diff options
Diffstat (limited to 'docs/reference')
41 files changed, 326 insertions, 22 deletions
diff --git a/docs/reference/DFOP.solution.html b/docs/reference/DFOP.solution.html index f89a66e2..b1b3cf50 100644 --- a/docs/reference/DFOP.solution.html +++ b/docs/reference/DFOP.solution.html @@ -27,6 +27,11 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="Double First-Order in Parallel kinetics — DFOP.solution" /> + +<meta property="og:description" content="Function describing decline from a defined starting value using the sum + of two exponential decline functions." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -182,3 +187,4 @@ </body> </html> + diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index 3b96f9ae..e554432f 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -27,6 +27,10 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="Subsetting method for mmkin objects — [.mmkin" /> + +<meta property="og:description" content="Subsetting method for mmkin objects." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -259,7 +263,7 @@ #> #> $time #> user system elapsed -#> 0.06 0.00 0.06 +#> 0.234 0.000 0.234 #> #> $mkinmod #> <mkinmod> model generated with @@ -448,8 +452,8 @@ #> } #> return(mC) #> } -#> <bytecode: 0x5555599fd348> -#> <environment: 0x555557684190> +#> <bytecode: 0x5555578e66e0> +#> <environment: 0x555559cd9780> #> #> $cost_notrans #> function (P) @@ -471,8 +475,8 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <bytecode: 0x555559feb960> -#> <environment: 0x555557684190> +#> <bytecode: 0x55555acf3f50> +#> <environment: 0x555559cd9780> #> #> $hessian_notrans #> parent_0 k_parent_sink @@ -539,7 +543,7 @@ #> 99.17407 #> #> $date -#> [1] "Fri Mar 9 23:08:11 2018" +#> [1] "Sun Mar 11 22:10:21 2018" #> #> $version #> [1] "0.9.47.1" @@ -582,3 +586,4 @@ </body> </html> + 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 ed5f29b3..f392bf64 100644 --- a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html +++ b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html @@ -27,6 +27,14 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="Results of fitting the DFOP model to Datasets A to B of FOCUS (2006) — FOCUS_2006_DFOP_ref_A_to_B" /> + +<meta property="og:description" content="A table with the fitted parameters and the resulting DT50 and DT90 values +generated with different software packages. Taken directly from FOCUS (2006). +The results from fitting the data with the Topfit software was removed, as +the initial concentration of the parent compound was fixed to a value of 100 +in this fit." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -167,3 +175,4 @@ in this fit.</p> </body> </html> + 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 e3e0d238..6e4c8d64 100644 --- a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html @@ -27,6 +27,14 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="Results of fitting the FOMC model to Datasets A to F of FOCUS (2006) — FOCUS_2006_FOMC_ref_A_to_F" /> + +<meta property="og:description" content="A table with the fitted parameters and the resulting DT50 and DT90 values +generated with different software packages. Taken directly from FOCUS (2006). +The results from fitting the data with the Topfit software was removed, as +the initial concentration of the parent compound was fixed to a value of 100 +in this fit." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -166,3 +174,4 @@ in this fit.</p> </body> </html> + 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 be785b0b..ed38ccae 100644 --- a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html @@ -27,6 +27,14 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="Results of fitting the HS model to Datasets A to F of FOCUS (2006) — FOCUS_2006_HS_ref_A_to_F" /> + +<meta property="og:description" content="A table with the fitted parameters and the resulting DT50 and DT90 values +generated with different software packages. Taken directly from FOCUS (2006). +The results from fitting the data with the Topfit software was removed, as +the initial concentration of the parent compound was fixed to a value of 100 +in this fit." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -167,3 +175,4 @@ in this fit.</p> </body> </html> + 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 6ca8e78e..107f3e5f 100644 --- a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html @@ -27,6 +27,14 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="Results of fitting the SFO model to Datasets A to F of FOCUS (2006) — FOCUS_2006_SFO_ref_A_to_F" /> + +<meta property="og:description" content="A table with the fitted parameters and the resulting DT50 and DT90 values +generated with different software packages. Taken directly from FOCUS (2006). +The results from fitting the data with the Topfit software was removed, as +the initial concentration of the parent compound was fixed to a value of 100 +in this fit." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -165,3 +173,4 @@ in this fit.</p> </body> </html> + diff --git a/docs/reference/FOCUS_2006_datasets.html b/docs/reference/FOCUS_2006_datasets.html index 9ea69f23..cc310ee3 100644 --- a/docs/reference/FOCUS_2006_datasets.html +++ b/docs/reference/FOCUS_2006_datasets.html @@ -27,6 +27,10 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="Datasets A to F from the FOCUS Kinetics report from 2006 — FOCUS_2006_datasets" /> + +<meta property="og:description" content="Data taken from FOCUS (2006), p. 258." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -167,3 +171,4 @@ </body> </html> + diff --git a/docs/reference/FOMC.solution.html b/docs/reference/FOMC.solution.html index b5b4c87c..397dc82d 100644 --- a/docs/reference/FOMC.solution.html +++ b/docs/reference/FOMC.solution.html @@ -27,6 +27,14 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="First-Order Multi-Compartment kinetics — FOMC.solution" /> + +<meta property="og:description" content="Function describing exponential decline from a defined starting value, with + a decreasing rate constant. +The form given here differs slightly from the original reference by Gustafson + and Holden (1990). The parameter beta corresponds to 1/beta in the + original equation." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -193,3 +201,4 @@ </body> </html> + diff --git a/docs/reference/HS.solution.html b/docs/reference/HS.solution.html index 0dc432ef..f633aa67 100644 --- a/docs/reference/HS.solution.html +++ b/docs/reference/HS.solution.html @@ -27,6 +27,11 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="Hockey-Stick kinetics — HS.solution" /> + +<meta property="og:description" content="Function describing two exponential decline functions with a break point + between them." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -183,3 +188,4 @@ </body> </html> + diff --git a/docs/reference/IORE.solution.html b/docs/reference/IORE.solution.html index b055534a..687dee5a 100644 --- a/docs/reference/IORE.solution.html +++ b/docs/reference/IORE.solution.html @@ -27,6 +27,11 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="Indeterminate order rate equation kinetics — IORE.solution" /> + +<meta property="og:description" content="Function describing exponential decline from a defined starting value, with + a concentration dependent rate constant." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -197,3 +202,4 @@ </body> </html> + diff --git a/docs/reference/SFO.solution.html b/docs/reference/SFO.solution.html index eda43e4d..1156c16f 100644 --- a/docs/reference/SFO.solution.html +++ b/docs/reference/SFO.solution.html @@ -27,6 +27,10 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="Single First-Order kinetics — SFO.solution" /> + +<meta property="og:description" content="Function describing exponential decline from a defined starting value." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -174,3 +178,4 @@ </body> </html> + diff --git a/docs/reference/SFORB.solution.html b/docs/reference/SFORB.solution.html index 2b6b2bc6..6901c435 100644 --- a/docs/reference/SFORB.solution.html +++ b/docs/reference/SFORB.solution.html @@ -27,6 +27,14 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="Single First-Order Reversible Binding kinetics — SFORB.solution" /> + +<meta property="og:description" content="Function describing the solution of the differential equations describing + the kinetic model with first-order terms for a two-way transfer from a free + to a bound fraction, and a first-order degradation term for the free + fraction. The initial condition is a defined amount in the free fraction and + no substance in the bound fraction." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -187,3 +195,4 @@ </body> </html> + diff --git a/docs/reference/add_err.html b/docs/reference/add_err.html index 407e1a3e..6d830113 100644 --- a/docs/reference/add_err.html +++ b/docs/reference/add_err.html @@ -27,6 +27,12 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="Add normally distributed errors to simulated kinetic degradation data — add_err" /> + +<meta property="og:description" content="Normally distributed errors are added to data predicted for a specific + degradation model using mkinpredict. The variance of the error + may depend on the predicted value and is specified as a standard deviation." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -241,3 +247,4 @@ </body> </html> + diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html index 4ab395cb..0f5ba0a4 100644 --- a/docs/reference/endpoints.html +++ b/docs/reference/endpoints.html @@ -27,6 +27,13 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="Function to calculate endpoints for further use from kinetic models fitted with mkinfit — endpoints" /> + +<meta property="og:description" content="This function calculates DT50 and DT90 values as well as formation fractions from kinetic models +fitted with mkinfit. If the SFORB model was specified for one of the parents or metabolites, +the Eigenvalues are returned. These are equivalent to the rate constantes of the DFOP model, but +with the advantage that the SFORB model can also be used for metabolites." