diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2020-05-12 19:10:32 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2020-05-12 19:10:32 +0200 |
| commit | 36bc31c52cbe4b686f5562e21ee110380481dff8 (patch) | |
| tree | f872beb978159d6f69b60505030fc1beedc1b747 | |
| parent | 20f235860c3d5a9c6319c516637021e02ecb6cae (diff) | |
Another documentation update
| -rw-r--r-- | R/mkinfit.R | 17 | ||||
| -rw-r--r-- | docs/pkgdown.yml | 2 | ||||
| -rw-r--r-- | docs/reference/mkinfit.html | 44 | ||||
| -rw-r--r-- | man/mkinfit.Rd | 19 |
4 files changed, 39 insertions, 43 deletions
diff --git a/R/mkinfit.R b/R/mkinfit.R index 0f478910..8231cd00 100644 --- a/R/mkinfit.R +++ b/R/mkinfit.R @@ -68,12 +68,11 @@ if(getRversion() >= '2.15.1') utils::globalVariables(c("name", "time", "value")) #' coefficient matrix in cases that this is possible. If set to "deSolve", a #' numerical ode solver from package \code{\link{deSolve}} is used. If set to #' "analytical", an analytical solution of the model is used. This is only -#' implemented for simple degradation experiments with only one state -#' variable, i.e. with no metabolites. The default is "auto", which uses -#' "analytical" if possible, otherwise "deSolve" if a compiler is present, -#' and "eigen" if no compiler is present and the model can be expressed using -#' eigenvalues and eigenvectors. This argument is passed on to the helper -#' function \code{\link{mkinpredict}}. +#' implemented for relatively simple degradation models. The default is +#' "auto", which uses "analytical" if possible, otherwise "deSolve" if a +#' compiler is present, and "eigen" if no compiler is present and the model +#' can be expressed using eigenvalues and eigenvectors. This argument is +#' passed on to the helper function \code{\link{mkinpredict}}. #' @param method.ode The solution method passed via \code{\link{mkinpredict}} #' to \code{\link{ode}} in case the solution type is "deSolve". The default #' "lsoda" is performant, but sometimes fails to converge. @@ -118,9 +117,9 @@ if(getRversion() >= '2.15.1') utils::globalVariables(c("name", "time", "value")) #' least squares fitting ("OLS") is selected. If the error model is "obs", or #' "tc", the "d_3" algorithm is selected. #' -#' The algorithm "d_3" will directly minimize the negative log-likelihood and -#' - independently - also use the three step algorithm described below. The -#' fit with the higher likelihood is returned. +#' The algorithm "d_3" will directly minimize the negative log-likelihood +#' and independently also use the three step algorithm described below. +#' The fit with the higher likelihood is returned. #' #' The algorithm "direct" will directly minimize the negative log-likelihood. #' diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 5147a265..cd82d482 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -10,7 +10,7 @@ articles: NAFTA_examples: web_only/NAFTA_examples.html benchmarks: web_only/benchmarks.html compiled_models: web_only/compiled_models.html -last_built: 2020-05-12T15:51Z +last_built: 2020-05-12T17:10Z urls: reference: https://pkgdown.jrwb.de/mkin/reference article: https://pkgdown.jrwb.de/mkin/articles diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 54ca377f..3438b8b1 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -115,6 +115,9 @@ likelihood function." /> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> + <li> + <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + </li> </ul> </li> <li> @@ -265,12 +268,11 @@ differential equations is based on the spectral decomposition of the coefficient matrix in cases that this is possible. If set to "deSolve", a numerical ode solver from package <code>deSolve</code> is used. If set to "analytical", an analytical solution of the model is used. This is only -implemented for simple degradation experiments with only one state -variable, i.e. with no metabolites. The default is "auto", which uses -"analytical" if possible, otherwise "deSolve" if a compiler is present, -and "eigen" if no compiler is present and the model can be expressed using -eigenvalues and eigenvectors. This argument is passed on to the helper -function <code><a href='mkinpredict.html'>mkinpredict</a></code>.</p></td> +implemented for relatively simple degradation models. The default is +"auto", which uses "analytical" if possible, otherwise "deSolve" if a +compiler is present, and "eigen" if no compiler is present and the model +can be expressed using eigenvalues and eigenvectors. This argument is +passed on to the helper function <code><a href='mkinpredict.html'>mkinpredict</a></code>.</p></td> </tr> <tr> <th>method.ode</th> @@ -342,11 +344,9 @@ normal distribution as assumed by this method.</p></td> the error model. If the error model is "const", unweighted nonlinear least squares fitting ("OLS") is selected. If the error model is "obs", or "tc", the "d_3" algorithm is selected.</p> -<p>The algorithm "d_3" will directly minimize the negative log-likelihood and</p><ul> -<li><p>independently - also use the three step algorithm described below. The -fit with the higher likelihood is returned.</p></li> -</ul> - +<p>The algorithm "d_3" will directly minimize the negative log-likelihood +and independently also use the three step algorithm described below. +The fit with the higher likelihood is returned.</p> <p>The algorithm "direct" will directly minimize the negative log-likelihood.</p> <p>The algorithm "twostep" will minimize the negative log-likelihood after an initial unweighted least squares optimisation step.