diff options
36 files changed, 62 insertions, 58 deletions
@@ -16,6 +16,10 @@ - 'transform_odeparms', 'backtransform_odeparms': Use logit transformation for solitary fractions like the g parameter of the DFOP model, or formation fractions for a pathway to only one target variable +- 'plot.mmkin': Add a ylab argument, making it possible to customize the y axis label of the panels on the left without affecting the residual plots + +- 'plot.mkinfit': Change default ylab from "Observed" to "Residue" + ## Mixed-effects models - 'mixed.mmkin' New container for mmkin objects for plotting with the 'plot.mixed.mmkin' method @@ -32,6 +36,7 @@ - 'saem' generic function to fit saemix models using 'saemix_model' and 'saemix_data', with a generator 'saem.mmkin', summary and plot methods + # mkin 0.9.50.3 (2020-10-08) - 'parms': Add a method for mmkin objects diff --git a/R/plot.mkinfit.R b/R/plot.mkinfit.R index 6ac4e45d..9dbc91d7 100644 --- a/R/plot.mkinfit.R +++ b/R/plot.mkinfit.R @@ -91,7 +91,7 @@ utils::globalVariables(c("type", "variable", "observed")) #' @export plot.mkinfit <- function(x, fit = x, obs_vars = names(fit$mkinmod$map), - xlab = "Time", ylab = "Observed", + xlab = "Time", ylab = "Residue", xlim = range(fit$data$time), ylim = "default", col_obs = 1:length(obs_vars), diff --git a/R/plot.mmkin.R b/R/plot.mmkin.R index 0523e4d3..f8ed1f9a 100644 --- a/R/plot.mmkin.R +++ b/R/plot.mmkin.R @@ -15,6 +15,7 @@ #' @param resplot Should the residuals plotted against time, using #' \code{\link{mkinresplot}}, or as squared residuals against predicted #' values, with the error model, using \code{\link{mkinerrplot}}. +#' @param ylab Label for the y axis. #' @param standardized Should the residuals be standardized? This option #' is passed to \code{\link{mkinresplot}}, it only takes effect if #' `resplot = "time"`. @@ -55,6 +56,7 @@ #' @export plot.mmkin <- function(x, main = "auto", legends = 1, resplot = c("time", "errmod"), + ylab = "Residue", standardized = FALSE, show_errmin = TRUE, errmin_var = "All data", errmin_digits = 3, @@ -117,9 +119,9 @@ plot.mmkin <- function(x, main = "auto", legends = 1, fit <- x[[i.fit]] if (ymax == "auto") { - plot(fit, legend = legends == i.fit, ...) + plot(fit, legend = legends == i.fit, ylab = ylab, ...) } else { - plot(fit, legend = legends == i.fit, ylim = c(0, ymax), ...) + plot(fit, legend = legends == i.fit, ylim = c(0, ymax), ylab = ylab, ...) } title(main, outer = TRUE, line = -2) diff --git a/docs/dev/pkgdown.yml b/docs/dev/pkgdown.yml index 3591cac8..2963e810 100644 --- a/docs/dev/pkgdown.yml +++ b/docs/dev/pkgdown.yml @@ -10,7 +10,7 @@ articles: web_only/NAFTA_examples: NAFTA_examples.html web_only/benchmarks: benchmarks.html web_only/compiled_models: compiled_models.html -last_built: 2021-01-11T11:41Z +last_built: 2021-01-25T13:41Z urls: reference: https://pkgdown.jrwb.de/mkin/reference article: https://pkgdown.jrwb.de/mkin/articles diff --git a/docs/dev/reference/Rplot001.png b/docs/dev/reference/Rplot001.png Binary files differindex 17a35806..bca41e2c 100644 --- a/docs/dev/reference/Rplot001.png +++ b/docs/dev/reference/Rplot001.png diff --git a/docs/dev/reference/Rplot006.png b/docs/dev/reference/Rplot006.png Binary files differindex 921e0394..da52f580 100644 --- a/docs/dev/reference/Rplot006.png +++ b/docs/dev/reference/Rplot006.png diff --git a/docs/dev/reference/Rplot007.png b/docs/dev/reference/Rplot007.png Binary files differindex fcca232c..fce3b6ee 100644 --- a/docs/dev/reference/Rplot007.png +++ b/docs/dev/reference/Rplot007.png diff --git a/docs/dev/reference/plot.mkinfit-1.png b/docs/dev/reference/plot.mkinfit-1.png Binary files differindex fc195031..e5da9f1c 100644 --- a/docs/dev/reference/plot.mkinfit-1.png +++ b/docs/dev/reference/plot.mkinfit-1.png diff --git a/docs/dev/reference/plot.mkinfit-2.png b/docs/dev/reference/plot.mkinfit-2.png Binary files differindex fa99f680..376c812f 100644 --- a/docs/dev/reference/plot.mkinfit-2.png +++ b/docs/dev/reference/plot.mkinfit-2.png diff --git a/docs/dev/reference/plot.mkinfit-3.png b/docs/dev/reference/plot.mkinfit-3.png Binary files differindex 28789544..c976d4b1 100644 --- a/docs/dev/reference/plot.mkinfit-3.png +++ b/docs/dev/reference/plot.mkinfit-3.png diff --git a/docs/dev/reference/plot.mkinfit-4.png b/docs/dev/reference/plot.mkinfit-4.png Binary files differindex 77b3422f..c8bc00fe 100644 --- a/docs/dev/reference/plot.mkinfit-4.png +++ b/docs/dev/reference/plot.mkinfit-4.png diff --git a/docs/dev/reference/plot.mkinfit-5.png b/docs/dev/reference/plot.mkinfit-5.png Binary files differindex b4b6528b..bc44de88 100644 --- a/docs/dev/reference/plot.mkinfit-5.png +++ b/docs/dev/reference/plot.mkinfit-5.png diff --git a/docs/dev/reference/plot.mkinfit-6.png b/docs/dev/reference/plot.mkinfit-6.png Binary files differindex f71f1769..eb8cbd92 100644 --- a/docs/dev/reference/plot.mkinfit-6.png +++ b/docs/dev/reference/plot.mkinfit-6.png diff --git a/docs/dev/reference/plot.mkinfit-7.png b/docs/dev/reference/plot.mkinfit-7.png Binary files differindex 98fee908..92a664f4 100644 --- a/docs/dev/reference/plot.mkinfit-7.png +++ b/docs/dev/reference/plot.mkinfit-7.png diff --git a/docs/dev/reference/plot.mkinfit.html b/docs/dev/reference/plot.mkinfit.html index c7eda78f..c5bfb528 100644 --- a/docs/dev/reference/plot.mkinfit.html +++ b/docs/dev/reference/plot.mkinfit.html @@ -123,7 +123,7 @@ observed data together with the solution of the fitted model." /> <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin/"> - <span class="fab fa fab fa-github fa-lg"></span> + <span class="fab fa-github fa-lg"></span> </a> </li> @@ -157,7 +157,7 @@ observed data together with the solution of the fitted model.