=</span> <span class='st'>"SFO_SFO"</span>, dll_dir <span class='op'>=</span> <span class='va'>DLL_dir</span>, unload <span class='op'>=</span> <span class='cn'>TRUE</span>, overwrite <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>Copied DLL from /tmp/Rtmp1BYo7R/file5c60502538f0.so to /home/jranke/.local/share/mkin/SFO_SFO.so</span></div><div class='input'><span class='co'># Now we can save the model and restore it in a new session</span> +</div><div class='output co'>#> <span class='message'>Copied DLL from /tmp/RtmpiJ2M4Z/filee097a4a94a921.so to /home/jranke/.local/share/mkin/SFO_SFO.so</span></div><div class='input'><span class='co'># Now we can save the model and restore it in a new session</span> <span class='fu'><a href='https://rdrr.io/r/base/readRDS.html'>saveRDS</a></span><span class='op'>(</span><span class='va'>SFO_SFO.2</span>, file <span class='op'>=</span> <span class='st'>"~/SFO_SFO.rds"</span><span class='op'>)</span> <span class='co'># Terminate the R session here if you would like to check, and then do</span> <span class='kw'><a href='https://rdrr.io/r/base/library.html'>library</a></span><span class='op'>(</span><span class='va'><a href='https://pkgdown.jrwb.de/mkin/'>mkin</a></span><span class='op'>)</span> @@ -397,7 +397,7 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p> #> }) #> return(predicted) #> } -#> <environment: 0x55555caa9ee0></div><div class='input'> +#> <environment: 0x55555b0c2760></div><div class='input'> <span class='co'># If we have several parallel metabolites</span> <span class='co'># (compare tests/testthat/test_synthetic_data_for_UBA_2014.R)</span> <span class='va'>m_synth_DFOP_par</span> <span class='op'><-</span> <span class='fu'>mkinmod</span><span class='op'>(</span> diff --git a/docs/reference/mkinparplot-1.png b/docs/reference/mkinparplot-1.png Binary files differindex dcf3e4b5..c9ed49eb 100644 --- a/docs/reference/mkinparplot-1.png +++ b/docs/reference/mkinparplot-1.png diff --git a/docs/reference/mkinparplot.html b/docs/reference/mkinparplot.html index b4d11dcb..c298f5d2 100644 --- a/docs/reference/mkinparplot.html +++ b/docs/reference/mkinparplot.html @@ -73,7 +73,7 @@ mkinfit." /> </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">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> @@ -176,7 +176,8 @@ effect, namely to produce a plot.</p> phenol <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"anisole"</span><span class='op'>)</span><span class='op'>)</span>, anisole <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>, use_of_ff <span class='op'>=</span> <span class='st'>"max"</span><span class='op'>)</span> </div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'><span class='va'>fit</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>model</span>, <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span><span class='op'>(</span><span class='va'>mccall81_245T</span>, <span class='va'>soil</span> <span class='op'>==</span> <span class='st'>"Commerce"</span><span class='op'>)</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'>mkinparplot</span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span> +</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#> <span class='warning'>Warning: Optimisation did not converge:</span> +#> <span class='warning'>false convergence (8)</span></div><div class='input'><span class='fu'>mkinparplot</span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span> </div><div class='img'><img src='mkinparplot-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># }</span> </div></pre> </div> diff --git a/docs/reference/mkinplot.html b/docs/reference/mkinplot.html index 1f0be544..b20a8c96 100644 --- a/docs/reference/mkinplot.html +++ b/docs/reference/mkinplot.html @@ -73,7 +73,7 @@ plot.mkinfit." /> </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">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index 035a21f9..25e26419 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -74,7 +74,7 @@ kinetic parameters and initial values for the state variables." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> @@ -410,8 +410,8 @@ as these always return mapped output.</p></td> </div><div class='output co'>#> test relative elapsed #> 2 deSolve_compiled 1.0 0.005 #> 4 analytical 1.0 0.005 -#> 1 eigen 4.0 0.020 -#> 3 deSolve 44.6 0.223</div><div class='input'> +#> 1 eigen 4.4 0.022 +#> 3 deSolve 47.0 0.235</div><div class='input'> <span class='co'># \dontrun{</span> <span class='co'># Predict from a fitted model</span> <span class='va'>f</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO</span>, <span class='va'>FOCUS_2006_C</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> diff --git a/docs/reference/mkinresplot.html b/docs/reference/mkinresplot.html index 69517f36..04ff15b8 100644 --- a/docs/reference/mkinresplot.html +++ b/docs/reference/mkinresplot.html @@ -75,7 +75,7 @@ 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">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/mmkin-1.png b/docs/reference/mmkin-1.png Binary files differindex cce02aed..0db3379f 100644 --- a/docs/reference/mmkin-1.png +++ b/docs/reference/mmkin-1.png diff --git a/docs/reference/mmkin-2.png b/docs/reference/mmkin-2.png Binary files differindex 4f2529fa..024a9892 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 fb5d4470..a23d7cb9 100644 --- a/docs/reference/mmkin-3.png +++ b/docs/reference/mmkin-3.png diff --git a/docs/reference/mmkin-4.png b/docs/reference/mmkin-4.png Binary files differindex 4f11753e..89975db5 100644 --- a/docs/reference/mmkin-4.png +++ b/docs/reference/mmkin-4.png diff --git a/docs/reference/mmkin-5.png b/docs/reference/mmkin-5.png Binary files differindex 5d653de9..a2f34983 100644 --- a/docs/reference/mmkin-5.png +++ b/docs/reference/mmkin-5.png diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index 77f815da..c9800fe7 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -75,7 +75,7 @@ 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">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> @@ -234,19 +234,19 @@ plotting.