diff options
| -rw-r--r-- | R/plot.mkinfit.R | 8 | ||||
| -rw-r--r-- | docs/reference/plot.mkinfit-3.png | bin | 62528 -> 57593 bytes | |||
| -rw-r--r-- | docs/reference/plot.mkinfit.html | 9 | ||||
| -rw-r--r-- | man/plot.mkinfit.Rd | 7 | ||||
| -rw-r--r-- | test.log | 4 | ||||
| -rw-r--r-- | tests/testthat/FOCUS_2006_D.csf | 2 |
6 files changed, 17 insertions, 13 deletions
diff --git a/R/plot.mkinfit.R b/R/plot.mkinfit.R index e0b3ad13..4b5bfa3a 100644 --- a/R/plot.mkinfit.R +++ b/R/plot.mkinfit.R @@ -33,7 +33,8 @@ if(getRversion() >= '2.15.1') utils::globalVariables(c("type", "variable", "obse #' to the right of the plots of the fitted curves. If this is set to #' 'standardized', a plot of the residuals divided by the standard deviation #' given by the fitted error model will be shown. -#' @param standardized For +#' @param standardized When calling 'plot_res', should the residuals be +#' standardized in the residual plot? #' @param show_errplot Should squared residuals and the error model be shown? #' If only one plot of the fits is shown, this plot is in the lower third of #' the plot. Otherwise, i.e. if "sep_obs" is given, the residual plots will @@ -298,10 +299,11 @@ plot_sep <- function(fit, show_errmin = TRUE, #' @rdname plot.mkinfit #' @export plot_res <- function(fit, sep_obs = FALSE, show_errmin = sep_obs, - show_residuals = ifelse(identical(fit$err_mod, "const"), TRUE, "standardized"), ...) + standardized = ifelse(identical(fit$err_mod, "const"), FALSE, TRUE), ...) { plot.mkinfit(fit, sep_obs = sep_obs, show_errmin = show_errmin, - show_residuals = show_residuals, row_layout = TRUE, ...) + show_residuals = ifelse(standardized, "standardized", TRUE), + row_layout = TRUE, ...) } #' @rdname plot.mkinfit diff --git a/docs/reference/plot.mkinfit-3.png b/docs/reference/plot.mkinfit-3.png Binary files differindex 72bc331e..6910ae47 100644 --- a/docs/reference/plot.mkinfit-3.png +++ b/docs/reference/plot.mkinfit-3.png diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html index a3b912bb..8dc21b06 100644 --- a/docs/reference/plot.mkinfit.html +++ b/docs/reference/plot.mkinfit.html @@ -155,8 +155,8 @@ observed data together with the solution of the fitted model.</p> <span class='st'>"standardized"</span>), <span class='no'>...</span>) <span class='fu'>plot_res</span>(<span class='no'>fit</span>, <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='no'>sep_obs</span>, - <span class='kw'>show_residuals</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/identical.html'>identical</a></span>(<span class='no'>fit</span>$<span class='no'>err_mod</span>, <span class='st'>"const"</span>), <span class='fl'>TRUE</span>, - <span class='st'>"standardized"</span>), <span class='no'>...</span>) + <span class='kw'>standardized</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/identical.html'>identical</a></span>(<span class='no'>fit</span>$<span class='no'>err_mod</span>, <span class='st'>"const"</span>), <span class='fl'>FALSE</span>, <span class='fl'>TRUE</span>), + <span class='no'>...</span>) <span class='fu'>plot_err</span>(<span class='no'>fit</span>, <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='no'>sep_obs</span>, <span class='no'>...</span>)</pre> @@ -282,7 +282,8 @@ chi2 error percentage.</p></td> </tr> <tr> <th>standardized</th> - <td><p>For</p></td> + <td><p>When calling 'plot_res', should the residuals be +standardized in the residual plot?</p></td> </tr> </table> @@ -301,7 +302,7 @@ latex is being used for the formatting of the chi2 error level, if <span class='co'># parent to sink included</span> <span class='co'># \dontrun{</span> <span class='no'>SFO_SFO</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'>full</span> <span class='kw'>=</span> <span class='st'>"Parent"</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'>full</span> <span class='kw'>=</span> <span class='st'>"Metabolite M1"</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'>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='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</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/graphics/plot.html'>plot</a></span>(<span class='no'>fit</span>)</div><div class='img'><img src='plot.mkinfit-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'>plot_res</span>(<span class='no'>fit</span>)</div><div class='img'><img src='plot.mkinfit-2.