</p> fit <span class='op'>=</span> <span class='va'>x</span>, obs_vars <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>fit</span><span class='op'>$</span><span class='va'>mkinmod</span><span class='op'>$</span><span class='va'>map</span><span class='op'>)</span>, xlab <span class='op'>=</span> <span class='st'>"Time"</span>, - ylab <span class='op'>=</span> <span class='st'>"Observed"</span>, + ylab <span class='op'>=</span> <span class='st'>"Residue"</span>, xlim <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/range.html'>range</a></span><span class='op'>(</span><span class='va'>fit</span><span class='op'>$</span><span class='va'>data</span><span class='op'>$</span><span class='va'>time</span><span class='op'>)</span>, ylim <span class='op'>=</span> <span class='st'>"default"</span>, col_obs <span class='op'>=</span> <span class='fl'>1</span><span class='op'>:</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>obs_vars</span><span class='op'>)</span>, diff --git a/docs/dev/reference/plot.mmkin-1.png b/docs/dev/reference/plot.mmkin-1.png Binary files differindex 438d5a53..f12b7907 100644 --- a/docs/dev/reference/plot.mmkin-1.png +++ b/docs/dev/reference/plot.mmkin-1.png diff --git a/docs/dev/reference/plot.mmkin-2.png b/docs/dev/reference/plot.mmkin-2.png Binary files differindex ee04b3c4..e3127554 100644 --- a/docs/dev/reference/plot.mmkin-2.png +++ b/docs/dev/reference/plot.mmkin-2.png diff --git a/docs/dev/reference/plot.mmkin-3.png b/docs/dev/reference/plot.mmkin-3.png Binary files differindex e06ed002..5448976e 100644 --- a/docs/dev/reference/plot.mmkin-3.png +++ b/docs/dev/reference/plot.mmkin-3.png diff --git a/docs/dev/reference/plot.mmkin-4.png b/docs/dev/reference/plot.mmkin-4.png Binary files differindex 5869df55..9a25fc50 100644 --- a/docs/dev/reference/plot.mmkin-4.png +++ b/docs/dev/reference/plot.mmkin-4.png diff --git a/docs/dev/reference/plot.mmkin-5.png b/docs/dev/reference/plot.mmkin-5.png Binary files differindex 927c573b..82b422b5 100644 --- a/docs/dev/reference/plot.mmkin-5.png +++ b/docs/dev/reference/plot.mmkin-5.png diff --git a/docs/dev/reference/plot.mmkin.html b/docs/dev/reference/plot.mmkin.html index 32da836d..ee80c6e4 100644 --- a/docs/dev/reference/plot.mmkin.html +++ b/docs/dev/reference/plot.mmkin.html @@ -125,7 +125,7 @@ the fit of at least one model to the same dataset is shown." /> <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin/"> - <span class="fab fa fab fa-github fa-lg"></span> + <span class="fab fa-github fa-lg"></span> </a> </li> @@ -160,6 +160,7 @@ the fit of at least one model to the same dataset is shown.</p> main <span class='op'>=</span> <span class='st'>"auto"</span>, legends <span class='op'>=</span> <span class='fl'>1</span>, resplot <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"time"</span>, <span class='st'>"errmod"</span><span class='op'>)</span>, + ylab <span class='op'>=</span> <span class='st'>"Residue"</span>, standardized <span class='op'>=</span> <span class='cn'>FALSE</span>, show_errmin <span class='op'>=</span> <span class='cn'>TRUE</span>, errmin_var <span class='op'>=</span> <span class='st'>"All data"</span>, @@ -193,6 +194,10 @@ column.</p></td> values, with the error model, using <code><a href='mkinerrplot.html'>mkinerrplot</a></code>.</p></td> </tr> <tr> + <th>ylab</th> + <td><p>Label for the y axis.</p></td> + </tr> + <tr> <th>standardized</th> <td><p>Should the residuals be standardized? This option is passed to <code><a href='mkinresplot.html'>mkinresplot</a></code>, it only takes effect if diff --git a/docs/dev/reference/saem.html b/docs/dev/reference/saem.html index a832e911..59589378 100644 --- a/docs/dev/reference/saem.html +++ b/docs/dev/reference/saem.html @@ -162,7 +162,6 @@ Expectation Maximisation algorithm (SAEM).</p> control <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>displayProgress <span class='op'>=</span> <span class='cn'>FALSE</span>, print <span class='op'>=</span> <span class='cn'>FALSE</span>, save <span class='op'>=</span> <span class='cn'>FALSE</span>, save.graphs <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>, verbose <span class='op'>=</span> <span class='cn'>FALSE</span>, - suppressPlot <span class='op'>=</span> <span class='cn'>TRUE</span>, quiet <span class='op'>=</span> <span class='cn'>FALSE</span>, <span class='va'>...</span> <span class='op'>)</span> @@ -221,11 +220,6 @@ automatic choice is not desired</p></td> type <a href='https://rdrr.io/pkg/saemix/man/SaemixModel-class.html'>saemix::SaemixModel</a> and <a href='https://rdrr.io/pkg/saemix/man/SaemixData-class.html'>saemix::SaemixData</a>?</p></td> </tr> <tr> - <th>suppressPlot</th> - <td><p>Should we suppress any plotting that is done -by the saemix function?</p></td> - </tr> - <tr> <th>quiet</th> <td><p>Should we suppress the messages saemix prints at the beginning and the end of the optimisation process?</p></td> @@ -267,36 +261,33 @@ using <a href='mmkin.html'>mmkin</a>.