diff options
author | Johannes Ranke <jranke@uni-bremen.de> | 2022-10-28 13:39:15 +0200 |
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committer | Johannes Ranke <jranke@uni-bremen.de> | 2022-10-28 13:39:15 +0200 |
commit | f820bf5b91be0f589de16c3e3250f5f79672df75 (patch) | |
tree | 2b1406e1c9286634ca017db586e09e2299dec048 /R/parplot.R | |
parent | b1740ade9a1746ccdb325b95915ef88872489f03 (diff) |
Rename parhist to parplot and make it generic
That parhist name was not the brightest idea, as it does
not show histograms.
Diffstat (limited to 'R/parplot.R')
-rw-r--r-- | R/parplot.R | 105 |
1 files changed, 105 insertions, 0 deletions
diff --git a/R/parplot.R b/R/parplot.R new file mode 100644 index 00000000..627a4eb8 --- /dev/null +++ b/R/parplot.R @@ -0,0 +1,105 @@ +#' Plot parameter variability of multistart objects +#' +#' Produces a boxplot with all parameters from the multiple runs, scaled +#' either by the parameters of the run with the highest likelihood, +#' or by their medians as proposed in the paper by Duchesne et al. (2021). +#' +#' @param object The [multistart] object +#' @param llmin The minimum likelihood of objects to be shown +#' @param scale By default, scale parameters using the best available fit. +#' If 'median', parameters are scaled using the median parameters from all fits. +#' @param main Title of the plot +#' @param lpos Positioning of the legend. +#' @param \dots Passed to [boxplot] +#' @references Duchesne R, Guillemin A, Gandrillon O, Crauste F. Practical +#' identifiability in the frame of nonlinear mixed effects models: the example +#' of the in vitro erythropoiesis. BMC Bioinformatics. 2021 Oct 4;22(1):478. +#' doi: 10.1186/s12859-021-04373-4. +#' @seealso [multistart] +#' @importFrom stats median +#' @export +parplot <- function(object, ...) { + UseMethod("parplot") +} + +#' @rdname parplot +#' @export +parplot.multistart.saem.mmkin <- function(object, llmin = -Inf, 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_parms <- orig$mean_dp_start + all_parms <- parms(object) + + if (inherits(object, "multistart.saem.mmkin")) { + llfunc <- function(object) { + if (inherits(object$so, "try-error")) return(NA) + else return(logLik(object$so)) + } + } else { + stop("parplot is only implemented for multistart.saem.mmkin objects") + } + ll <- sapply(object, llfunc) + selected <- which(ll > llmin) + selected_parms <- all_parms[selected, ] + + par(las = 1) + if (orig$transformations == "mkin") { + degparm_names_transformed <- names(start_parms) + degparm_index <- which(names(orig_parms) %in% degparm_names_transformed) + orig_parms[degparm_names_transformed] <- backtransform_odeparms( + orig_parms[degparm_names_transformed], + orig$mmkin[[1]]$mkinmod, + transform_rates = orig$mmkin[[1]]$transform_rates, + transform_fractions = orig$mmkin[[1]]$transform_fractions) + start_parms <- backtransform_odeparms(start_parms, + orig$mmkin[[1]]$mkinmod, + transform_rates = orig$mmkin[[1]]$transform_rates, + transform_fractions = orig$mmkin[[1]]$transform_fractions) + degparm_names <- names(start_parms) + + names(orig_parms) <- c(degparm_names, names(orig_parms[-degparm_index])) + + 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 + } + + scale <- match.arg(scale) + parm_scale <- switch(scale, + best = selected_parms[which.best(object[selected]), ], + median = apply(selected_parms, 2, median) + ) + + # Boxplots of all scaled parameters + selected_scaled_parms <- t(apply(selected_parms, 1, function(x) x / parm_scale)) + boxplot(selected_scaled_parms, log = "y", main = main, , + ylab = "Normalised parameters", ...) + + # Show starting parameters + start_scaled_parms <- rep(NA_real_, length(orig_parms)) + names(start_scaled_parms) <- names(orig_parms) + start_scaled_parms[names(start_parms)] <- + start_parms / parm_scale[names(start_parms)] + points(start_scaled_parms, col = 3, cex = 3) + + # Show parameters of original run + orig_scaled_parms <- orig_parms / parm_scale + points(orig_scaled_parms, col = 2, cex = 2) + + abline(h = 1, lty = 2) + + legend(lpos, inset = c(0.05, 0.05), bty = "n", + pch = 1, col = 3:1, lty = c(NA, NA, 1), + legend = c( + "Starting parameters", + "Original run", + "Multistart runs")) +} |