diff options
Diffstat (limited to 'docs/reference')
57 files changed, 19 insertions, 282 deletions
diff --git a/docs/reference/DFOP.solution-1.png b/docs/reference/DFOP.solution-1.png Binary files differindex 1549a73b..e9268f94 100644 --- a/docs/reference/DFOP.solution-1.png +++ b/docs/reference/DFOP.solution-1.png diff --git a/docs/reference/DFOP.solution.html b/docs/reference/DFOP.solution.html index ff1ad823..f89a66e2 100644 --- a/docs/reference/DFOP.solution.html +++ b/docs/reference/DFOP.solution.html @@ -27,11 +27,6 @@ <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> diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index 11738484..3b96f9ae 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -27,10 +27,6 @@ <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> @@ -263,7 +259,7 @@ #> #> $time #> user system elapsed -#> 0.058 0.000 0.057 +#> 0.06 0.00 0.06 #> #> $mkinmod #> <mkinmod> model generated with @@ -452,8 +448,8 @@ #> } #> return(mC) #> } -#> <bytecode: 0x55555ad80908> -#> <environment: 0x55555b1b4b90> +#> <bytecode: 0x5555599fd348> +#> <environment: 0x555557684190> #> #> $cost_notrans #> function (P) @@ -475,8 +471,8 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <bytecode: 0x55555b174428> -#> <environment: 0x55555b1b4b90> +#> <bytecode: 0x555559feb960> +#> <environment: 0x555557684190> #> #> $hessian_notrans #> parent_0 k_parent_sink @@ -543,7 +539,7 @@ #> 99.17407 #> #> $date -#> [1] "Thu Mar 1 14:26:09 2018" +#> [1] "Fri Mar 9 23:08:11 2018" #> #> $version #> [1] "0.9.47.1" 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 5fb3ccfe..de986f3f 100644 --- a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html +++ b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html @@ -27,14 +27,6 @@ <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> 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 c1665dee..4bc0fd4b 100644 --- a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html @@ -27,14 +27,6 @@ <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> 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 db3d228d..bf0331cc 100644 --- a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html @@ -27,14 +27,6 @@ <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> 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 cc4fcb1d..6f05cbb9 100644 --- a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html @@ -27,14 +27,6 @@ <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> diff --git a/docs/reference/FOCUS_2006_datasets.html b/docs/reference/FOCUS_2006_datasets.html index 4548c983..9ea69f23 100644 --- a/docs/reference/FOCUS_2006_datasets.html +++ b/docs/reference/FOCUS_2006_datasets.html @@ -27,10 +27,6 @@ <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> diff --git a/docs/reference/FOMC.solution-1.png b/docs/reference/FOMC.solution-1.png Binary files differindex 58178df5..f10cff4e 100644 --- a/docs/reference/FOMC.solution-1.png +++ b/docs/reference/FOMC.solution-1.png diff --git a/docs/reference/FOMC.solution.html b/docs/reference/FOMC.solution.html index 810b0eba..b5b4c87c 100644 --- a/docs/reference/FOMC.solution.html +++ b/docs/reference/FOMC.solution.html @@ -27,14 +27,6 @@ <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> diff --git a/docs/reference/HS.solution-1.png b/docs/reference/HS.solution-1.png Binary files differindex e259134e..5e04d343 100644 --- a/docs/reference/HS.solution-1.png +++ b/docs/reference/HS.solution-1.png diff --git a/docs/reference/HS.solution.html b/docs/reference/HS.solution.html index 79358efb..0dc432ef 100644 --- a/docs/reference/HS.solution.html +++ b/docs/reference/HS.solution.html @@ -27,11 +27,6 @@ <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> diff --git a/docs/reference/IORE.solution-1.png b/docs/reference/IORE.solution-1.png Binary files differindex 674c25d3..e421d562 100644 --- a/docs/reference/IORE.solution-1.png +++ b/docs/reference/IORE.solution-1.png diff --git a/docs/reference/IORE.solution.html b/docs/reference/IORE.solution.html index f705ab2f..b055534a 100644 --- a/docs/reference/IORE.solution.html +++ b/docs/reference/IORE.solution.html @@ -27,11 +27,6 @@ <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> diff --git a/docs/reference/SFO.solution.html b/docs/reference/SFO.solution.html index a7934a35..eda43e4d 100644 --- a/docs/reference/SFO.solution.html +++ b/docs/reference/SFO.solution.html @@ -27,10 +27,6 @@ <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> diff --git a/docs/reference/SFORB.solution.html b/docs/reference/SFORB.solution.html index aaae7cdd..2b6b2bc6 100644 --- a/docs/reference/SFORB.solution.html +++ b/docs/reference/SFORB.solution.html @@ -27,14 +27,6 @@ <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> diff --git a/docs/reference/add_err-1.png b/docs/reference/add_err-1.png Binary files differindex 4f9b1534..fecfc52d 100644 --- a/docs/reference/add_err-1.png +++ b/docs/reference/add_err-1.png diff --git a/docs/reference/add_err-2.png b/docs/reference/add_err-2.png Binary files differindex 8fcf4625..907001ed 100644 --- a/docs/reference/add_err-2.png +++ b/docs/reference/add_err-2.png diff --git a/docs/reference/add_err-3.png b/docs/reference/add_err-3.png Binary files differindex e44839a6..3786d934 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 42bec993..407e1a3e 100644 --- a/docs/reference/add_err.html +++ b/docs/reference/add_err.html @@ -27,12 +27,6 @@ <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> diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html index c45a0b7c..4ab395cb 100644 --- a/docs/reference/endpoints.html +++ b/docs/reference/endpoints.html @@ -27,13 +27,6 @@ <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> diff --git a/docs/reference/geometric_mean.html b/docs/reference/geometric_mean.html index 2d46b4de..7e27c1dc 100644 --- a/docs/reference/geometric_mean.html +++ b/docs/reference/geometric_mean.html @@ -27,10 +27,6 @@ <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> diff --git a/docs/reference/ilr.html b/docs/reference/ilr.html index 2c51001f..7ed15db5 100644 --- a/docs/reference/ilr.html +++ b/docs/reference/ilr.html @@ -27,10 +27,6 @@ <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> diff --git a/docs/reference/index.html b/docs/reference/index.html index 218194ad..84bc1dfc 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -27,7 +27,6 @@ <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> diff --git a/docs/reference/max_twa_parent.html b/docs/reference/max_twa_parent.html index 5d6baf6a..9e1e3974 100644 --- a/docs/reference/max_twa_parent.html +++ b/docs/reference/max_twa_parent.html @@ -27,14 +27,6 @@ <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> diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index ec7f8ccd..30aa894e 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -27,12 +27,6 @@ <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> @@ -151,8 +145,8 @@ <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: Thu Mar 1 14:26:15 2018 -#> Date of summary: Thu Mar 1 14:26:15 2018 +#> Date of fit: Fri Mar 9 23:08:18 2018 +#> Date of summary: Fri Mar 9 23:08:18 2018 #> #> Equations: #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245 diff --git a/docs/reference/mkin_long_to_wide.html b/docs/reference/mkin_long_to_wide.html index a5432dac..dc781aaf 100644 --- a/docs/reference/mkin_long_to_wide.html +++ b/docs/reference/mkin_long_to_wide.html @@ -27,12 +27,6 @@ <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> diff --git a/docs/reference/mkin_wide_to_long.html b/docs/reference/mkin_wide_to_long.html index 6798efa6..2a8d20a3 100644 --- a/docs/reference/mkin_wide_to_long.html +++ b/docs/reference/mkin_wide_to_long.html @@ -27,11 +27,6 @@ <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> diff --git a/docs/reference/mkinds.html b/docs/reference/mkinds.html index ab06e903..fd707cfd 100644 --- a/docs/reference/mkinds.html +++ b/docs/reference/mkinds.html @@ -27,10 +27,6 @@ <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> diff --git a/docs/reference/mkinerrmin.html b/docs/reference/mkinerrmin.html index 