</p> state.ini <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fl'>100</span><span class='op'>)</span>, fixed_initials <span class='op'>=</span> <span class='st'>"parent"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> <span class='va'>f_saem_p0_fixed</span> <span class='op'><-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent_p0_fixed</span><span class='op'>)</span> </div><div class='output co'>#> Running main SAEM algorithm -#> [1] "Mon Jan 11 12:42:01 2021" +#> [1] "Mon Jan 25 14:41:42 2021" #> .... #> Minimisation finished -#> [1] "Mon Jan 11 12:42:03 2021"</div><div class='input'> +#> [1] "Mon Jan 25 14:41:43 2021"</div><div class='input'> <span class='va'>f_mmkin_parent</span> <span class='op'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"FOMC"</span>, <span class='st'>"DFOP"</span><span class='op'>)</span>, <span class='va'>ds</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> <span class='va'>f_saem_sfo</span> <span class='op'><-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"SFO"</span>, <span class='op'>]</span><span class='op'>)</span> </div><div class='output co'>#> Running main SAEM algorithm -#> [1] "Mon Jan 11 12:42:04 2021" +#> [1] "Mon Jan 25 14:41:45 2021" #> .... #> Minimisation finished -#> [1] "Mon Jan 11 12:42:06 2021"</div><div class='input'><span class='va'>f_saem_fomc</span> <span class='op'><-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span><span class='op'>)</span> +#> [1] "Mon Jan 25 14:41:46 2021"</div><div class='input'><span class='va'>f_saem_fomc</span> <span class='op'><-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span><span class='op'>)</span> </div><div class='output co'>#> Running main SAEM algorithm -#> [1] "Mon Jan 11 12:42:06 2021" +#> [1] "Mon Jan 25 14:41:47 2021" #> .... #> Minimisation finished -#> [1] "Mon Jan 11 12:42:08 2021"</div><div class='input'><span class='va'>f_saem_dfop</span> <span class='op'><-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"DFOP"</span>, <span class='op'>]</span><span class='op'>)</span> +#> [1] "Mon Jan 25 14:41:49 2021"</div><div class='input'><span class='va'>f_saem_dfop</span> <span class='op'><-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"DFOP"</span>, <span class='op'>]</span><span class='op'>)</span> </div><div class='output co'>#> Running main SAEM algorithm -#> [1] "Mon Jan 11 12:42:09 2021" +#> [1] "Mon Jan 25 14:41:49 2021" #> .... #> Minimisation finished -#> [1] "Mon Jan 11 12:42:12 2021"</div><div class='input'> +#> [1] "Mon Jan 25 14:41:52 2021"</div><div class='input'> <span class='co'># The returned saem.mmkin object contains an SaemixObject, therefore we can use</span> <span class='co'># functions from saemix</span> <span class='kw'><a href='https://rdrr.io/r/base/library.html'>library</a></span><span class='op'>(</span><span class='va'>saemix</span><span class='op'>)</span> </div><div class='output co'>#> <span class='message'>Package saemix, version 3.1.9000</span> #> <span class='message'> please direct bugs, questions and feedback to emmanuelle.comets@inserm.fr</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/compare.saemix.html'>compare.saemix</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='va'>f_saem_sfo</span><span class='op'>$</span><span class='va'>so</span>, <span class='va'>f_saem_fomc</span><span class='op'>$</span><span class='va'>so</span>, <span class='va'>f_saem_dfop</span><span class='op'>$</span><span class='va'>so</span><span class='op'>)</span><span class='op'>)</span> -</div><div class='output co'>#> Likelihoods computed by importance sampling </div><div class='output co'>#> AIC BIC -#> 1 624.2484 622.2956 -#> 2 467.7096 464.9757 -#> 3 495.4373 491.9222</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html'>plot</a></span><span class='op'>(</span><span class='va'>f_saem_fomc</span><span class='op'>$</span><span class='va'>so</span>, plot.type <span class='op'>=</span> <span class='st'>"convergence"</span><span class='op'>)</span> +</div><div class='output co'>#> <span class='error'>Error in compare.saemix(list(f_saem_sfo$so, f_saem_fomc$so, f_saem_dfop$so)): 'compare.saemix' requires at least two models.</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html'>plot</a></span><span class='op'>(</span><span class='va'>f_saem_fomc</span><span class='op'>$</span><span class='va'>so</span>, plot.type <span class='op'>=</span> <span class='st'>"convergence"</span><span class='op'>)</span> </div><div class='output co'>#> Plotting convergence plots</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html'>plot</a></span><span class='op'>(</span><span class='va'>f_saem_fomc</span><span class='op'>$</span><span class='va'>so</span>, plot.type <span class='op'>=</span> <span class='st'>"individual.fit"</span><span class='op'>)</span> </div><div class='img'><img src='saem-1.png' alt='' width='700' height='433' /></div><div class='output co'>#> Plotting individual fits</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html'>plot</a></span><span class='op'>(</span><span class='va'>f_saem_fomc</span><span class='op'>$</span><span class='va'>so</span>, plot.type <span class='op'>=</span> <span class='st'>"npde"</span><span class='op'>)</span> </div><div class='img'><img src='saem-2.png' alt='' width='700' height='433' /></div><div class='output co'>#> Simulating data using nsim = 1000 simulated datasets @@ -333,13 +324,11 @@ using <a href='mmkin.html'>mmkin</a>.