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'>plot_res</span>(<span class='no'>fit</span>, <span class='kw'>standardized</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#> <span class='warning'>Warning: "standardized" ist kein Grafikparameter</span></div><div class='output co'>#> <span class='warning'>Warning: "standardized" ist kein Grafikparameter</span></div><div class='output co'>#> <span class='warning'>Warning: "standardized" ist kein Grafikparameter</span></div><div class='output co'>#> <span class='warning'>Warning: "standardized" ist kein Grafikparameter</span></div><div class='output co'>#> <span class='warning'>Warning: "standardized" ist kein Grafikparameter</span></div><div class='output co'>#> <span class='warning'>Warning: "standardized" ist kein Grafikparameter</span></div><div class='img'><img src='plot.mkinfit-3.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'>plot_err</span>(<span class='no'>fit</span>)</div><div class='img'><img src='plot.mkinfit-4.png' alt='' width='700' height='433' /></div><div class='input'> + <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'>full</span> <span class='kw'>=</span> <span class='st'>"Metabolite M1"</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'>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='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</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/graphics/plot.html'>plot</a></span>(<span class='no'>fit</span>)</div><div class='img'><img src='plot.mkinfit-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'>plot_res</span>(<span class='no'>fit</span>)</div><div class='img'><img src='plot.mkinfit-2.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'>plot_res</span>(<span class='no'>fit</span>, <span class='kw'>standardized</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='img'><img src='plot.mkinfit-3.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'>plot_err</span>(<span class='no'>fit</span>)</div><div class='img'><img src='plot.mkinfit-4.png' alt='' width='700' height='433' /></div><div class='input'> <span class='co'># Show the observed variables separately, with residuals</span> <span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>fit</span>, <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>show_residuals</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"topright"</span>, <span class='st'>"bottomright"</span>), <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='img'><img src='plot.mkinfit-5.png' alt='' width='700' height='433' /></div><div class='input'> diff --git a/man/plot.mkinfit.Rd b/man/plot.mkinfit.Rd index 6824f8a5..47cc08a4 100644 --- a/man/plot.mkinfit.Rd +++ b/man/plot.mkinfit.Rd @@ -21,8 +21,8 @@ plot_sep(fit, show_errmin = TRUE, "standardized"), ...) plot_res(fit, sep_obs = FALSE, show_errmin = sep_obs, - show_residuals = ifelse(identical(fit$err_mod, "const"), TRUE, - "standardized"), ...) + standardized = ifelse(identical(fit$err_mod, "const"), FALSE, TRUE), + ...) plot_err(fit, sep_obs = FALSE, show_errmin = sep_obs, ...) } @@ -96,7 +96,8 @@ chi2 error percentage.} \item{\dots}{Further arguments passed to \code{\link{plot}}.} -\item{standardized}{For} +\item{standardized}{When calling 'plot_res', should the residuals be +standardized in the residual plot?} } \value{ The function is called for its side effect. @@ -3,7 +3,7 @@ Testing mkin ✔ | OK F W S | Context ✔ | 2 | Export dataset for reading into CAKE ✔ | 10 | Confidence intervals and p-values [9.7 s] -✔ | 14 | Error model fitting [36.6 s] +✔ | 14 | Error model fitting [36.5 s] ✔ | 4 | Calculation of FOCUS chi2 error levels [2.2 s] ✔ | 13 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [3.3 s] ✔ | 6 | Test fitting the decline of metabolites from their maximum [0.7 s] @@ -18,7 +18,7 @@ Testing mkin ✔ | 11 | Plotting [0.6 s] ✔ | 4 | AIC calculation ✔ | 2 | Residuals extracted from mkinfit models -✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [5.2 s] +✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [5.3 s] ✔ | 4 | Fitting the SFORB model [1.7 s] ✔ | 1 | Summaries of old mkinfit objects ✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [7.1 s] diff --git a/tests/testthat/FOCUS_2006_D.csf b/tests/testthat/FOCUS_2006_D.csf index d5d807ab..528e2b61 100644 --- a/tests/testthat/FOCUS_2006_D.csf +++ b/tests/testthat/FOCUS_2006_D.csf @@ -5,7 +5,7 @@ Description: MeasurementUnits: % AR TimeUnits: days Comments: Created using mkin::CAKE_export -Date: 2019-11-04 +Date: 2019-11-05 Optimiser: IRLS [Data] |
