Rename parhist to parplot and make it generic

That parhist name was not the brightest idea, as it does
not show histograms.

1 files changed, 0 insertions, 99 deletions

diff --git a/R/parhist.R b/R/parhist.R
deleted file mode 100644
index 0f9c9964..00000000
--- a/R/parhist.R
+++ /dev/null
@@ -1,99 +0,0 @@
-#' Plot parameter distributions from 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
-parhist <- 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$so))
-    }
-  } else {
-    stop("parhist is only implemented for multistart.saem.mmkin objects")
-  }
-  ll <- sapply(object, llfunc)
-  selected <- which(ll > llmin)
-  selected_parms <- all_parms[selected, ]
-
-  par(las = 1)
-  if (orig$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"))
-}