</p> <span class='va'>f_mmkin_parent_tc</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span><span class='op'>(</span><span class='va'>f_mmkin_parent</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span><span class='op'>)</span> <span class='va'>f_saem_fomc_tc</span> <span class='op'><-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent_tc</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span><span class='op'>)</span> </div><div class='output co'>#> Running main SAEM algorithm -#> [1] "Mon Jan 11 12:42:14 2021" +#> [1] "Mon Jan 25 14:41:55 2021" #> .... #> Minimisation finished -#> [1] "Mon Jan 11 12:42:19 2021"</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/compare.saemix.html'>compare.saemix</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='va'>f_saem_fomc</span><span class='op'>$</span><span class='va'>so</span>, <span class='va'>f_saem_fomc_tc</span><span class='op'>$</span><span class='va'>so</span><span class='op'>)</span><span class='op'>)</span> -</div><div class='output co'>#> Likelihoods computed by importance sampling </div><div class='output co'>#> AIC BIC -#> 1 467.7096 464.9757 -#> 2 469.5208 466.3963</div><div class='input'> +#> [1] "Mon Jan 25 14:42:00 2021"</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/compare.saemix.html'>compare.saemix</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='va'>f_saem_fomc</span><span class='op'>$</span><span class='va'>so</span>, <span class='va'>f_saem_fomc_tc</span><span class='op'>$</span><span class='va'>so</span><span class='op'>)</span><span class='op'>)</span> +</div><div class='output co'>#> <span class='error'>Error in compare.saemix(list(f_saem_fomc$so, f_saem_fomc_tc$so)): 'compare.saemix' requires at least two models.</span></div><div class='input'> <span class='va'>sfo_sfo</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"A1"</span><span class='op'>)</span>, A1 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span><span class='op'>)</span> </div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'><span class='va'>fomc_sfo</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"FOMC"</span>, <span class='st'>"A1"</span><span class='op'>)</span>, @@ -357,15 +346,15 @@ using <a href='mmkin.html'>mmkin</a>.</p> <span class='co'># four minutes</span> <span class='va'>f_saem_sfo_sfo</span> <span class='op'><-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin</span><span class='op'>[</span><span class='st'>"SFO-SFO"</span>, <span class='op'>]</span><span class='op'>)</span> </div><div class='output co'>#> Running main SAEM algorithm -#> [1] "Mon Jan 11 12:42:22 2021" +#> [1] "Mon Jan 25 14:42:02 2021" #> .... #> Minimisation finished -#> [1] "Mon Jan 11 12:42:27 2021"</div><div class='input'><span class='va'>f_saem_dfop_sfo</span> <span class='op'><-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin</span><span class='op'>[</span><span class='st'>"DFOP-SFO"</span>, <span class='op'>]</span><span class='op'>)</span> +#> [1] "Mon Jan 25 14:42:07 2021"</div><div class='input'><span class='va'>f_saem_dfop_sfo</span> <span class='op'><-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin</span><span class='op'>[</span><span class='st'>"DFOP-SFO"</span>, <span class='op'>]</span><span class='op'>)</span> </div><div class='output co'>#> Running main SAEM algorithm -#> [1] "Mon Jan 11 12:42:28 2021" +#> [1] "Mon Jan 25 14:42:08 2021" #> .... #> Minimisation finished -#> [1] "Mon Jan 11 12:42:37 2021"</div><div class='input'><span class='co'># We can use print, plot and summary methods to check the results</span> +#> [1] "Mon Jan 25 14:42:17 2021"</div><div class='input'><span class='co'># We can use print, plot and summary methods to check the results</span> <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>f_saem_dfop_sfo</span><span class='op'>)</span> </div><div class='output co'>#> Kinetic nonlinear mixed-effects model fit by SAEM #> Structural model: @@ -408,8 +397,8 @@ using <a href='mmkin.html'>mmkin</a>.</p> </div><div class='output co'>#> saemix version used for fitting: 3.1.9000 #> mkin version used for pre-fitting: 0.9.50.4 #> R version used for fitting: 4.0.3 -#> Date of fit: Mon Jan 11 12:42:38 2021 -#> Date of summary: Mon Jan 11 12:42:38 2021 +#> Date of fit: Mon Jan 25 14:42:18 2021 +#> Date of summary: Mon Jan 25 14:42:18 2021 #> #> Equations: #> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -424,7 +413,7 @@ using <a href='mmkin.html'>mmkin</a>.</p> #> #> Model predictions using solution type analytical #> -#> Fitted in 10.092 s using 300, 100 iterations +#> Fitted in 9.954 s using 300, 100 iterations #> #> Variance model: Constant variance #> diff --git a/man/plot.mkinfit.Rd b/man/plot.mkinfit.Rd index bf38c5a5..9fd4c038 100644 --- a/man/plot.mkinfit.Rd +++ b/man/plot.mkinfit.Rd @@ -12,7 +12,7 @@ fit = x, obs_vars = names(fit$mkinmod$map), xlab = "Time", - ylab = "Observed", + ylab = "Residue", xlim = range(fit$data$time), ylim = "default", col_obs = 1:length(obs_vars), diff --git a/man/plot.mmkin.Rd b/man/plot.mmkin.Rd index 998e25e1..c127be8c 100644 --- a/man/plot.mmkin.Rd +++ b/man/plot.mmkin.Rd @@ -10,6 +10,7 @@ of an mmkin object} main = "auto", legends = 1, resplot = c("time", "errmod"), + ylab = "Residue", standardized = FALSE, show_errmin = TRUE, errmin_var = "All data", @@ -32,6 +33,8 @@ column.