</p></div> <span class='va'>time_default</span> </div><div class='output co'>#> user system elapsed -#> 4.634 0.317 1.280 </div><div class='input'><span class='va'>time_1</span> +#> 4.630 0.415 1.717 </div><div class='input'><span class='va'>time_1</span> </div><div class='output co'>#> user system elapsed -#> 5.249 0.016 5.267 </div><div class='input'> +#> 5.694 0.000 5.694 </div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>fits.0</span><span class='op'>[[</span><span class='st'>"SFO_lin"</span>, <span class='fl'>2</span><span class='op'>]</span><span class='op'>]</span><span class='op'>)</span> </div><div class='output co'>#> $ff #> parent_M1 parent_sink M1_M2 M1_sink -#> 0.7340478 0.2659522 0.7505687 0.2494313 +#> 0.7340481 0.2659519 0.7505683 0.2494317 #> #> $distimes #> DT50 DT90 #> parent 0.877769 2.915885 -#> M1 2.325746 7.725960 -#> M2 33.720083 112.015691 +#> M1 2.325744 7.725956 +#> M2 33.720100 112.015749 #> </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.default.html'>plot</a></span><span class='op'>(</span><span class='va'>fits.0</span><span class='op'>[</span><span class='fl'>1</span>, <span class='op'>]</span><span class='op'>)</span> @@ -273,12 +273,10 @@ plotting.</p></div> #> dataset #> model A B C D #> SFO OK OK OK OK -#> FOMC C OK OK OK +#> FOMC OK OK OK OK #> DFOP OK OK OK OK #> -#> OK: No warnings -#> C: Optimisation did not converge: -#> false convergence (8)</div><div class='input'><span class='co'># We get false convergence for the FOMC fit to FOCUS_2006_A because this</span> +#> OK: No warnings</div><div class='input'><span class='co'># We get false convergence for the FOMC fit to FOCUS_2006_A because this</span> <span class='co'># dataset is really SFO, and the FOMC fit is overparameterised</span> <span class='fu'>stopCluster</span><span class='op'>(</span><span class='va'>cl</span><span class='op'>)</span> <span class='co'># }</span> diff --git a/docs/reference/nafta-1.png b/docs/reference/nafta-1.png Binary files differindex 76d724f0..4f0d7833 100644 --- a/docs/reference/nafta-1.png +++ b/docs/reference/nafta-1.png diff --git a/docs/reference/nafta.html b/docs/reference/nafta.html index c6c1b173..29e03251 100644 --- a/docs/reference/nafta.html +++ b/docs/reference/nafta.html @@ -76,7 +76,7 @@ order of increasing model complexity, i.e. SFO, then IORE, and finally DFOP." /> </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">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/nlme-1.png b/docs/reference/nlme-1.png Binary files differindex 82b952f7..728cc557 100644 --- a/docs/reference/nlme-1.png +++ b/docs/reference/nlme-1.png diff --git a/docs/reference/nlme-2.png b/docs/reference/nlme-2.png Binary files differindex 6bc121d1..e8167455 100644 --- a/docs/reference/nlme-2.png +++ b/docs/reference/nlme-2.png diff --git a/docs/reference/nlme.html b/docs/reference/nlme.html index f9e68b7f..7b0c6a97 100644 --- a/docs/reference/nlme.html +++ b/docs/reference/nlme.html @@ -75,7 +75,7 @@ datasets. They are used internally by the nlme.mmkin() method." /> </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">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/nlme.mmkin-1.png b/docs/reference/nlme.mmkin-1.png Binary files differindex 546a3731..9186c135 100644 --- a/docs/reference/nlme.mmkin-1.png +++ b/docs/reference/nlme.mmkin-1.png diff --git a/docs/reference/nlme.mmkin-2.png b/docs/reference/nlme.mmkin-2.png Binary files differindex 7b5b4ab0..d395fe02 100644 --- a/docs/reference/nlme.mmkin-2.png +++ b/docs/reference/nlme.mmkin-2.png diff --git a/docs/reference/nlme.mmkin-3.png b/docs/reference/nlme.mmkin-3.png Binary files differindex 7c04df4b..40518a59 100644 --- a/docs/reference/nlme.mmkin-3.png +++ b/docs/reference/nlme.mmkin-3.png diff --git a/docs/reference/nlme.mmkin.html b/docs/reference/nlme.mmkin.html index 2e4f6337..189e34ef 100644 --- a/docs/reference/nlme.mmkin.html +++ b/docs/reference/nlme.mmkin.html @@ -74,7 +74,7 @@ have been obtained by fitting the same model to a list of datasets." /> </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">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> @@ -157,7 +157,7 @@ have been obtained by fitting the same model to a list of datasets.</p> data <span class='op'>=</span> <span class='st'>"auto"</span>, fixed <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>as.list</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='fu'><a href='nlme_function.html'>mean_degparms</a></span><span class='op'>(</span><span class='va'>model</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>, <span class='kw'>function</span><span class='op'>(</span><span class='va'>el</span><span class='op'>)</span> <span class='fu'><a href='https://rdrr.io/r/base/eval.html'>eval</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/parse.html'>parse</a></span><span class='op'>(</span>text <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='va'>el</span>, <span class='fl'>1</span>, sep <span class='op'>=</span> <span class='st'>"~"</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>, - random <span class='op'>=</span> <span class='fu'>pdDiag</span><span class='op'>(</span><span class='va'>fixed</span><span class='op'>)</span>, + random <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/pdDiag.html'>pdDiag</a></span><span class='op'>(</span><span class='va'>fixed</span><span class='op'>)</span>, <span class='va'>groups</span>, start <span class='op'>=</span> <span class='fu'><a href='nlme_function.html'>mean_degparms</a></span><span class='op'>(</span><span class='va'>model</span>, random <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>, correlation <span class='op'>=</span> <span class='cn'>NULL</span>, @@ -290,7 +290,7 @@ methods that will automatically work on 'nlme.mmkin' objects, such as <span class='fu'><a href='https://rdrr.io/r/stats/anova.html'>anova</a></span><span class='op'>(</span><span class='va'>f_nlme_sfo</span>, <span class='va'>f_nlme_dfop</span><span class='op'>)</span> </div><div class='output co'>#> Model df AIC BIC logLik Test L.Ratio p-value #> f_nlme_sfo 1 5 625.0539 637.5529 -307.5269 -#> f_nlme_dfop 2 9 495.1270 517.6253 -238.5635 1 vs 2 137.9268 <.0001</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop</span><span class='op'>)</span> +#> f_nlme_dfop 2 9 495.1270 517.6253 -238.5635 1 vs 2 137.9269 <.0001</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop</span><span class='op'>)</span> </div><div class='output co'>#> Kinetic nonlinear mixed-effects model fit by maximum likelihood #> #> Structural model: @@ -318,7 +318,7 @@ methods that will automatically work on 'nlme.mmkin' objects, such as </div><div class='img'><img src='nlme.mmkin-1.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop</span><span class='op'>)</span> </div><div class='output co'>#> $distimes #> DT50 DT90 DT50back DT50_k1 DT50_k2 -#> parent 10.79857 100.7937 30.34192 4.193937 43.85442 +#> parent 10.79857 100.7937 30.34193 4.193938 43.85443 #> </div><div class='input'> <span class='va'>ds_2</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span><span class='op'>(</span><span class='va'>experimental_data_for_UBA_2019</span><span class='op'>[</span><span class='fl'>6</span><span class='op'>:</span><span class='fl'>10</span><span class='op'>]</span>, <span class='kw'>function</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span> <span class='va'>x</span><span class='op'>$</span><span class='va'>data</span><span class='op'>[</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"name"</span>, <span class='st'>"time"</span>, <span class='st'>"value"</span><span class='op'>)</span><span class='op'>]</span><span class='op'>)</span> @@ -350,8 +350,8 @@ methods that will automatically work on 'nlme.mmkin' objects, such as </div><div class='img'><img src='nlme.mmkin-3.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/stats/anova.html'>anova</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop_sfo</span>, <span class='va'>f_nlme_sfo_sfo</span><span class='op'>)</span> </div><div class='output co'>#> Model df AIC BIC logLik Test L.Ratio p-value -#> f_nlme_dfop_sfo 1 13 843.8547 884.6201 -408.9274 -#> f_nlme_sfo_sfo 2 9 1085.1821 1113.4043 -533.5910 1 vs 2 249.3274 <.0001</div><div class='input'> +#> f_nlme_dfop_sfo 1 13 843.8548 884.6201 -408.9274 +#> f_nlme_sfo_sfo 2 9 1085.1821 1113.4043 -533.5910 1 vs 2 249.3273 <.0001</div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>f_nlme_sfo_sfo</span><span class='op'>)</span> </div><div class='output co'>#> $ff #> parent_sink parent_A1 A1_sink @@ -364,12 +364,12 @@ methods that will automatically work on 'nlme.mmkin' objects, such as #> </div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop_sfo</span><span class='op'>)</span> </div><div class='output co'>#> $ff #> parent_A1 parent_sink -#> 0.2768574 0.7231426 +#> 0.2768575 0.7231425 #> #> $distimes #> DT50 DT90 DT50back DT50_k1 DT50_k2 -#> parent 11.07091 104.6320 31.49738 4.462384 46.20825 -#> A1 162.30523 539.1663 NA NA NA +#> parent 11.07091 104.6320 31.49737 4.462384 46.20825 +#> A1 162.30492 539.1653 NA NA NA #> </div><div class='input'> <span class='kw'>if</span> <span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='fu'>findFunction</span><span class='op'>(</span><span class='st'>"varConstProp"</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>></span> <span class='fl'>0</span><span class='op'>)</span> <span class='op'>{</span> <span class='co'># tc error model for nlme available</span> <span class='co'># Attempts to fit metabolite kinetics with the tc error model are possible,</span> @@ -396,7 +396,7 @@ methods that will automatically work on 'nlme.mmkin' objects, such as #> Fixed effects: #> list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1) #> parent_0 log_k1 log_k2 g_qlogis -#> 94.04775 -1.82340 -4.16715 0.05685 +#> 94.04774 -1.82340 -4.16716 0.05686 #> #> Random effects: #> Formula: list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1) @@ -410,7 +410,7 @@ methods that will automatically work on 'nlme.mmkin' objects, such as #> Formula: ~fitted(.) #> Parameter estimates: #> const prop -#> 2.23224114 0.01262341 </div><div class='input'> +#> 2.23223147 0.01262395 </div><div class='input'> <span class='va'>f_2_obs</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span><span class='op'>(</span><span class='va'>f_2</span>, error_model <span class='op'>=</span> <span class='st'>"obs"</span><span class='op'>)</span> <span class='va'>f_nlme_sfo_sfo_obs</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f_2_obs</span><span class='op'>[</span><span class='st'>"SFO-SFO"</span>, <span class='op'>]</span><span class='op'>)</span> <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>f_nlme_sfo_sfo_obs</span><span class='op'>)</span> @@ -442,7 +442,7 @@ methods that will automatically work on 'nlme.mmkin' objects, such as #> Formula: ~1 | name #> Parameter estimates: #> parent A1 -#> 1.0000000 0.2050003 </div><div class='input'> <span class='va'>f_nlme_dfop_sfo_obs</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f_2_obs</span><span class='op'>[</span><span class='st'>"DFOP-SFO"</span>, <span class='op'>]</span>, +#> 1.0000000 0.2049995 </div><div class='input'> <span class='va'>f_nlme_dfop_sfo_obs</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f_2_obs</span><span class='op'>[</span><span class='st'>"DFOP-SFO"</span>, <span class='op'>]</span>, control <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>pnlsMaxIter <span class='op'>=</span> <span class='fl'>120</span>, tolerance <span class='op'>=</span> <span class='fl'>5e-4</span><span