496cce15..045e5805 100644 --- a/docs/reference/mkinerrmin.html +++ b/docs/reference/mkinerrmin.html @@ -27,11 +27,6 @@ <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> diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 4fb5ef9a..10052053 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -27,20 +27,6 @@ <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> @@ -414,15 +400,15 @@ <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: Thu Mar 1 14:26:18 2018 -#> Date of summary: Thu Mar 1 14:26:18 2018 +#> Date of fit: Fri Mar 9 23:08:20 2018 +#> Date of summary: Fri Mar 9 23:08:20 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 0.135 s +#> Fitted with method Port using 64 model solutions performed in 0.148 s #> #> Weighting: none #> @@ -491,7 +477,7 @@ <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 -#> 0.84 0.00 0.84 </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 +#> 0.839 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 #> 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 diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index c1287905..032fcbb6 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -27,15 +27,6 @@ <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> diff --git a/docs/reference/mkinparplot-1.png b/docs/reference/mkinparplot-1.png Binary files differindex 42811535..1e7603d7 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 30954168..e416d67c 100644 --- a/docs/reference/mkinparplot.html +++ b/docs/reference/mkinparplot.html @@ -27,11 +27,6 @@ <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> diff --git a/docs/reference/mkinplot.html b/docs/reference/mkinplot.html index 5df3f872..e1ee1607 100644 --- a/docs/reference/mkinplot.html +++ b/docs/reference/mkinplot.html @@ -27,10 +27,6 @@ <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> diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index df6316e1..7354c496 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -27,12 +27,6 @@ <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> @@ -311,7 +305,7 @@ <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 0.001 </div><div class='input'> <span class='fu'>system.time</span>( +#> 0.002 0.000 0.002 </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 diff --git a/docs/reference/mkinresplot-1.png b/docs/reference/mkinresplot-1.png Binary files differindex 8636baf2..5b201616 100644 --- a/docs/reference/mkinresplot-1.png +++ b/docs/reference/mkinresplot-1.png diff --git a/docs/reference/mkinresplot.html b/docs/reference/mkinresplot.html index 036917f1..b4b6b116 100644 --- a/docs/reference/mkinresplot.html +++ b/docs/reference/mkinresplot.html @@ -27,13 +27,6 @@ <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> diff --git a/docs/reference/mkinsub.html b/docs/reference/mkinsub.html index 7724220f..b4915112 100644 --- a/docs/reference/mkinsub.html +++ b/docs/reference/mkinsub.html @@ -27,11 +27,6 @@ <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> diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index e97e3f81..78033dd2 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -27,11 +27,6 @@ <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> diff --git a/docs/reference/plot.mkinfit-1.png b/docs/reference/plot.mkinfit-1.png Binary files differindex 2bb8f5dd..0d54d2fe 100644 --- a/docs/reference/plot.mkinfit-1.png +++ b/docs/reference/plot.mkinfit-1.png diff --git a/docs/reference/plot.mkinfit-2.png b/docs/reference/plot.mkinfit-2.png Binary files differindex 22a3f8b0..377d63b6 100644 --- a/docs/reference/plot.mkinfit-2.png +++ b/docs/reference/plot.mkinfit-2.png diff --git a/docs/reference/plot.mkinfit-3.png b/docs/reference/plot.mkinfit-3.png Binary files differindex 93e859c7..b23ddfe7 100644 --- a/docs/reference/plot.mkinfit-3.png +++ b/docs/reference/plot.mkinfit-3.png diff --git a/docs/reference/plot.mkinfit-4.png b/docs/reference/plot.mkinfit-4.png Binary files differindex 27edd6f3..0dd9f4d6 100644 --- a/docs/reference/plot.mkinfit-4.png +++ b/docs/reference/plot.mkinfit-4.png diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html index 4bdad93f..b6dd1525 100644 --- a/docs/reference/plot.mkinfit.html +++ b/docs/reference/plot.mkinfit.html @@ -27,15 +27,6 @@ <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> diff --git a/docs/reference/plot.mmkin-1.png b/docs/reference/plot.mmkin-1.png Binary files differindex 2554b68b..c2c25e90 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 9a66294f..b40ae0d5 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 b0f7fa21..dfbe014f 100644 --- a/docs/reference/plot.mmkin-3.png +++ b/docs/reference/plot.mmkin-3.png diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html index 11da6685..8b80273c 100644 --- a/docs/reference/plot.mmkin.html +++ b/docs/reference/plot.mmkin.html @@ -27,14 +27,6 @@ <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> diff --git a/docs/reference/print.mkinds.html b/docs/reference/print.mkinds.html index 8e0d18b2..02882776 100644 --- a/docs/reference/print.mkinds.html +++ b/docs/reference/print.mkinds.html @@ -27,10 +27,6 @@ <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> diff --git a/docs/reference/print.mkinmod.html b/docs/reference/print.mkinmod.html index db15cc60..cd6678a6 100644 --- a/docs/reference/print.mkinmod.html +++ b/docs/reference/print.mkinmod.html @@ -27,10 +27,6 @@ <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> diff --git a/docs/reference/schaefer07_complex_case.html b/docs/reference/schaefer07_complex_case.html index 6c53f805..04c72edd 100644 --- a/docs/reference/schaefer07_complex_case.html +++ b/docs/reference/schaefer07_complex_case.html @@ -27,12 +27,6 @@ <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> diff --git a/docs/reference/sigma_rl.html b/docs/reference/sigma_rl.html index 868c0d4f..4b287e55 100644 --- a/docs/reference/sigma_rl.html +++ b/docs/reference/sigma_rl.html @@ -27,12 +27,6 @@ <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> diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index 977ff8d8..f34736b3 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -27,13 +27,6 @@ <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> @@ -191,15 +184,15 @@ <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: Thu Mar 1 14:26:27 2018 -#> Date of summary: Thu Mar 1 14:26:27 2018 +#> Date of fit: Fri Mar 9 23:08:29 2018 +#> Date of summary: Fri Mar 9 23:08:29 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 0.076 s +#> Fitted with method Port using 35 model solutions performed in 0.075 s #> #> Weighting: none #> diff --git a/docs/reference/synthetic_data_for_UBA.html b/docs/reference/synthetic_data_for_UBA.html index 192e8dc2..396a6e2b 100644 --- a/docs/reference/synthetic_data_for_UBA.html +++ b/docs/reference/synthetic_data_for_UBA.html @@ -27,22 +27,6 @@ <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> diff --git a/docs/reference/test_data_from_UBA_2014.html b/docs/reference/test_data_from_UBA_2014.html index c4292d9c..13e072c6 100644 --- a/docs/reference/test_data_from_UBA_2014.html +++ b/docs/reference/test_data_from_UBA_2014.html @@ -27,11 +27,6 @@ <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> diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index 630a5103..266db603 100644 --- a/docs/reference/transform_odeparms.html +++ b/docs/reference/transform_odeparms.html @@ -27,18 +27,6 @@ <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> @@ -185,8 +173,8 @@ The transformation of sets of formation fractions is fragile, as it supposes <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: Thu Mar 1 14:26:28 2018 -#> Date of summary: Thu Mar 1 14:26:28 2018 +#> Date of fit: Fri Mar 9 23:08:30 2018 +#> Date of summary: Fri Mar 9 23:08:30 2018 #> #> Equations: #> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent @@ -194,7 +182,7 @@ The transformation of sets of formation fractions is fragile, as it supposes #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 153 model solutions performed in 0.571 s +#> Fitted with method Port using 153 model solutions performed in 0.657 s #> #> Weighting: none #> |
