diff options
| -rw-r--r-- | DESCRIPTION | 2 | ||||
| -rw-r--r-- | NEWS.md | 2 | ||||
| -rw-r--r-- | R/parplot.R | 19 |
3 files changed, 15 insertions, 8 deletions
diff --git a/DESCRIPTION b/DESCRIPTION index 3c1c4f7d..50c6cec3 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,7 +2,7 @@ Package: mkin Type: Package Title: Kinetic Evaluation of Chemical Degradation Data Version: 1.2.9 -Date: 2024-04-27 +Date: 2024-09-06 Authors@R: c( person("Johannes", "Ranke", role = c("aut", "cre", "cph"), email = "johannes.ranke@jrwb.de", @@ -1,5 +1,7 @@ # mkin 1.2.9 +- 'R/parplot.R': Support multistart objects with covariate models and filter negative values of scaled parameters (with a warning) for plotting. + - 'R/create_deg_func.R: Make sure that no reversible reactions are specified in the case of two observed variables, as this is not supported # mkin 1.2.8 (unreleased) diff --git a/R/parplot.R b/R/parplot.R index 3da4b51a..a33112a5 100644 --- a/R/parplot.R +++ b/R/parplot.R @@ -35,9 +35,6 @@ parplot.multistart.saem.mmkin <- function(object, llmin = -Inf, llquant = NA, scale = c("best", "median"), lpos = "bottomleft", main = "", ...) { - oldpar <- par(no.readonly = TRUE) - on.exit(par(oldpar, no.readonly = TRUE)) - orig <- attr(object, "orig") orig_parms <- parms(orig) start_degparms <- orig$mean_dp_start @@ -59,11 +56,10 @@ parplot.multistart.saem.mmkin <- function(object, llmin = -Inf, llquant = NA, selected <- which(ll > llmin) selected_parms <- all_parms[selected, ] - par(las = 1) if (orig$transformations == "mkin") { degparm_names_transformed <- names(start_degparms) degparm_index <- which(names(orig_parms) %in% degparm_names_transformed) - orig_parms[degparm_names_transformed] <- backtransform_odeparms( + orig_degparms <- backtransform_odeparms( orig_parms[degparm_names_transformed], orig$mmkin[[1]]$mkinmod, transform_rates = orig$mmkin[[1]]$transform_rates, @@ -74,14 +70,17 @@ parplot.multistart.saem.mmkin <- function(object, llmin = -Inf, llquant = NA, transform_fractions = orig$mmkin[[1]]$transform_fractions) degparm_names <- names(start_degparms) - names(orig_parms) <- c(degparm_names, names(orig_parms[-degparm_index])) + orig_parms_back <- orig_parms + orig_parms_back[degparm_index] <- orig_degparms + names(orig_parms_back)[degparm_index] <- degparm_names + orig_parms <- orig_parms_back selected_parms[, degparm_names_transformed] <- t(apply(selected_parms[, degparm_names_transformed], 1, backtransform_odeparms, orig$mmkin[[1]]$mkinmod, transform_rates = orig$mmkin[[1]]$transform_rates, transform_fractions = orig$mmkin[[1]]$transform_fractions)) - colnames(selected_parms)[1:length(degparm_names)] <- degparm_names + colnames(selected_parms)[degparm_index] <- degparm_names } start_errparms <- orig$so@model@error.init @@ -99,6 +98,12 @@ parplot.multistart.saem.mmkin <- function(object, llmin = -Inf, llquant = NA, # Boxplots of all scaled parameters selected_scaled_parms <- t(apply(selected_parms, 1, function(x) x / parm_scale)) + i_negative <- selected_scaled_parms <= 0 + parms_with_negative_scaled_values <- paste(names(which(apply(i_negative, 2, any))), collapse = ", ") + if (any(i_negative)) { + warning("There are negative values for ", parms_with_negative_scaled_values, " which are set to NA for plotting") + } + selected_scaled_parms[i_negative] <- NA boxplot(selected_scaled_parms, log = "y", main = main, , ylab = "Normalised parameters", ...) |