class='op'>)</span><span class='op'>)</span> <span class='va'>f_2_tc</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span><span class='op'>(</span><span class='va'>f_2</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span><span class='op'>)</span> @@ -452,8 +452,8 @@ methods that will automatically work on 'nlme.mmkin' objects, such as <span class='fu'><a href='https://rdrr.io/r/stats/anova.html'>anova</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop_sfo</span>, <span class='va'>f_nlme_dfop_sfo_obs</span><span class='op'>)</span> </div><div class='output co'>#> Model df AIC BIC logLik Test L.Ratio -#> f_nlme_dfop_sfo 1 13 843.8547 884.6201 -408.9274 -#> f_nlme_dfop_sfo_obs 2 14 817.5338 861.4350 -394.7669 1 vs 2 28.32089 +#> f_nlme_dfop_sfo 1 13 843.8548 884.6201 -408.9274 +#> f_nlme_dfop_sfo_obs 2 14 817.5338 861.4350 -394.7669 1 vs 2 28.32093 #> p-value #> f_nlme_dfop_sfo #> f_nlme_dfop_sfo_obs <.0001</div><div class='input'> diff --git a/docs/reference/nobs.mkinfit.html b/docs/reference/nobs.mkinfit.html index dff8a285..6b9948c3 100644 --- a/docs/reference/nobs.mkinfit.html +++ b/docs/reference/nobs.mkinfit.html @@ -72,7 +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">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/parms.html b/docs/reference/parms.html index ab5888fa..e45d6a5c 100644 --- a/docs/reference/parms.html +++ b/docs/reference/parms.html @@ -74,7 +74,7 @@ considering the error structure that was assumed for the fit." /> </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">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> @@ -219,10 +219,10 @@ such matrices is returned.</p> #> #> $DFOP #> Dataset 7 -#> parent_0 91.058971597 +#> parent_0 91.058971589 #> k1 0.044946770 #> k2 0.002868336 -#> g 0.526942414 +#> g 0.526942415 #> sigma 2.221302196 #> </div><div class='input'><span class='fu'>parms</span><span class='op'>(</span><span class='va'>fits</span><span class='op'>)</span> </div><div class='output co'>#> $SFO @@ -233,17 +233,17 @@ such matrices is returned.</p> #> #> $FOMC #> Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10 -#> parent_0 95.558575 92.6837649 90.719787 98.383939 94.8481458 +#> parent_0 95.558575 92.6837649 90.719787 98.383939 94.8481459 #> alpha 1.338667 0.4967832 1.639099 1.074460 0.2805272 #> beta 13.033315 14.1451255 5.007077 4.397126 6.9052224 #> sigma 1.847671 1.9167519 1.066063 3.146056 1.6222778 #> #> $DFOP #> Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10 -#> parent_0 96.55213663 91.058971597 90.34509493 98.14858820 94.311323733 +#> parent_0 96.55213663 91.058971589 90.34509493 98.14858820 94.311323734 #> k1 0.21954588 0.044946770 0.41232288 0.31697588 0.080663857 #> k2 0.02957934 0.002868336 0.07581766 0.03260384 0.003425417 -#> g 0.44845068 0.526942414 0.66091967 0.65322767 0.342652880 +#> g 0.44845068 0.526942415 0.66091967 0.65322767 0.342652880 #> sigma 1.35690468 2.221302196 1.34169076 2.87159846 1.942067831 #> </div><div class='input'><span class='fu'>parms</span><span class='op'>(</span><span class='va'>fits</span>, transformed <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> </div><div class='output co'>#> $SFO diff --git a/docs/reference/plot.mixed.mmkin.html b/docs/reference/plot.mixed.mmkin.html index 46303c44..4b72a308 100644 --- a/docs/reference/plot.mixed.mmkin.html +++ b/docs/reference/plot.mixed.mmkin.html @@ -72,7 +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">1.0.2</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/plot.mkinfit-2.png b/docs/reference/plot.mkinfit-2.png Binary files differindex 376c812f..a11d1680 100644 --- a/docs/reference/plot.mkinfit-2.png +++ b/docs/reference/plot.mkinfit-2.png diff --git a/docs/reference/plot.mkinfit-5.png b/docs/reference/plot.mkinfit-5.png Binary files differindex bc44de88..6631aa68 100644 --- a/docs/reference/plot.mkinfit-5.png +++ b/docs/reference/plot.mkinfit-5.png diff --git a/docs/reference/plot.mkinfit-6.png b/docs/reference/plot.mkinfit-6.png Binary files differindex eb8cbd92..946b20c5 100644 --- a/docs/reference/plot.mkinfit-6.png +++ b/docs/reference/plot.mkinfit-6.png diff --git a/docs/reference/plot.mkinfit-7.png b/docs/reference/plot.mkinfit-7.png Binary files differindex 92a664f4..10807ea8 100644 --- a/docs/reference/plot.mkinfit-7.png +++ b/docs/reference/plot.mkinfit-7.png diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html index 1be0f9af..b80c672d 100644 --- a/docs/reference/plot.mkinfit.html +++ b/docs/reference/plot.mkinfit.html @@ -74,7 +74,7 @@ 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">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/plot.mmkin-1.png b/docs/reference/plot.mmkin-1.png Binary files differindex f12b7907..647dfb8a 100644 --- a/docs/reference/plot.mmkin-1.png +++ b/docs/reference/plot.mmkin-1.png diff --git a/docs/reference/plot.mmkin-2.png b/docs/reference/plot.mmkin-2.png Binary files differindex e3127554..1bc1c9db 100644 --- a/docs/reference/plot.mmkin-2.png +++ b/docs/reference/plot.mmkin-2.png diff --git a/docs/reference/plot.mmkin-3.png b/docs/reference/plot.mmkin-3.png Binary files differindex 5448976e..50d6ffac 100644 --- a/docs/reference/plot.mmkin-3.png +++ b/docs/reference/plot.mmkin-3.png diff --git a/docs/reference/plot.mmkin-4.png b/docs/reference/plot.mmkin-4.png Binary files differindex 9a25fc50..e049fa16 100644 --- a/docs/reference/plot.mmkin-4.png +++ b/docs/reference/plot.mmkin-4.png diff --git a/docs/reference/plot.mmkin-5.png b/docs/reference/plot.mmkin-5.png Binary files differindex 82b422b5..2421995b 100644 --- a/docs/reference/plot.mmkin-5.png +++ b/docs/reference/plot.mmkin-5.png diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html index 4e9836ec..20f9033d 100644 --- a/docs/reference/plot.mmkin.html +++ b/docs/reference/plot.mmkin.html @@ -76,7 +76,7 @@ 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">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/plot.nafta.html