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -177,3 +184,4 @@ with the advantage that the SFORB model can also be used for metabolites.</p> </body> </html> + diff --git a/docs/reference/geometric_mean.html b/docs/reference/geometric_mean.html index 7e27c1dc..9d91b5a8 100644 --- a/docs/reference/geometric_mean.html +++ b/docs/reference/geometric_mean.html @@ -27,6 +27,10 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="Calculate the geometric mean — geometric_mean" /> + +<meta property="og:description" content="Function calculating the geometric mean of numeric vectors" /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -158,3 +162,4 @@ </body> </html> + diff --git a/docs/reference/ilr.html b/docs/reference/ilr.html index 7ed15db5..33d749ce 100644 --- a/docs/reference/ilr.html +++ b/docs/reference/ilr.html @@ -27,6 +27,10 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="Function to perform isometric log-ratio transformation — ilr" /> + +<meta property="og:description" content="This implementation is a special case of the class of isometric log-ratio transformations." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -182,3 +186,4 @@ </body> </html> + diff --git a/docs/reference/index.html b/docs/reference/index.html index 157eaad3..6c05941d 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -27,6 +27,7 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="Function reference" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -453,3 +454,4 @@ </body> </html> + diff --git a/docs/reference/max_twa_parent.html b/docs/reference/max_twa_parent.html index 9e1e3974..696ca729 100644 --- a/docs/reference/max_twa_parent.html +++ b/docs/reference/max_twa_parent.html @@ -27,6 +27,14 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="Function to calculate maximum time weighted average concentrations from kinetic models fitted with mkinfit — max_twa_parent" /> + +<meta property="og:description" content="This function calculates maximum moving window time weighted average concentrations +(TWAs) for kinetic models fitted with mkinfit. Currently, only +calculations for the parent are implemented for the SFO, FOMC and DFOP models, +using the analytical formulas given in the PEC soil section of the FOCUS +guidance." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -178,3 +186,4 @@ guidance.</p> </body> </html> + diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index 30aa894e..80cac442 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -27,6 +27,12 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="Datasets on aerobic soil metabolism of 2,4,5-T in six soils — mccall81_245T" /> + +<meta property="og:description" content="Time course of 2,4,5-trichlorophenoxyacetic acid, and the corresponding + 2,4,5-trichlorophenol and 2,4,5-trichloroanisole as recovered in diethylether + extracts." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -145,8 +151,8 @@ <span class='kw'>fixed_parms</span> <span class='kw'>=</span> <span class='st'>"k_phenol_sink"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'>summary</span>(<span class='no'>fit.2</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.1 #> R version used for fitting: 3.4.3 -#> Date of fit: Fri Mar 9 23:08:18 2018 -#> Date of summary: Fri Mar 9 23:08:18 2018 +#> Date of fit: Sun Mar 11 22:10:30 2018 +#> Date of summary: Sun Mar 11 22:10:30 2018 #> #> Equations: #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245 @@ -156,7 +162,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 246 model solutions performed in 1.359 s +#> Fitted with method Port using 246 model solutions performed in 1.318 s #> #> Weighting: none #> @@ -266,3 +272,4 @@ </body> </html> + diff --git a/docs/reference/mkin_long_to_wide.html b/docs/reference/mkin_long_to_wide.html index dc781aaf..3c498a76 100644 --- a/docs/reference/mkin_long_to_wide.html +++ b/docs/reference/mkin_long_to_wide.html @@ -27,6 +27,12 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="Convert a dataframe from long to wide format — mkin_long_to_wide" /> + +<meta property="og:description" content="This function takes a dataframe in the long form as required by modCost + and converts it into a dataframe with one independent variable and several + dependent variables as columns." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -192,3 +198,4 @@ </body> </html> + diff --git a/docs/reference/mkin_wide_to_long.html b/docs/reference/mkin_wide_to_long.html index 2a8d20a3..f40cb7cf 100644 --- a/docs/reference/mkin_wide_to_long.html +++ b/docs/reference/mkin_wide_to_long.html @@ -27,6 +27,11 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="Convert a dataframe with observations over time into long format — mkin_wide_to_long" /> + +<meta property="og:description" content="This function simply takes a dataframe with one independent variable and several + dependent variable and converts it into the long form as required by modCost." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -171,3 +176,4 @@ </body> </html> + diff --git a/docs/reference/mkinds.html b/docs/reference/mkinds.html index fd707cfd..7f5ec78e 100644 --- a/docs/reference/mkinds.html +++ b/docs/reference/mkinds.html @@ -27,6 +27,10 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="A dataset class for mkin — mkinds" /> + +<meta property="og:description" content="A dataset class for mkin" /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -160,3 +164,4 @@ in order to be compatible with mkinfit</p></dd> </body> </html> + diff --git a/docs/reference/mkinerrmin.html b/docs/reference/mkinerrmin.html index 045e5805..f172cba1 100644 --- a/docs/reference/mkinerrmin.html +++ b/docs/reference/mkinerrmin.html @@ -27,6 +27,11 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="Calculate the minimum error to assume in order to pass the variance test — mkinerrmin" /> + +<meta property="og:description" content="This function finds the smallest relative error still resulting in passing the +chi-squared test as defined in the FOCUS kinetics report from 2006." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -195,3 +200,4 @@ chi-squared test as defined in the FOCUS kinetics report from 2006.</p> </body> </html> + diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 10052053..991df1cc 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -27,6 +27,20 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="Fit a kinetic model to data with one or more state variables — mkinfit" /> + +<meta property="og:description" content="This function uses the Flexible Modelling Environment package + FME to create a function calculating the model cost, i.e. the + deviation between the kinetic model and the observed data. This model cost is + then minimised using the Port algorithm nlminb, + using the specified initial or fixed parameters and starting values. + Per default, parameters in the kinetic models are internally transformed in order + to better satisfy the assumption of a normal distribution of their estimators. + In each step of the optimsation, the kinetic model is solved using the + function mkinpredict. The variance of the residuals for each + observed variable can optionally be iteratively reweighted until convergence + using the argument reweight.method = "obs"." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -400,15 +414,15 @@ <span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'>summary</span>(<span class='no'>fit</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.1 #> R version used for fitting: 3.4.3 -#> Date of fit: Fri Mar 9 23:08:20 2018 -#> Date of summary: Fri Mar 9 23:08:20 2018 +#> Date of fit: Sun Mar 11 22:10:32 2018 +#> Date of summary: Sun Mar 11 22:10:32 2018 #> #> Equations: #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent #> #> Model predictions using solution type analytical #> -#> Fitted with method Port using 64 model solutions performed in 0.148 s +#> Fitted with method Port using 64 model solutions performed in 0.135 s #> #> Weighting: none #> @@ -477,7 +491,7 @@ <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</span> <span class='fu'>print</span>(<span class='fu'>system.time</span>(<span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)))</div><div class='output co'>#> user system elapsed -#> 0.839 0.000 0.840 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit</span>)</div><div class='output co'>#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink +#> 0.829 0.000 0.829 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit</span>)</div><div class='output co'>#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink #> 99.59848 -3.03822 -2.98030 -5.24750 </div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> $ff #> parent_sink parent_m1 m1_sink #> 0.485524 0.514476 1.000000 @@ -585,3 +599,4 @@ </body> </html> + diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index 032fcbb6..7d3c0f94 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -27,6 +27,15 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="Function to set up a kinetic model with one or more state variables — mkinmod" /> + +<meta property="og:description" content="The function usually takes several expressions, each assigning a compound name to + a list, specifying the kinetic model type and reaction or transfer to other + observed compartments. Instead of specifying several expressions, a list + of lists can be given in the speclist argument. +For the definition of model types and their parameters, the equations given + in the FOCUS and NAFTA guidance documents are used." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -255,3 +264,4 @@ </body> </html> + diff --git a/docs/reference/mkinparplot.html b/docs/reference/mkinparplot.html index e416d67c..81f52fc3 100644 --- a/docs/reference/mkinparplot.html +++ b/docs/reference/mkinparplot.html @@ -27,6 +27,11 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="Function to plot the confidence intervals obtained using mkinfit — mkinparplot" /> + +<meta property="og:description" content="This function plots the confidence intervals for the parameters + fitted using mkinfit." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -163,3 +168,4 @@ </body> </html> + diff --git a/docs/reference/mkinplot.html b/docs/reference/mkinplot.html index e1ee1607..cfd72521 100644 --- a/docs/reference/mkinplot.html +++ b/docs/reference/mkinplot.html @@ -27,6 +27,10 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="Plot the observed data and the fitted model of an mkinfit object — mkinplot" /> + +<meta property="og:description" content="Deprecated function. It now only calls the plot method plot.mkinfit." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -158,3 +162,4 @@ </body> </html> + diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index 7354c496..044b2d92 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -27,6 +27,12 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="Produce predictions from a kinetic model using specific parameters — mkinpredict" /> + +<meta property="og:description" content="This function produces a time series for all the observed variables in a + kinetic model as specified by mkinmod, using a specific set of + kinetic parameters and initial values for the state variables." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -300,17 +306,17 @@ <span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>), <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#> time parent m1 #> 201 20 4.978707 27.46227</div><div class='output co'>#> user system elapsed -#> 0.003 0.000 0.003 </div><div class='input'> <span class='fu'>system.time</span>( +#> 0.002 0.000 0.003 </div><div class='input'> <span class='fu'>system.time</span>( <span class='fu'>print</span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_parent_m1</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>k_m1_sink</span> <span class='kw'>=</span> <span class='fl'>0.01</span>), <span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>), <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#> time parent m1 #> 201 20 4.978707 27.46227</div><div class='output co'>#> user system elapsed -#> 0.002 0.000 0.002 </div><div class='input'> <span class='fu'>system.time</span>( +#> 0.002 0.000 0.001 </div><div class='input'> <span class='fu'>system.time</span>( <span class='fu'>print</span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_parent_m1</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>k_m1_sink</span> <span class='kw'>=</span> <span class='fl'>0.01</span>), <span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>), <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#> time parent m1 #> 201 20 4.978707 27.46227</div><div class='output co'>#> user system elapsed -#> 0.031 0.000 0.031 </div></pre> +#> 0.029 0.000 0.029 </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> @@ -343,3 +349,4 @@ </body> </html> + diff --git a/docs/reference/mkinresplot.html b/docs/reference/mkinresplot.html index b4b6b116..df83f693 100644 --- a/docs/reference/mkinresplot.html +++ b/docs/reference/mkinresplot.html @@ -27,6 +27,13 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="Function to plot residuals stored in an mkin object — mkinresplot" /> + +<meta property="og:description" content="This function plots the residuals for the specified subset of the + observed variables from an mkinfit object. A combined plot of the fitted + model and the residuals can be obtained using plot.mkinfit + using the argument show_residuals = TRUE." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -208,3 +215,4 @@ </body> </html> + diff --git a/docs/reference/mkinsub.html b/docs/reference/mkinsub.html index b4915112..db727427 100644 --- a/docs/reference/mkinsub.html +++ b/docs/reference/mkinsub.html @@ -27,6 +27,11 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="Function to set up a kinetic submodel for one state variable — mkinsub" /> + +<meta property="og:description" content="This is a convenience function to set up the lists used as arguments for + mkinmod." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -188,3 +193,4 @@ </body> </html> + diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index 78033dd2..65c37898 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -27,6 +27,11 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="Fit one or more kinetic models with one or more state variables to one or more datasets — mmkin" /> + +<meta property="og:description" content="This function calls mkinfit on all combinations of models and datasets + specified in its first two arguments." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -220,3 +225,4 @@ </body> </html> + diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html index b6dd1525..319ba75b 100644 --- a/docs/reference/plot.mkinfit.html +++ b/docs/reference/plot.mkinfit.html @@ -27,6 +27,15 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="Plot the observed data and the fitted model of an mkinfit object — plot.mkinfit" /> + +<meta property="og:description" content="Solves the differential equations with the optimised and fixed parameters + from a previous successful call to mkinfit and plots + the observed data together with the solution of the fitted model. +If the current plot device is a tikz device, + then latex is being used for the formatting of the chi2 error level, + if show_errmin = TRUE." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -275,3 +284,4 @@ plot_sep(fit, sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE, … </body> </html> + diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html index 8b80273c..f1aa789f 100644 --- a/docs/reference/plot.mmkin.html +++ b/docs/reference/plot.mmkin.html @@ -27,6 +27,14 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="Plot model fits (observed and fitted) and the residuals for a row or column of an mmkin object — plot.mmkin" /> + +<meta property="og:description" content="When x is a row selected from an mmkin object ([.mmkin), the same model + fitted for at least one dataset is shown. When it is a column, the fit of at least one model + to the same dataset is shown. +If the current plot device is a tikz device, + then latex is being used for the formatting of the chi2 error level." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -200,3 +208,4 @@ </body> </html> + diff --git a/docs/reference/print.mkinds.html b/docs/reference/print.mkinds.html index 02882776..2a469fc2 100644 --- a/docs/reference/print.mkinds.html +++ b/docs/reference/print.mkinds.html @@ -27,6 +27,10 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="Print mkinds objects — print.mkinds" /> + +<meta property="og:description" content="Print mkinds objects." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -149,3 +153,4 @@ </body> </html> + diff --git a/docs/reference/print.mkinmod.html b/docs/reference/print.mkinmod.html index cd6678a6..30703dfd 100644 --- a/docs/reference/print.mkinmod.html +++ b/docs/reference/print.mkinmod.html @@ -27,6 +27,10 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="Print mkinmod objects — print.mkinmod" /> + +<meta property="og:description" content="Print mkinmod objects in a way that the user finds his way to get to its components." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -170,3 +174,4 @@ </body> </html> + diff --git a/docs/reference/schaefer07_complex_case.html b/docs/reference/schaefer07_complex_case.html index 15c23fd3..2c06b1dd 100644 --- a/docs/reference/schaefer07_complex_case.html +++ b/docs/reference/schaefer07_complex_case.html @@ -27,6 +27,12 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="Metabolism data set used for checking the software quality of KinGUI — schaefer07_complex_case" /> + +<meta property="og:description" content="This dataset was used for a comparison of KinGUI and ModelMaker to check the + software quality of KinGUI in the original publication (Schäfer et al., 2007). + The results from the fitting are also included." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -188,3 +194,4 @@ </body> </html> + diff --git a/docs/reference/sigma_rl.html b/docs/reference/sigma_rl.html index 4b287e55..fd714224 100644 --- a/docs/reference/sigma_rl.html +++ b/docs/reference/sigma_rl.html @@ -27,6 +27,12 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="Two component error model of Rocke and Lorenzato — sigma_rl" /> + +<meta property="og:description" content="Function describing the standard deviation of the measurement error + in dependence of the measured value \(y\): +$$\sigma = \sqrt{ \sigma_{low}^2 + y^2 * {rsd}_{high}^2}$$" /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -168,3 +174,4 @@ </body> </html> + diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index f34736b3..e462fd17 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -27,6 +27,13 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="Summary method for class "mkinfit" — summary.mkinfit" /> + +<meta property="og:description" content="Lists model equations, the summary as returned by summary.modFit, + the chi2 error levels calculated according to FOCUS guidance (2006) as far + as defined therein, and optionally the data, consisting of observed, predicted + and residual values." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -184,15 +191,15 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> <span class='fu'>summary</span>(<span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>)), <span class='no'>FOCUS_2006_A</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))</div><div class='output co'>#> mkin version used for fitting: 0.9.47.1 #> R version used for fitting: 3.4.3 -#> Date of fit: Fri Mar 9 23:08:29 2018 -#> Date of summary: Fri Mar 9 23:08:29 2018 +#> Date of fit: Sun Mar 11 22:10:41 2018 +#> Date of summary: Sun Mar 11 22:10:41 2018 #> #> Equations: #> d_parent/dt = - k_parent_sink * parent #> #> Model predictions using solution type analytical #> -#> Fitted with method Port using 35 model solutions performed in 0.075 s +#> Fitted with method Port using 35 model solutions performed in 0.07 s #> #> Weighting: none #> @@ -286,3 +293,4 @@ </body> </html> + diff --git a/docs/reference/synthetic_data_for_UBA.html b/docs/reference/synthetic_data_for_UBA.html index 396a6e2b..18da9ff6 100644 --- a/docs/reference/synthetic_data_for_UBA.html +++ b/docs/reference/synthetic_data_for_UBA.html @@ -27,6 +27,22 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="Synthetic datasets for one parent compound with two metabolites — synthetic_data_for_UBA_2014" /> + +<meta property="og:description" content="The 12 datasets were generated using four different models and three different + variance components. The four models are either the SFO or the DFOP model with either + two sequential or two parallel metabolites. +Variance component 'a' is based on a normal distribution with standard deviation of 3, + Variance component 'b' is also based on a normal distribution, but with a standard deviation of 7. + Variance component 'c' is based on the error model from Rocke and Lorenzato (1995), with the + minimum standard deviation (for small y values) of 0.5, and a proportionality constant of 0.07 + for the increase of the standard deviation with y. +Initial concentrations for metabolites and all values where adding the variance component resulted + in a value below the assumed limit of detection of 0.1 were set to NA. +As an example, the first dataset has the title SFO_lin_a and is based on the SFO model + with two sequential metabolites (linear pathway), with added variance component 'a'. +Compare also the code in the example section to see the degradation models." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -269,3 +285,4 @@ summary(fit) </body> </html> + diff --git a/docs/reference/test_data_from_UBA_2014.html b/docs/reference/test_data_from_UBA_2014.html index 13e072c6..b1b5e617 100644 --- a/docs/reference/test_data_from_UBA_2014.html +++ b/docs/reference/test_data_from_UBA_2014.html @@ -27,6 +27,11 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="Three experimental datasets from two water sediment systems and one soil — test_data_from_UBA_2014" /> + +<meta property="og:description" content="The datasets were used for the comparative validation of several kinetic evaluation + software packages (Ranke, 2014)." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -184,3 +189,4 @@ </body> </html> + diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index 266db603..5c89f8e2 100644 --- a/docs/reference/transform_odeparms.html +++ b/docs/reference/transform_odeparms.html @@ -27,6 +27,18 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="Functions to transform and backtransform kinetic parameters for fitting — transform_odeparms" /> + +<meta property="og:description" content="The transformations are intended to map parameters that should only take + on restricted values to the full scale of real numbers. For kinetic rate + constants and other paramters that can only take on positive values, a + simple log transformation is used. For compositional parameters, such as + the formations fractions that should always sum up to 1 and can not be + negative, the ilr transformation is used. +The transformation of sets of formation fractions is fragile, as it supposes + the same ordering of the components in forward and backward transformation. + This is no problem for the internal use in mkinfit." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -173,8 +185,8 @@ <span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'>summary</span>(<span class='no'>fit</span>, <span class='kw'>data</span><span class='kw'>=</span><span class='fl'>FALSE</span>) <span class='co'># See transformed and backtransformed parameters</span></div><div class='output co'>#> mkin version used for fitting: 0.9.47.1 #> R version used for fitting: 3.4.3 -#> Date of fit: Fri Mar 9 23:08:30 2018 -#> Date of summary: Fri Mar 9 23:08:30 2018 +#> Date of fit: Sun Mar 11 22:10:42 2018 +#> Date of summary: Sun Mar 11 22:10:42 2018 #> #> Equations: #> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent @@ -182,7 +194,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 153 model solutions performed in 0.657 s +#> Fitted with method Port using 153 model solutions performed in 0.564 s #> #> Weighting: none #> @@ -312,3 +324,4 @@ </body> </html> + |