} \code{\link{mkinresplot}}, or as squared residuals against predicted values, with the error model, using \code{\link{mkinerrplot}}.} +\item{ylab}{Label for the y axis.} + \item{standardized}{Should the residuals be standardized? This option is passed to \code{\link{mkinresplot}}, it only takes effect if \code{resplot = "time"}.} diff --git a/tests/figs/evaluations-according-to-2015-nafta-guidance/nafta-sop-appendix-b.svg b/tests/figs/evaluations-according-to-2015-nafta-guidance/nafta-sop-appendix-b.svg index 617e39b3..d63d8da2 100644 --- a/tests/figs/evaluations-according-to-2015-nafta-guidance/nafta-sop-appendix-b.svg +++ b/tests/figs/evaluations-according-to-2015-nafta-guidance/nafta-sop-appendix-b.svg @@ -47,7 +47,7 @@ </clipPath> </defs> <g clip-path='url(#cpMC4wMHwzNjAuMDB8MTk4LjYyfDAuMDA=)'><text x='180.92' y='206.68' style='font-size: 8.40px; font-family: Liberation Sans;' textLength='18.33px' lengthAdjust='spacingAndGlyphs'>Time</text></g> -<g clip-path='url(#cpMC4wMHwzNjAuMDB8MTk4LjYyfDAuMDA=)'><text transform='translate(9.07,123.07) rotate(-90)' style='font-size: 8.40px; font-family: Liberation Sans;' textLength='36.42px' lengthAdjust='spacingAndGlyphs'>Observed</text></g> +<g clip-path='url(#cpMC4wMHwzNjAuMDB8MTk4LjYyfDAuMDA=)'><text transform='translate(9.07,120.26) rotate(-90)' style='font-size: 8.40px; font-family: Liberation Sans;' textLength='30.81px' lengthAdjust='spacingAndGlyphs'>Residue</text></g> <defs> <clipPath id='cpNDEuMzN8MzM4LjgzfDE2OC4zOHw0MS4zMw=='> <rect x='41.33' y='41.33' width='297.50' height='127.05' /> @@ -195,7 +195,7 @@ </clipPath> </defs> <g clip-path='url(#cpMC4wMHwzNjAuMDB8Mzc3LjM4fDE5OC42Mg==)'><text x='180.92' y='385.44' style='font-size: 8.40px; font-family: Liberation Sans;' textLength='18.33px' lengthAdjust='spacingAndGlyphs'>Time</text></g> -<g clip-path='url(#cpMC4wMHwzNjAuMDB8Mzc3LjM4fDE5OC42Mg==)'><text transform='translate(9.07,301.67) rotate(-90)' style='font-size: 8.40px; font-family: Liberation Sans;' textLength='36.42px' lengthAdjust='spacingAndGlyphs'>Observed</text></g> +<g clip-path='url(#cpMC4wMHwzNjAuMDB8Mzc3LjM4fDE5OC42Mg==)'><text transform='translate(9.07,298.87) rotate(-90)' style='font-size: 8.40px; font-family: Liberation Sans;' textLength='30.81px' lengthAdjust='spacingAndGlyphs'>Residue</text></g> <defs> <clipPath id='cpNDEuMzN8MzM4LjgzfDM0Ny4xNHwyMTkuNzk='> <rect x='41.33' y='219.79' width='297.50' height='127.35' /> @@ -343,7 +343,7 @@ </clipPath> </defs> <g clip-path='url(#cpMC4wMHwzNjAuMDB8NTc2LjAwfDM3Ny4zOA==)'><text x='180.92' y='562.90' style='font-size: 8.40px; font-family: Liberation Sans;' textLength='18.33px' lengthAdjust='spacingAndGlyphs'>Time</text></g> -<g clip-path='url(#cpMC4wMHwzNjAuMDB8NTc2LjAwfDM3Ny4zOA==)'><text transform='translate(9.07,479.78) rotate(-90)' style='font-size: 8.40px; font-family: Liberation Sans;' textLength='36.42px' lengthAdjust='spacingAndGlyphs'>Observed</text></g> +<g clip-path='url(#cpMC4wMHwzNjAuMDB8NTc2LjAwfDM3Ny4zOA==)'><text transform='translate(9.07,476.98) rotate(-90)' style='font-size: 8.40px; font-family: Liberation Sans;' textLength='30.81px' lengthAdjust='spacingAndGlyphs'>Residue</text></g> <defs> <clipPath id='cpNDEuMzN8MzM4LjgzfDUyNC41OXwzOTguNTU='> <rect x='41.33' y='398.55' width='297.50' height='126.04' /> diff --git a/tests/figs/evaluations-according-to-2015-nafta-guidance/plot-nafta-analysis.svg b/tests/figs/evaluations-according-to-2015-nafta-guidance/plot-nafta-analysis.svg index 5e98487b..283c5c9e 100644 --- a/tests/figs/evaluations-according-to-2015-nafta-guidance/plot-nafta-analysis.svg +++ b/tests/figs/evaluations-according-to-2015-nafta-guidance/plot-nafta-analysis.svg @@ -41,7 +41,7 @@ </clipPath> </defs> <g clip-path='url(#cpMC4wMHwzNjAuMDB8MTk4LjYyfDAuMDA=)'><text x='180.92' y='206.68' style='font-size: 8.40px; font-family: Liberation Sans;' textLength='18.33px' lengthAdjust='spacingAndGlyphs'>Time</text></g> -<g clip-path='url(#cpMC4wMHwzNjAuMDB8MTk4LjYyfDAuMDA=)'><text transform='translate(9.07,123.07) rotate(-90)' style='font-size: 8.40px; font-family: Liberation Sans;' textLength='36.42px' lengthAdjust='spacingAndGlyphs'>Observed</text></g> +<g clip-path='url(#cpMC4wMHwzNjAuMDB8MTk4LjYyfDAuMDA=)'><text transform='translate(9.07,120.26) rotate(-90)' style='font-size: 8.40px; font-family: Liberation Sans;' textLength='30.81px' lengthAdjust='spacingAndGlyphs'>Residue</text></g> <defs> <clipPath id='cpNDEuMzN8MzM4LjgzfDE2OC4zOHw0MS4zMw=='> <rect x='41.33' y='41.33' width='297.50' height='127.05' /> @@ -189,7 +189,7 @@ </clipPath> </defs> <g clip-path='url(#cpMC4wMHwzNjAuMDB8Mzc3LjM4fDE5OC42Mg==)'><text x='180.92' y='385.44' style='font-size: 8.40px; font-family: Liberation Sans;' textLength='18.33px' lengthAdjust='spacingAndGlyphs'>Time</text></g> -<g clip-path='url(#cpMC4wMHwzNjAuMDB8Mzc3LjM4fDE5OC42Mg==)'><text transform='translate(9.07,301.67) rotate(-90)' style='font-size: 8.40px; font-family: Liberation Sans;' textLength='36.42px' lengthAdjust='spacingAndGlyphs'>Observed</text></g> +<g clip-path='url(#cpMC4wMHwzNjAuMDB8Mzc3LjM4fDE5OC42Mg==)'><text transform='translate(9.07,298.87) rotate(-90)' style='font-size: 