b/docs/reference/plot.nafta.html index 29cc984a..544ee5eb 100644 --- a/docs/reference/plot.nafta.html +++ b/docs/reference/plot.nafta.html @@ -73,7 +73,7 @@ function (SFO, then IORE, then DFOP)." /> </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">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html index 2bfeb582..864c4ff9 100644 --- a/docs/reference/reexports.html +++ b/docs/reference/reexports.html @@ -79,7 +79,7 @@ below to see their documentation. </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">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/residuals.mkinfit.html b/docs/reference/residuals.mkinfit.html index db7c1a40..c5c2dcaf 100644 --- a/docs/reference/residuals.mkinfit.html +++ b/docs/reference/residuals.mkinfit.html @@ -72,7 +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">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> @@ -175,7 +175,7 @@ standard deviation obtained from the fitted error model?</p></td> </div><div class='output co'>#> [1] 0.09726374 -0.13912142 -0.15351210 0.73388322 -0.08657004 -0.93204702 #> [7] -0.03269080 1.45347823 -0.88423697</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/stats/residuals.html'>residuals</a></span><span class='op'>(</span><span class='va'>f</span>, standardized <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> </div><div class='output co'>#> [1] 0.13969917 -0.19981904 -0.22048826 1.05407091 -0.12433989 -1.33869208 -#> [7] -0.04695354 2.08761977 -1.27002287</div></pre> +#> [7] -0.04695355 2.08761977 -1.27002287</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> <nav id="toc" data-toggle="toc" class="sticky-top"> diff --git a/docs/reference/schaefer07_complex_case-1.png b/docs/reference/schaefer07_complex_case-1.png Binary files differindex be903641..96aab2dc 100644 --- a/docs/reference/schaefer07_complex_case-1.png +++ b/docs/reference/schaefer07_complex_case-1.png diff --git a/docs/reference/schaefer07_complex_case.html b/docs/reference/schaefer07_complex_case.html index 74f71f46..979e4c29 100644 --- a/docs/reference/schaefer07_complex_case.html +++ b/docs/reference/schaefer07_complex_case.html @@ -74,7 +74,7 @@ </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">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> @@ -186,15 +186,15 @@ </div><div class='img'><img src='schaefer07_complex_case-1.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span> </div><div class='output co'>#> $ff #> parent_A1 parent_B1 parent_C1 parent_sink A1_A2 A1_sink -#> 0.3809620 0.1954665 0.4235715 0.0000000 0.4479662 0.5520338 +#> 0.3809620 0.1954667 0.4235713 0.0000000 0.4479619 0.5520381 #> #> $distimes #> DT50 DT90 #> parent 13.95078 46.34350 -#> A1 49.75343 165.27731 -#> B1 37.26912 123.80533 -#> C1 11.23131 37.30959 -#> A2 28.50569 94.69386 +#> A1 49.75342 165.27728 +#> B1 37.26908 123.80520 +#> C1 11.23131 37.30961 +#> A2 28.50624 94.69567 #> </div><div class='input'> <span class='co'># }</span> <span class='co'># Compare with the results obtained in the original publication</span> <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>schaefer07_complex_results</span><span class='op'>)</span> diff --git a/docs/reference/sigma_twocomp.html b/docs/reference/sigma_twocomp.html index 46ca562a..397582f0 100644 --- a/docs/reference/sigma_twocomp.html +++ b/docs/reference/sigma_twocomp.html @@ -73,7 +73,7 @@ dependence of the measured value \(y\):" /> </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">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> @@ -188,6 +188,10 @@ Additive, Multiplicative, and Mixed Analytical Errors. Clinical Chemistry 24(11), 1895-1898.</p> <p>Rocke, David M. and Lorenzato, Stefan (1995) A two-component model for measurement error in analytical chemistry. Technometrics 37(2), 176-184.</p> +<p>Ranke J and Meinecke S (2019) Error Models for the Kinetic Evaluation of Chemical +Degradation Data. <em>Environments</em> 6(12) 124 +doi: <a href='https://doi.org/10.3390/environments6120124'>10.3390/environments6120124</a> +.</p> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='va'>times</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>3</span>, <span class='fl'>7</span>, <span class='fl'>14</span>, <span class='fl'>28</span>, <span class='fl'>60</span>, <span class='fl'>90</span>, <span class='fl'>120</span><span class='op'>)</span> diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index 7be427bf..67a50216 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -76,7 +76,7 @@ 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">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> @@ -236,17 +236,17 @@ EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, <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='op'>(</span><span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span><span class='op'>)</span>, <span class='va'>FOCUS_2006_A</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span><span class='op'>)</span> -</div><div class='output co'>#> mkin version used for fitting: 1.0.0 +</div><div class='output co'>#> mkin version used for fitting: 1.0.3 #> R version used for fitting: 4.0.3 -#> Date of fit: Wed Feb 3 17:32:02 2021 -#> Date of summary: Wed Feb 3 17:32:02 2021 +#> Date of fit: Mon Feb 15 13:46:11 2021 +#> Date of summary: Mon Feb 15 13:46:11 2021 #> #> Equations: #> d_parent/dt = - k_parent * parent #> #> Model predictions using solution type analytical #> -#> Fitted using 131 model solutions performed in 0.028 s +#> Fitted using 131 model solutions performed in 0.029 s #> #> Error model: Constant variance #> diff --git a/docs/reference/summary.nlme.mmkin.html b/docs/reference/summary.nlme.mmkin.html index bc60b53e..d6840425 100644 --- a/docs/reference/summary.nlme.mmkin.html +++ b/docs/reference/summary.nlme.mmkin.html @@ -76,7 +76,7 @@ endpoints such as formation fractions and DT50 values. Optionally </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">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> @@ -264,11 +264,11 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p> </div><div class='output co'>#> <span class='warning'>Warning: Optimisation did not converge:</span> #> <span class='warning'>iteration limit reached without convergence (10)</span></div><div class='input'><span class='va'>f_nlme</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f_mmkin</span><span class='op'>)</span> </div><div class='output co'>#> <span class='warning'>Warning: Iteration 4, LME step: nlminb() did not converge (code = 1). PORT message: false convergence (8)</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>f_nlme</span>, data <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -</div><div class='output co'>#> nlme version used for fitting: 3.1.151 -#> mkin version used for pre-fitting: 1.0.0 +</div><div class='output co'>#> nlme version used for fitting: 3.1.152 +#> mkin version used for pre-fitting: 1.0.3 #> R version used for fitting: 4.0.3 -#> Date of fit: Wed Feb 3 17:32:05 2021 -#> Date of summary: Wed Feb 3 17:32:05 2021 +#> Date of fit: Mon Feb 15 13:46:13 2021 +#> Date of summary: Mon Feb 15 13:46:13 2021 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -278,7 +278,7 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p> #> #> Model predictions using solution type analytical #> -#> Fitted in 0.526 s using 4 iterations +#> Fitted in 0.553 s using 4 iterations #> #> Variance model: Two-component variance function #> @@ -307,19 +307,19 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p> #> Formula: list(parent_0 ~ 1, log_k_parent ~ 1) #> Level: ds #> Structure: Diagonal -#> parent_0 log_k_parent Residual -#> StdDev: 6.91e-05 0.5863 1 +#> parent_0 log_k_parent Residual +#> StdDev: 6.924e-05 0.5863 1 #> #> Variance function: #> Structure: Constant plus proportion of variance covariate #> Formula: ~fitted(.) #> Parameter estimates: #> const prop -#> 0.0001206605 0.0789967776 +#> 0.0001208853 0.0789968036 #> #> Backtransformed parameters with asymmetric confidence intervals: #> lower est. upper -#> parent_0 99.370883 101.59243 103.81398 +#> parent_0 99.370882 101.59243 103.81398 #> k_parent 0.006923 0.01168 0.01972 #> #> Estimated disappearance times: @@ -330,68 +330,68 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p> #> ds name time observed predicted residual std standardized #> ds 1 parent 0 104.1 101.592 2.50757 8.0255 0.312451 #> ds 1 parent 0 105.0 101.592 3.40757 8.0255 0.424594 -#> ds 1 parent 1 98.5 100.796 -2.29571 7.9625 -0.288314 +#> ds 1 parent 1 98.5 100.796 -2.29571 7.9625 -0.288313 #> ds 1 parent 1 96.1 100.796 -4.69571 7.9625 -0.589725 #> ds 1 parent 3 101.9 99.221 2.67904 7.8381 0.341796 -#> ds 1 parent 3 85.2 99.221 -14.02096 7.8381 -1.788813 +#> ds 1 parent 3 85.2 99.221 -14.02096 7.8381 -1.788812 #> ds 1 parent 7 99.1 96.145 2.95512 7.5951 0.389081 #> ds 1 parent 7 93.0 96.145 -3.14488 7.5951 -0.414065 -#> ds 1 parent 14 88.1 90.989 -2.88944 7.1879 -0.401988 +#> ds 1 parent 14 88.1 90.989 -2.88944 7.1879 -0.401987 #> ds 1 parent 14 84.1 90.989 -6.88944 7.1879 -0.958480 #> ds 1 parent 28 80.2 81.493 -1.29305 6.4377 -0.200857 -#> ds 1 parent 28 91.3 81.493 9.80695 6.4377 1.523365 +#> ds 1 parent 28 91.3 81.493 9.80695 6.4377 1.523364 #> ds 1 parent 60 65.1 63.344 1.75642 5.0039 0.351008 #> ds 1 parent 60 65.8 63.344 2.45642 5.0039 0.490898 -#> ds 1 parent 90 47.8 50.018 -2.21764 3.9512 -0.561253 +#> ds 1 parent 90 47.8 50.018 -2.21764 3.9512 -0.561252 #> ds 1 parent 90 53.5 50.018 3.48236 3.9512 0.881335 #> ds 1 parent 120 37.6 39.495 -1.89515 3.1200 -0.607423 #> ds 1 parent 120 39.3 39.495 -0.19515 3.1200 -0.062549 -#> ds 2 parent 0 107.9 101.592 6.30757 8.0255 0.785944 +#> ds 2 parent 0 107.9 101.592 6.30757 8.0255 0.785943 #> ds 2 parent 0 102.1 101.592 0.50757 8.0255 0.063245 -#> ds 2 parent 1 103.8 100.058 3.74159 7.9043 0.473362 -#> ds 2 parent 1 108.6 100.058 8.54159 7.9043 1.080627 +#> ds 2 parent 1 103.8 100.058 3.74159 7.9043 0.473361 +#> ds 2 parent 1 108.6 100.058 8.54159 7.9043 1.080626 #> ds 2 parent 3 91.0 97.060 -6.05952 7.6674 -0.790297 #> ds 2 parent 3 84.9 97.060 -12.15952 7.6674 -1.585874 -#> ds 2 parent 7 79.3 91.329 -12.02867 7.2147 -1.667252 -#> ds 2 parent 7 100.9 91.329 9.57133 7.2147 1.326648 +#> ds 2 parent 7 79.3 91.329 -12.02867 7.2147 -1.667251 +#> ds 2 parent 7 100.9 91.329 9.57133 7.2147 1.326647 #> ds 2 parent 14 77.3 82.102 -4.80185 6.4858 -0.740366 #> ds 2 parent 14 83.5 82.102 1.39815 6.4858 0.215571 #> ds 2 parent 28 66.8 66.351 0.44945 5.2415 0.085748 #> ds 2 parent 28 63.3 66.351 -3.05055 5.2415 -0.582002 #> ds 2 parent 60 40.8 40.775 0.02474 3.2211 0.007679 -#> ds 2 parent 60 44.8 40.775 4.02474 3.2211 1.249486 +#> ds 2 parent 60 44.8 40.775 4.02474 3.2211 1.249485 #> ds 2 parent 90 27.8 25.832 1.96762 2.0407 0.964198 #> ds 2 parent 90 27.0 25.832 1.16762 2.0407 0.572171 -#> ds 2 parent 120 15.2 16.366 -1.16561 1.2928 -0.901596 +#> ds 2 parent 120 15.2 16.366 -1.16561 1.2928 -0.901595 #> ds 2 parent 120 15.5 16.366 -0.86561 1.2928 -0.669547 #> ds 3 parent 0 97.7 101.592 -3.89243 8.0255 -0.485009 -#> ds 3 parent 0 88.2 101.592 -13.39243 8.0255 -1.668740 -#> ds 3 parent 1 109.9 99.218 10.68196 7.8379 1.362859 +#> ds 3 parent 0 88.2 101.592 -13.39243 8.0255 -1.668739 +#> ds 3 parent 1 109.9 99.218 10.68196 7.8379 1.362858 #> ds 3 parent 1 97.8 99.218 -1.41804 7.8379 -0.180921 #> ds 3 parent 3 100.5 94.634 5.86555 7.4758 0.784603 #> ds 3 parent 3 77.4 94.634 -17.23445 7.4758 -2.305360 -#> ds 3 parent 7 78.3 86.093 -7.79273 6.8010 -1.145813 -#> ds 3 parent 7 90.3 86.093 4.20727 6.8010 0.618621 -#> ds 3 parent 14 76.0 72.958 3.04222 5.7634 0.527849 -#> ds 3 parent 14 79.1 72.958 6.14222 5.7634 1.065723 +#> ds 3 parent 7 78.3 86.093 -7.79273 6.8011 -1.145813 +#> ds 3 parent 7 90.3 86.093 4.20727 6.8011 0.618620 +#> ds 3 parent 