</p> @@ -422,15 +422,15 @@ Degradation Data. <em>Environments</em> 6(12) 124 <span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.50.2 #> R version used for fitting: 4.0.0 -#> Date of fit: Tue May 12 15:29:48 2020 -#> Date of summary: Tue May 12 15:29:48 2020 +#> Date of fit: Tue May 12 19:10:13 2020 +#> Date of summary: Tue May 12 19:10:13 2020 #> #> Equations: #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent #> #> Model predictions using solution type analytical #> -#> Fitted using 222 model solutions performed in 0.043 s +#> Fitted using 222 model solutions performed in 0.047 s #> #> Error model: Constant variance #> @@ -597,7 +597,7 @@ Degradation Data. <em>Environments</em> 6(12) 124 #> Sum of squared residuals at call 166: 371.2134 #> Sum of squared residuals at call 168: 371.2134 #> Negative log-likelihood at call 178: 97.22429</div><div class='output co'>#> <span class='message'>Optimisation successfully terminated.</span></div><div class='output co'>#> User System verstrichen -#> 0.363 0.001 0.364 </div><div class='input'><span class='fu'><a href='parms.html'>parms</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#> parent_0 k_parent k_m1 f_parent_to_m1 sigma +#> 0.351 0.000 0.352 </div><div class='input'><span class='fu'><a href='parms.html'>parms</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#> parent_0 k_parent k_m1 f_parent_to_m1 sigma #> 99.598480759 0.098697739 0.005260651 0.514475958 3.125503874 </div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#> $ff #> parent_m1 parent_sink #> 0.514476 0.485524 @@ -631,8 +631,8 @@ Degradation Data. <em>Environments</em> 6(12) 124 <span class='no'>SFO_SFO.ff</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>f.noweight</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>f.noweight</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.50.2 #> R version used for fitting: 4.0.0 -#> Date of fit: Tue May 12 15:29:53 2020 -#> Date of summary: Tue May 12 15:29:53 2020 +#> Date of fit: Tue May 12 19:10:18 2020 +#> Date of summary: Tue May 12 19:10:18 2020 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -640,7 +640,7 @@ Degradation Data. <em>Environments</em> 6(12) 124 #> #> Model predictions using solution type analytical #> -#> Fitted using 421 model solutions performed in 0.13 s +#> Fitted using 421 model solutions performed in 0.146 s #> #> Error model: Constant variance #> @@ -753,8 +753,8 @@ Degradation Data. <em>Environments</em> 6(12) 124 #> 120 m1 25.15 28.78984 -3.640e+00 #> 120 m1 33.31 28.78984 4.520e+00</div><div class='input'><span class='no'>f.obs</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"obs"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>f.obs</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.50.2 #> R version used for fitting: 4.0.0 -#> Date of fit: Tue May 12 15:29:53 2020 -#> Date of summary: Tue May 12 15:29:53 2020 +#> Date of fit: Tue May 12 19:10:19 2020 +#> Date of summary: Tue May 12 19:10:19 2020 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -890,8 +890,8 @@ Degradation Data. <em>Environments</em> 6(12) 124 #> 120 m1 25.15 28.80429 -3.654e+00 #> 120 m1 33.31 28.80429 4.506e+00</div><div class='input'><span class='no'>f.tc</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>f.tc</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.50.2 #> R version used for fitting: 4.0.0 -#> Date of fit: Tue May 12 15:29:54 2020 -#> Date of summary: Tue May 12 15:29:54 2020 +#> Date of fit: Tue May 12 19:10:19 2020 +#> Date of summary: Tue May 12 19:10:19 2020 #> #> Equations: #> d_parent/dt = - k_parent * parent diff --git a/man/mkinfit.Rd b/man/mkinfit.Rd index 5a2b3e53..b8d44fba 100644 --- a/man/mkinfit.Rd +++ b/man/mkinfit.Rd @@ -94,12 +94,11 @@ differential equations is based on the spectral decomposition of the coefficient matrix in cases that this is possible. If set to "deSolve", a numerical ode solver from package \code{\link{deSolve}} is used. If set to "analytical", an analytical solution of the model is used. This is only -implemented for simple degradation experiments with only one state -variable, i.e. with no metabolites. The default is "auto", which uses -"analytical" if possible, otherwise "deSolve" if a compiler is present, -and "eigen" if no compiler is present and the model can be expressed using -eigenvalues and eigenvectors. This argument is passed on to the helper -function \code{\link{mkinpredict}}.} +implemented for relatively simple degradation models. The default is +"auto", which uses "analytical" if possible, otherwise "deSolve" if a +compiler is present, and "eigen" if no compiler is present and the model +can be expressed using eigenvalues and eigenvectors. This argument is +passed on to the helper function \code{\link{mkinpredict}}.} \item{method.ode}{The solution method passed via \code{\link{mkinpredict}} to \code{\link{ode}} in case the solution type is "deSolve". The default @@ -154,11 +153,9 @@ the error model. If the error model is "const", unweighted nonlinear least squares fitting ("OLS") is selected. If the error model is "obs", or "tc", the "d_3" algorithm is selected. -The algorithm "d_3" will directly minimize the negative log-likelihood and -\itemize{ -\item independently - also use the three step algorithm described below. The -fit with the higher likelihood is returned. -} +The algorithm "d_3" will directly minimize the negative log-likelihood +and independently also use the three step algorithm described below. +The fit with the higher likelihood is returned. The algorithm "direct" will directly minimize the negative log-likelihood. |