8.40px; font-family: Liberation Sans;' textLength='30.81px' lengthAdjust='spacingAndGlyphs'>Residue</text></g> <defs> <clipPath id='cpNDEuMzN8MzM4LjgzfDM0Ny4xNHwyMTkuNzk='> <rect x='41.33' y='219.79' width='297.50' height='127.35' /> @@ -337,7 +337,7 @@ </clipPath> </defs> <g clip-path='url(#cpMC4wMHwzNjAuMDB8NTc2LjAwfDM3Ny4zOA==)'><text x='180.92' y='562.90' style='font-size: 8.40px; font-family: Liberation Sans;' textLength='18.33px' lengthAdjust='spacingAndGlyphs'>Time</text></g> -<g clip-path='url(#cpMC4wMHwzNjAuMDB8NTc2LjAwfDM3Ny4zOA==)'><text transform='translate(9.07,479.78) rotate(-90)' style='font-size: 8.40px; font-family: Liberation Sans;' textLength='36.42px' lengthAdjust='spacingAndGlyphs'>Observed</text></g> +<g clip-path='url(#cpMC4wMHwzNjAuMDB8NTc2LjAwfDM3Ny4zOA==)'><text transform='translate(9.07,476.98) rotate(-90)' style='font-size: 8.40px; font-family: Liberation Sans;' textLength='30.81px' lengthAdjust='spacingAndGlyphs'>Residue</text></g> <defs> <clipPath id='cpNDEuMzN8MzM4LjgzfDUyNC41OXwzOTguNTU='> <rect x='41.33' y='398.55' width='297.50' height='126.04' /> diff --git a/tests/figs/plotting/mkinfit-plot-for-focus-c-with-defaults.svg b/tests/figs/plotting/mkinfit-plot-for-focus-c-with-defaults.svg index 82577502..ef238a51 100644 --- a/tests/figs/plotting/mkinfit-plot-for-focus-c-with-defaults.svg +++ b/tests/figs/plotting/mkinfit-plot-for-focus-c-with-defaults.svg @@ -40,7 +40,7 @@ <text transform='translate(41.76,106.75) rotate(-90)' style='font-size: 12.00px; font-family: Liberation Sans;' textLength='13.34px' lengthAdjust='spacingAndGlyphs'>80</text> <polyline points='59.04,502.56 689.76,502.56 689.76,59.04 59.04,59.04 59.04,502.56 ' style='stroke-width: 0.75;' /> <text x='361.29' y='557.28' style='font-size: 12.00px; font-family: Liberation Sans;' textLength='26.22px' lengthAdjust='spacingAndGlyphs'>Time</text> -<text transform='translate(12.96,306.81) rotate(-90)' style='font-size: 12.00px; font-family: Liberation Sans;' textLength='52.02px' lengthAdjust='spacingAndGlyphs'>Observed</text> +<text transform='translate(12.96,302.82) rotate(-90)' style='font-size: 12.00px; font-family: Liberation Sans;' textLength='44.03px' lengthAdjust='spacingAndGlyphs'>Residue</text> <defs> <clipPath id='cpNTkuMDR8Njg5Ljc2fDUwMi41Nnw1OS4wNA=='> <rect x='59.04' y='59.04' width='630.72' height='443.52' /> diff --git a/tests/figs/plotting/mkinfit-plot-for-focus-c-with-residuals-like-in-gmkin.svg b/tests/figs/plotting/mkinfit-plot-for-focus-c-with-residuals-like-in-gmkin.svg index 8d16bfd3..a84e170d 100644 --- a/tests/figs/plotting/mkinfit-plot-for-focus-c-with-residuals-like-in-gmkin.svg +++ b/tests/figs/plotting/mkinfit-plot-for-focus-c-with-residuals-like-in-gmkin.svg @@ -45,7 +45,7 @@ </clipPath> </defs> <g clip-path='url(#cpMC4wMHw3MjAuMDB8MzQ5LjA5fDAuMDA=)'><text x='361.29' y='359.17' style='font-size: 12.00px; font-family: Liberation Sans;' textLength='26.22px' lengthAdjust='spacingAndGlyphs'>Time</text></g> -<g clip-path='url(#cpMC4wMHw3MjAuMDB8MzQ5LjA5fDAuMDA=)'><text transform='translate(12.96,207.75) rotate(-90)' style='font-size: 12.00px; font-family: Liberation Sans;' textLength='52.02px' lengthAdjust='spacingAndGlyphs'>Observed</text></g> +<g clip-path='url(#cpMC4wMHw3MjAuMDB8MzQ5LjA5fDAuMDA=)'><text transform='translate(12.96,203.76) rotate(-90)' style='font-size: 12.00px; font-family: Liberation Sans;' textLength='44.03px' lengthAdjust='spacingAndGlyphs'>Residue</text></g> <defs> <clipPath id='cpNTkuMDR8Njg5Ljc2fDMwNC40NXw1OS4wNA=='> <rect x='59.04' y='59.04' width='630.72' height='245.41' /> diff --git a/tests/figs/plotting/mkinfit-plot-for-focus-c-with-sep-true.svg b/tests/figs/plotting/mkinfit-plot-for-focus-c-with-sep-true.svg index 327161da..9b16c583 100644 --- a/tests/figs/plotting/mkinfit-plot-for-focus-c-with-sep-true.svg +++ b/tests/figs/plotting/mkinfit-plot-for-focus-c-with-sep-true.svg @@ -45,7 +45,7 @@ </clipPath> </defs> <g clip-path='url(#cpMC4wMHwzNjAuMDB8NTc2LjAwfDAuMDA=)'><text x='181.29' y='557.28' style='font-size: 12.00px; font-family: Liberation Sans;' textLength='26.22px' lengthAdjust='spacingAndGlyphs'>Time</text></g> -<g clip-path='url(#cpMC4wMHwzNjAuMDB8NTc2LjAwfDAuMDA=)'><text transform='translate(12.96,306.81) rotate(-90)' style='font-size: 12.00px; font-family: Liberation Sans;' textLength='52.02px' lengthAdjust='spacingAndGlyphs'>Observed</text></g> +<g clip-path='url(#cpMC4wMHwzNjAuMDB8NTc2LjAwfDAuMDA=)'><text transform='translate(12.96,302.82) rotate(-90)' style='font-size: 12.00px; font-family: Liberation Sans;' textLength='44.03px' lengthAdjust='spacingAndGlyphs'>Residue</text></g> <defs> <clipPath id='cpNTkuMDR8MzI5Ljc2fDUwMi41Nnw1OS4wNA=='> <rect x='59.04' y='59.04' width='270.72' height='443.52' /> diff --git a/tests/figs/plotting/mmkin-plot-for-focus-c.svg b/tests/figs/plotting/mmkin-plot-for-focus-c.svg index 1c697328..0f824e6c 100644 --- a/tests/figs/plotting/mmkin-plot-for-focus-c.svg +++ b/tests/figs/plotting/mmkin-plot-for-focus-c.svg @@ -45,7 +45,7 @@ </clipPath> </defs> <g clip-path='url(#cpMC4wMHwzNjAuMDB8MTUxLjU4fDAuMDA=)'><text x='180.92' y='159.64' style='font-size: 8.40px; font-family: Liberation Sans;' textLength='18.33px' lengthAdjust='spacingAndGlyphs'>Time</text></g> -<g clip-path='url(#cpMC4wMHwzNjAuMDB8MTUxLjU4fDAuMDA=)'><text