14 76.0 72.958 3.04222 5.7634 0.527848 +#> ds 3 parent 14 79.1 72.958 6.14222 5.7634 1.065722 #> ds 3 parent 28 46.0 52.394 -6.39404 4.1390 -1.544842 #> ds 3 parent 28 53.4 52.394 1.00596 4.1390 0.243046 #> ds 3 parent 60 25.1 24.582 0.51786 1.9419 0.266676 -#> ds 3 parent 60 21.4 24.582 -3.18214 1.9419 -1.638665 -#> ds 3 parent 90 11.0 12.092 -1.09202 0.9552 -1.143200 -#> ds 3 parent 90 14.2 12.092 2.10798 0.9552 2.206777 +#> ds 3 parent 60 21.4 24.582 -3.18214 1.9419 -1.638664 +#> ds 3 parent 90 11.0 12.092 -1.09202 0.9552 -1.143199 +#> ds 3 parent 90 14.2 12.092 2.10798 0.9552 2.206776 #> ds 3 parent 120 5.8 5.948 -0.14810 0.4699 -0.315178 #> ds 3 parent 120 6.1 5.948 0.15190 0.4699 0.323282 #> ds 4 parent 0 95.3 101.592 -6.29243 8.0255 -0.784057 -#> ds 4 parent 0 102.0 101.592 0.40757 8.0255 0.050785 +#> ds 4 parent 0 102.0 101.592 0.40757 8.0255 0.050784 #> ds 4 parent 1 104.4 101.125 3.27549 7.9885 0.410025 #> ds 4 parent 1 105.4 101.125 4.27549 7.9885 0.535205 #> ds 4 parent 3 113.7 100.195 13.50487 7.9151 1.706218 -#> ds 4 parent 3 82.3 100.195 -17.89513 7.9151 -2.260887 +#> ds 4 parent 3 82.3 100.195 -17.89513 7.9151 -2.260886 #> ds 4 parent 7 98.1 98.362 -0.26190 7.7703 -0.033706 #> ds 4 parent 7 87.8 98.362 -10.56190 7.7703 -1.359270 #> ds 4 parent 14 97.9 95.234 2.66590 7.5232 0.354357 -#> ds 4 parent 14 104.8 95.234 9.56590 7.5232 1.271522 +#> ds 4 parent 14 104.8 95.234 9.56590 7.5232 1.271521 #> ds 4 parent 28 85.0 89.274 -4.27372 7.0523 -0.606001 #> ds 4 parent 28 77.2 89.274 -12.07372 7.0523 -1.712017 #> ds 4 parent 60 82.2 77.013 5.18661 6.0838 0.852526 @@ -400,18 +400,18 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p> #> ds 4 parent 90 61.7 67.053 -5.35308 5.2970 -1.010591 #> ds 4 parent 120 60.0 58.381 1.61905 4.6119 0.351058 #> ds 4 parent 120 56.4 58.381 -1.98095 4.6119 -0.429530 -#> ds 5 parent 0 92.6 101.592 -8.99243 8.0255 -1.120486 +#> ds 5 parent 0 92.6 101.592 -8.99243 8.0255 -1.120485 #> ds 5 parent 0 116.5 101.592 14.90757 8.0255 1.857531 #> ds 5 parent 1 108.0 99.914 8.08560 7.8929 1.024413 -#> ds 5 parent 1 104.9 99.914 4.98560 7.8929 0.631656 +#> ds 5 parent 1 104.9 99.914 4.98560 7.8929 0.631655 #> ds 5 parent 3 100.5 96.641 3.85898 7.6343 0.505477 -#> ds 5 parent 3 89.5 96.641 -7.14102 7.6343 -0.935383 +#> ds 5 parent 3 89.5 96.641 -7.14102 7.6343 -0.935382 #> ds 5 parent 7 91.7 90.412 1.28752 7.1423 0.180267 -#> ds 5 parent 7 95.1 90.412 4.68752 7.1423 0.656305 -#> ds 5 parent 14 82.2 80.463 1.73715 6.3563 0.273296 +#> ds 5 parent 7 95.1 90.412 4.68752 7.1423 0.656304 +#> ds 5 parent 14 82.2 80.463 1.73715 6.3563 0.273295 #> ds 5 parent 14 84.5 80.463 4.03715 6.3563 0.635141 #> ds 5 parent 28 60.5 63.728 -3.22788 5.0343 -0.641178 -#> ds 5 parent 28 72.8 63.728 9.07212 5.0343 1.802063 +#> ds 5 parent 28 72.8 63.728 9.07212 5.0343 1.802062 #> ds 5 parent 60 38.3 37.399 0.90061 2.9544 0.304835 #> ds 5 parent 60 40.7 37.399 3.30061 2.9544 1.117174 #> ds 5 parent 90 22.5 22.692 -0.19165 1.7926 -0.106913 diff --git a/docs/reference/synthetic_data_for_UBA_2014-1.png b/docs/reference/synthetic_data_for_UBA_2014-1.png Binary files differindex 4f11753e..89975db5 100644 --- a/docs/reference/synthetic_data_for_UBA_2014-1.png +++ b/docs/reference/synthetic_data_for_UBA_2014-1.png diff --git a/docs/reference/synthetic_data_for_UBA_2014.html b/docs/reference/synthetic_data_for_UBA_2014.html index af8bdcb2..c37b986e 100644 --- a/docs/reference/synthetic_data_for_UBA_2014.html +++ b/docs/reference/synthetic_data_for_UBA_2014.html @@ -87,7 +87,7 @@ Compare also the code in the example section to see the degradation models." /> </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">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> @@ -297,10 +297,10 @@ Compare also the code in the example section to see the degradation models." /> quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span> </div><div class='img'><img src='synthetic_data_for_UBA_2014-1.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span> -</div><div class='output co'>#> mkin version used for fitting: 1.0.0 +</div><div class='output co'>#> mkin version used for fitting: 1.0.3 #> R version used for fitting: 4.0.3 -#> Date of fit: Wed Feb 3 17:32:06 2021 -#> Date of summary: Wed Feb 3 17:32:06 2021 +#> Date of fit: Mon Feb 15 13:46:15 2021 +#> Date of summary: Mon Feb 15 13:46:15 2021 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -309,7 +309,7 @@ Compare also the code in the example section to see the degradation models." /> #> #> Model predictions using solution type deSolve #> -#> Fitted using 822 model solutions performed in 0.645 s +#> Fitted using 833 model solutions performed in 0.665 s #> #> Error model: Constant variance #> @@ -361,15 +361,15 @@ Compare also the code in the example section to see the degradation models." /> #> log_k_M2 2.819e-02 7.166e-02 -3.929e-01 1.000e+00 -2.658e-01 #> f_parent_qlogis -4.624e-01 -5.682e-01 7.478e-01 -2.658e-01 1.000e+00 #> f_M1_qlogis 1.614e-01 4.102e-01 -8.109e-01 5.419e-01 -8.605e-01 -#> sigma -7.941e-08 -9.143e-09 -1.268e-08 5.947e-08 5.657e-08 +#> sigma -2.900e-08 -8.030e-09 -2.741e-08 3.938e-08 -2.681e-08 #> f_M1_qlogis sigma -#> parent_0 1.614e-01 -7.941e-08 -#> log_k_parent 4.102e-01 -9.143e-09 -#> log_k_M1 -8.109e-01 -1.268e-08 -#> log_k_M2 5.419e-01 5.947e-08 -#> f_parent_qlogis -8.605e-01 5.657e-08 -#> f_M1_qlogis 1.000e+00 -2.382e-10 -#> sigma -2.382e-10 1.000e+00 +#> parent_0 1.614e-01 -2.900e-08 +#> log_k_parent 4.102e-01 -8.030e-09 +#> log_k_M1 -8.109e-01 -2.741e-08 +#> log_k_M2 5.419e-01 3.938e-08 +#> f_parent_qlogis -8.605e-01 -2.681e-08 +#> f_M1_qlogis 1.000e+00 4.971e-08 +#> sigma 4.971e-08 1.000e+00 #> #> Backtransformed parameters: #> Confidence intervals for internally transformed parameters are asymmetric. @@ -416,7 +416,7 @@ Compare also the code in the example section to see the degradation models." /> #> 7 parent 0.3 