From ead1f286271923f57d83aed41cb34181a10773ef Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 5 Nov 2019 00:05:34 +0100 Subject: Fix standardized residual plots in 'plot_res' --- R/plot.mkinfit.R | 8 +++++--- docs/reference/plot.mkinfit-3.png | Bin 62528 -> 57593 bytes docs/reference/plot.mkinfit.html | 9 +++++---- man/plot.mkinfit.Rd | 7 ++++--- test.log | 4 ++-- 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 index 72bc331e..6910ae47 100644 Binary files a/docs/reference/plot.mkinfit-3.png and b/docs/reference/plot.mkinfit-3.png differ 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.

"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, ...) @@ -282,7 +282,8 @@ chi2 error percentage.

standardized -

For

+

When calling 'plot_res', should the residuals be +standardized in the residual plot?

@@ -301,7 +302,7 @@ latex is being used for the formatting of the chi2 error level, if # parent to sink included # \dontrun{ SFO_SFO <- mkinmod(parent = mkinsub("SFO", "m1", full = "Parent"), - m1 = mkinsub("SFO", full = "Metabolite M1" ))
#> Successfully compiled differential equation model from auto-generated C code.
fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE, error_model = "tc")
#> Warning: Observations with value of zero were removed from the data
plot(fit)
plot_res(fit)
plot_res(fit, standardized = FALSE)
#> Warning: "standardized" ist kein Grafikparameter
#> Warning: "standardized" ist kein Grafikparameter
#> Warning: "standardized" ist kein Grafikparameter
#> Warning: "standardized" ist kein Grafikparameter
#> Warning: "standardized" ist kein Grafikparameter
#> Warning: "standardized" ist kein Grafikparameter
plot_err(fit)
+ m1 = mkinsub("SFO", full = "Metabolite M1" ))
#> Successfully compiled differential equation model from auto-generated C code.
fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE, error_model = "tc")
#> Warning: Observations with value of zero were removed from the data
plot(fit)
plot_res(fit)
plot_res(fit, standardized = FALSE)
plot_err(fit)
# Show the observed variables separately, with residuals plot(fit, sep_obs = TRUE, show_residuals = TRUE, lpos = c("topright", "bottomright"), show_errmin = TRUE)
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. diff --git a/test.log b/test.log index f0f09d41..806c72b3 100644 --- a/test.log +++ b/test.log @@ -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] -- cgit v1.2.1