transform='translate(9.07,99.54) rotate(-90)' style='font-size: 8.40px; font-family: Liberation Sans;' textLength='36.42px' lengthAdjust='spacingAndGlyphs'>Observed</text></g> +<g clip-path='url(#cpMC4wMHwzNjAuMDB8MTUxLjU4fDAuMDA=)'><text transform='translate(9.07,96.74) rotate(-90)' style='font-size: 8.40px; font-family: Liberation Sans;' textLength='30.81px' lengthAdjust='spacingAndGlyphs'>Residue</text></g> <defs> <clipPath id='cpNDEuMzN8MzM4LjgzfDEyMS4zNHw0MS4zMw=='> <rect x='41.33' y='41.33' width='297.50' height='80.01' /> @@ -187,7 +187,7 @@ </clipPath> </defs> <g clip-path='url(#cpMC4wMHwzNjAuMDB8Mjg4LjAwfDE1MS41OA==)'><text x='180.92' y='296.06' style='font-size: 8.40px; font-family: Liberation Sans;' textLength='18.33px' lengthAdjust='spacingAndGlyphs'>Time</text></g> -<g clip-path='url(#cpMC4wMHwzNjAuMDB8Mjg4LjAwfDE1MS41OA==)'><text transform='translate(9.07,233.46) rotate(-90)' style='font-size: 8.40px; font-family: Liberation Sans;' textLength='36.42px' lengthAdjust='spacingAndGlyphs'>Observed</text></g> +<g clip-path='url(#cpMC4wMHwzNjAuMDB8Mjg4LjAwfDE1MS41OA==)'><text transform='translate(9.07,230.66) rotate(-90)' style='font-size: 8.40px; font-family: Liberation Sans;' textLength='30.81px' lengthAdjust='spacingAndGlyphs'>Residue</text></g> <defs> <clipPath id='cpNDEuMzN8MzM4LjgzfDI1Ny43NnwxNzIuNzU='> <rect x='41.33' y='172.75' width='297.50' height='85.01' /> @@ -327,7 +327,7 @@ </clipPath> </defs> <g clip-path='url(#cpMC4wMHwzNjAuMDB8NDI0LjQyfDI4OC4wMA==)'><text x='180.92' y='432.49' style='font-size: 8.40px; font-family: Liberation Sans;' textLength='18.33px' lengthAdjust='spacingAndGlyphs'>Time</text></g> -<g clip-path='url(#cpMC4wMHwzNjAuMDB8NDI0LjQyfDI4OC4wMA==)'><text transform='translate(9.07,369.89) rotate(-90)' style='font-size: 8.40px; font-family: Liberation Sans;' textLength='36.42px' lengthAdjust='spacingAndGlyphs'>Observed</text></g> +<g clip-path='url(#cpMC4wMHwzNjAuMDB8NDI0LjQyfDI4OC4wMA==)'><text transform='translate(9.07,367.08) rotate(-90)' style='font-size: 8.40px; font-family: Liberation Sans;' textLength='30.81px' lengthAdjust='spacingAndGlyphs'>Residue</text></g> <defs> <clipPath id='cpNDEuMzN8MzM4LjgzfDM5NC4xOHwzMDkuMTc='> <rect x='41.33' y='309.17' width='297.50' height='85.01' /> @@ -466,7 +466,7 @@ </clipPath> </defs> <g clip-path='url(#cpMC4wMHwzNjAuMDB8NTc2LjAwfDQyNC40Mg==)'><text x='180.92' y='562.90' style='font-size: 8.40px; font-family: Liberation Sans;' textLength='18.33px' lengthAdjust='spacingAndGlyphs'>Time</text></g> -<g clip-path='url(#cpMC4wMHwzNjAuMDB8NTc2LjAwfDQyNC40Mg==)'><text transform='translate(9.07,503.30) rotate(-90)' style='font-size: 8.40px; font-family: Liberation Sans;' textLength='36.42px' lengthAdjust='spacingAndGlyphs'>Observed</text></g> +<g clip-path='url(#cpMC4wMHwzNjAuMDB8NTc2LjAwfDQyNC40Mg==)'><text transform='translate(9.07,500.50) rotate(-90)' style='font-size: 8.40px; font-family: Liberation Sans;' textLength='30.81px' lengthAdjust='spacingAndGlyphs'>Residue</text></g> <defs> <clipPath id='cpNDEuMzN8MzM4LjgzfDUyNC41OXw0NDUuNTk='> <rect x='41.33' y='445.59' width='297.50' height='79.00' /> diff --git a/tests/figs/plotting/mmkin-plot-for-sfo-focus-c-and-d.svg b/tests/figs/plotting/mmkin-plot-for-sfo-focus-c-and-d.svg index 72496e86..40aa6bef 100644 --- a/tests/figs/plotting/mmkin-plot-for-sfo-focus-c-and-d.svg +++ b/tests/figs/plotting/mmkin-plot-for-sfo-focus-c-and-d.svg @@ -45,7 +45,7 @@ </clipPath> </defs> <g clip-path='url(#cpMC4wMHwzNjAuMDB8Mjg4LjAwfDAuMDA=)'><text x='180.92' y='296.06' style='font-size: 8.40px; font-family: Liberation Sans;' textLength='18.33px' lengthAdjust='spacingAndGlyphs'>Time</text></g> -<g clip-path='url(#cpMC4wMHwzNjAuMDB8Mjg4LjAwfDAuMDA=)'><text transform='translate(9.07,167.75) rotate(-90)' style='font-size: 8.40px; font-family: Liberation Sans;' textLength='36.42px' lengthAdjust='spacingAndGlyphs'>Observed</text></g> +<g clip-path='url(#cpMC4wMHwzNjAuMDB8Mjg4LjAwfDAuMDA=)'><text transform='translate(9.07,164.95) rotate(-90)' style='font-size: 8.40px; font-family: Liberation Sans;' textLength='30.81px' lengthAdjust='spacingAndGlyphs'>Residue</text></g> <defs> <clipPath id='cpNDEuMzN8MzM4LjgzfDI1Ny43Nnw0MS4zMw=='> <rect x='41.33' y='41.33' width='297.50' height='216.43' /> @@ -183,7 +183,7 @@ </clipPath> </defs> <g clip-path='url(#cpMC4wMHwzNjAuMDB8NTc2LjAwfDI4OC4wMA==)'><text x='180.92' y='562.90' style='font-size: 8.40px; font-family: Liberation Sans;' textLength='18.33px' lengthAdjust='spacingAndGlyphs'>Time</text></g> -<g clip-path='url(#cpMC4wMHwzNjAuMDB8NTc2LjAwfDI4OC4wMA==)'><text transform='translate(9.07,435.09) rotate(-90)' style='font-size: 8.40px; font-family: Liberation Sans;' textLength='36.42px' lengthAdjust='spacingAndGlyphs'>Observed</text></g> +<g clip-path='url(#cpMC4wMHwzNjAuMDB8NTc2LjAwfDI4OC4wMA==)'><text transform='translate(9.07,432.29) rotate(-90)' style='font-size: 8.40px; font-family: Liberation Sans;' textLength='30.81px' lengthAdjust='spacingAndGlyphs'>Residue</text></g> <defs> <clipPath id='cpNDEuMzN8MzM4LjgzfDUyNC41OXwzMDkuMTc='> <rect x='41.33' y='309.17' width='297.50' height='215.42' /> diff --git a/tests/figs/plotting/plot-err-for-focus-d.svg b/tests/figs/plotting/plot-err-for-focus-d.svg index e7f05168..53049f6e 100644 --- a/tests/figs/plotting/plot-err-for-focus-d.svg +++ b/tests/figs/plotting/plot-err-for-focus-d.svg @@ -47,7 +47,7 @@ </clipPath> </defs> <g clip-path='url(#cpMC4wMHwzNjAuMDB8NTc2LjAwfDAuMDA=)'><text x='181.29' y='557.28' style='font-size: 12.00px; font-family: Liberation Sans;' textLength='26.22px' lengthAdjust='spacingAndGlyphs'>Time</text></g> -<g clip-path='url(#cpMC4wMHwzNjAuMDB8NTc2LjAwfDAuMDA=)'><text transform='translate(12.96,306.81) rotate(-90)' style='font-size: 12.00px; font-family: Liberation Sans;' textLength='52.02px' lengthAdjust='spacingAndGlyphs'>Observed</text></g> +<g clip-path='url(#cpMC4wMHwzNjAuMDB8NTc2LjAwfDAuMDA=)'><text transform='translate(12.96,302.82) rotate(-90)' style='font-size: 12.00px; font-family: Liberation Sans;' textLength='44.03px' lengthAdjust='spacingAndGlyphs'>Residue</text></g> <defs> <clipPath id='cpNTkuMDR8MzI5Ljc2fDUwMi41Nnw1OS4wNA=='> <rect x='59.04' y='59.04' width='270.72' height='443.52' /> diff --git a/tests/figs/plotting/plot-errmod-with-focus-c-tc.svg b/tests/figs/plotting/plot-errmod-with-focus-c-tc.svg index 8adefc27..b0d84808 100644 --- a/tests/figs/plotting/plot-errmod-with-focus-c-tc.svg +++ b/tests/figs/plotting/plot-errmod-with-focus-c-tc.svg @@ -45,7 +45,7 @@ </clipPath> </defs> <g clip-path='url(#cpMC4wMHwzNjAuMDB8NTc2LjAwfDAuMDA=)'><text x='181.29' y='557.28' style='font-size: 12.00px; font-family: Liberation Sans;' textLength='26.22px' lengthAdjust='spacingAndGlyphs'>Time</text></g> -<g clip-path='url(#cpMC4wMHwzNjAuMDB8NTc2LjAwfDAuMDA=)'><text transform='translate(12.96,306.81) rotate(-90)' style='font-size: 12.00px; font-family: Liberation Sans;' textLength='52.02px' lengthAdjust='spacingAndGlyphs'>Observed</text></g> +<g clip-path='url(#cpMC4wMHwzNjAuMDB8NTc2LjAwfDAuMDA=)'><text transform='translate(12.96,302.82) rotate(-90)' style='font-size: 12.00px; font-family: Liberation Sans;' textLength='44.03px' lengthAdjust='spacingAndGlyphs'>Residue</text></g> <defs> <clipPath id='cpNTkuMDR8MzI5Ljc2fDUwMi41Nnw1OS4wNA=='> <rect x='59.04' y='59.04' width='270.72' height='443.52' /> diff --git a/tests/figs/plotting/plot-errmod-with-focus-d-obs-eigen.svg b/tests/figs/plotting/plot-errmod-with-focus-d-obs-eigen.svg index afd3e064..d5e1b6b2 100644 --- a/tests/figs/plotting/plot-errmod-with-focus-d-obs-eigen.svg +++ b/tests/figs/plotting/plot-errmod-with-focus-d-obs-eigen.svg @@ -47,7 +47,7 @@ </clipPath> </defs> <g clip-path='url(#cpMC4wMHwzNjAuMDB8NTc2LjAwfDAuMDA=)'><text x='181.29' y='557.28' style='font-size: 12.00px; font-family: Liberation Sans;' textLength='26.22px' lengthAdjust='spacingAndGlyphs'>Time</text></g> -<g clip-path='url(#cpMC4wMHwzNjAuMDB8NTc2LjAwfDAuMDA=)'><text transform='translate(12.96,306.81) rotate(-90)' style='font-size: 12.00px; font-family: Liberation Sans;' textLength='52.02px' lengthAdjust='spacingAndGlyphs'>Observed</text></g> +<g clip-path='url(#cpMC4wMHwzNjAuMDB8NTc2LjAwfDAuMDA=)'><text transform='translate(12.96,302.82) rotate(-90)' style='font-size: 12.00px; font-family: Liberation Sans;' textLength='44.03px' lengthAdjust='spacingAndGlyphs'>Residue</text></g> <defs> <clipPath id='cpNTkuMDR8MzI5Ljc2fDUwMi41Nnw1OS4wNA=='> <rect x='59.04' y='59.04' width='270.72' height='443.52' /> diff --git a/tests/figs/plotting/plot-res-for-focus-c.svg b/tests/figs/plotting/plot-res-for-focus-c.svg index 43b94055..226d9014 100644 --- a/tests/figs/plotting/plot-res-for-focus-c.svg +++ b/tests/figs/plotting/plot-res-for-focus-c.svg @@ -45,7 +45,7 @@ </clipPath> </defs> <g clip-path='url(#cpMC4wMHwzNjAuMDB8NTc2LjAwfDAuMDA=)'><text x='181.29' y='557.28' style='font-size: 12.00px; font-family: Liberation Sans;' textLength='26.22px' lengthAdjust='spacingAndGlyphs'>Time</text></g> -<g clip-path='url(#cpMC4wMHwzNjAuMDB8NTc2LjAwfDAuMDA=)'><text transform='translate(12.96,306.81) rotate(-90)' style='font-size: 12.00px; font-family: Liberation Sans;' textLength='52.02px' lengthAdjust='spacingAndGlyphs'>Observed</text></g> +<g clip-path='url(#cpMC4wMHwzNjAuMDB8NTc2LjAwfDAuMDA=)'><text transform='translate(12.96,302.82) rotate(-90)' style='font-size: 12.00px; font-family: Liberation Sans;' textLength='44.03px' lengthAdjust='spacingAndGlyphs'>Residue</text></g> <defs> <clipPath id='cpNTkuMDR8MzI5Ljc2fDUwMi41Nnw1OS4wNA=='> <rect x='59.04' y='59.04' width='270.72' height='443.52' /> diff --git a/tests/figs/plotting/plot-res-for-focus-d.svg b/tests/figs/plotting/plot-res-for-focus-d.svg index ea3388ed..6504365c 100644 --- a/tests/figs/plotting/plot-res-for-focus-d.svg +++ b/tests/figs/plotting/plot-res-for-focus-d.svg @@ -47,7 +47,7 @@ </clipPath> </defs> <g clip-path='url(#cpMC4wMHwzNjAuMDB8NTc2LjAwfDAuMDA=)'><text x='181.29' y='557.28' style='font-size: 12.00px; font-family: Liberation Sans;' textLength='26.22px' lengthAdjust='spacingAndGlyphs'>Time</text></g> -<g clip-path='url(#cpMC4wMHwzNjAuMDB8NTc2LjAwfDAuMDA=)'><text transform='translate(12.96,306.81) rotate(-90)' style='font-size: 12.00px; font-family: Liberation Sans;' textLength='52.02px' lengthAdjust='spacingAndGlyphs'>Observed</text></g> +<g clip-path='url(#cpMC4wMHwzNjAuMDB8NTc2LjAwfDAuMDA=)'><text transform='translate(12.96,302.82) rotate(-90)' style='font-size: 12.00px; font-family: Liberation Sans;' textLength='44.03px' lengthAdjust='spacingAndGlyphs'>Residue</text></g> <defs> <clipPath id='cpNTkuMDR8MzI5Ljc2fDUwMi41Nnw1OS4wNA=='> <rect x='59.04' y='59.04' width='270.72' height='443.52' /> |