5.772e-01 -0.27717 #> 14 parent 3.5 3.264e-03 3.49674 #> 28 parent 3.2 1.045e-07 3.20000 -#> 90 parent 0.6 9.532e-10 0.60000 +#> 90 parent 0.6 9.530e-10 0.60000 #> 120 parent 3.5 -5.940e-10 3.50000 #> 1 M1 36.4 3.479e+01 1.61088 #> 1 M1 37.4 3.479e+01 2.61088 @@ -427,7 +427,7 @@ Compare also the code in the example section to see the degradation models." /> #> 14 M1 5.8 1.995e+00 3.80469 #> 14 M1 1.2 1.995e+00 -0.79531 #> 60 M1 0.5 2.111e-06 0.50000 -#> 90 M1 3.2 -9.671e-10 3.20000 +#> 90 M1 3.2 -9.670e-10 3.20000 #> 120 M1 1.5 7.670e-10 1.50000 #> 120 M1 0.6 7.670e-10 0.60000 #> 1 M2 4.8 4.455e+00 0.34517 diff --git a/docs/reference/test_data_from_UBA_2014-1.png b/docs/reference/test_data_from_UBA_2014-1.png Binary files differindex 168103ee..7bf0bd0f 100644 --- a/docs/reference/test_data_from_UBA_2014-1.png +++ b/docs/reference/test_data_from_UBA_2014-1.png diff --git a/docs/reference/test_data_from_UBA_2014-2.png b/docs/reference/test_data_from_UBA_2014-2.png Binary files differindex 68288aed..fc1f77e0 100644 --- a/docs/reference/test_data_from_UBA_2014-2.png +++ b/docs/reference/test_data_from_UBA_2014-2.png diff --git a/docs/reference/test_data_from_UBA_2014.html b/docs/reference/test_data_from_UBA_2014.html index eeaef9e0..c0056d45 100644 --- a/docs/reference/test_data_from_UBA_2014.html +++ b/docs/reference/test_data_from_UBA_2014.html @@ -73,7 +73,7 @@ </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">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> @@ -203,25 +203,25 @@ </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='plot.mkinfit.html'>plot_sep</a></span><span class='op'>(</span><span class='va'>f_soil</span>, lpos <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"topright"</span>, <span class='st'>"topright"</span>, <span class='st'>"topright"</span>, <span class='st'>"bottomright"</span><span class='op'>)</span><span class='op'>)</span> </div><div class='img'><img src='test_data_from_UBA_2014-2.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>f_soil</span><span class='op'>)</span><span class='op'>$</span><span class='va'>bpar</span> </div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower -#> parent_0 76.55425649 0.859186399 89.1008710 1.113861e-26 74.755959406 +#> parent_0 76.55425650 0.859186399 89.1008710 1.113861e-26 74.755959418 #> k_parent 0.12081956 0.004601918 26.2541722 1.077359e-16 0.111561575 -#> k_M1 0.84258614 0.806159820 1.0451850 1.545267e-01 0.113779670 -#> k_M2 0.04210880 0.017083035 2.4649483 1.170188e-02 0.018013857 -#> k_M3 0.01122918 0.007245855 1.5497385 6.885052e-02 0.002909431 -#> f_parent_to_M1 0.32240200 0.240783909 1.3389682 9.819073e-02 NA -#> f_parent_to_M2 0.16099855 0.033691953 4.7785463 6.531137e-05 NA -#> f_M1_to_M3 0.27921507 0.269423745 1.0363417 1.565266e-01 0.022978220 -#> f_M2_to_M3 0.55641253 0.595119954 0.9349586 1.807707e-01 0.008002509 +#> k_M1 0.84258615 0.806160102 1.0451846 1.545268e-01 0.113779609 +#> k_M2 0.04210880 0.017083034 2.4649483 1.170188e-02 0.018013857 +#> k_M3 0.01122918 0.007245856 1.5497385 6.885052e-02 0.002909431 +#> f_parent_to_M1 0.32240200 0.240783943 1.3389680 9.819076e-02 NA +#> f_parent_to_M2 0.16099855 0.033691952 4.7785464 6.531136e-05 NA +#> f_M1_to_M3 0.27921507 0.269423780 1.0363416 1.565267e-01 0.022978205 +#> f_M2_to_M3 0.55641252 0.595119966 0.9349586 1.807707e-01 0.008002509 #> sigma 1.14005399 0.149696423 7.6157731 1.727024e-07 0.826735778 #> Upper -#> parent_0 78.35255357 +#> parent_0 78.35255358 #> k_parent 0.13084582 -#> k_M1 6.23970352 +#> k_M1 6.23970702 #> k_M2 0.09843260 #> k_M3 0.04333992 #> f_parent_to_M1 NA #> f_parent_to_M2 NA -#> f_M1_to_M3 0.86450768 +#> f_M1_to_M3 0.86450775 #> f_M2_to_M3 0.99489895 #> sigma 1.45337221</div><div class='input'> <span class='fu'><a href='mkinerrmin.html'>mkinerrmin</a></span><span class='op'>(</span><span class='va'>f_soil</span><span class='op'>)</span> </div><div class='output co'>#> err.min n.optim df diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index e2cb876b..c3c756f6 100644 --- a/docs/reference/transform_odeparms.html +++ b/docs/reference/transform_odeparms.html @@ -77,7 +77,7 @@ 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">1.0.1</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> @@ -259,13 +259,13 @@ This is no problem for the internal use in <a href='mkinfit.html'>mkinfit</a>.</ <span class='va'>fit.2.s</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>fit.2</span><span class='op'>)</span> <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>fit.2.s</span><span class='op'>$</span><span class='va'>par</span>, <span class='fl'>3</span><span class='op'>)</span> </div><div class='output co'>#> Estimate Std. Error Lower Upper -#> parent_0 99.59849 1.57022 96.40385 1.03e+02 +#> parent_0 99.59848 1.57022 96.40384 1.03e+02 #> k_parent_sink 0.04792 0.00365 0.04049 5.54e-02 #> k_parent_m1 0.05078 0.00205 0.04661 5.49e-02 #> k_m1_sink 0.00526 0.00070 0.00384 6.69e-03 #> sigma 3.12550 0.35852 2.39609 3.85e+00</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>fit.2.s</span><span class='op'>$</span><span class='va'>bpar</span>, <span class='fl'>3</span><span class='op'>)</span> </div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower Upper -#> parent_0 99.59849 1.57022 63.43 2.30e-36 96.40385 1.03e+02 +#> parent_0 99.59848 1.57022 63.43 2.30e-36 96.40384 1.03e+02 #> k_parent_sink 0.04792 0.00365 13.11 6.13e-15 0.04049 5.54e-02 #> k_parent_m1 0.05078 0.00205 24.80 3.27e-23 0.04661 5.49e-02 #> k_m1_sink 0.00526 0.00070 7.51 6.16e-09 0.00384 6.69e-03 diff --git a/docs/reference/update.mkinfit.html b/docs/reference/update.mkinfit.html index f7149d84..09050e53 100644 --- a/docs/reference/update.mkinfit.html +++ b/docs/reference/update.mkinfit.html @@ -75,7 +75,7 @@ override these starting 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">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> |
