From 478c6d5eec4c84b22b43adcbdf36888b302ead00 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Tue, 6 Dec 2022 10:33:24 +0100
Subject: Some parplot improvements

llquant argument, improved legend text, tests
---
 R/parplot.R | 16 ++++++++++++----
 1 file changed, 12 insertions(+), 4 deletions(-)

(limited to 'R')

diff --git a/R/parplot.R b/R/parplot.R
index 98579779..63306ac2 100644
--- a/R/parplot.R
+++ b/R/parplot.R
@@ -10,7 +10,10 @@
 #'
 #' @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.
+#' @param llquant Fractional value for selecting only the fits with higher
+#' likelihoods. Overrides 'llmin'.
+#' @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.
@@ -28,7 +31,8 @@ parplot <- function(object, ...) {
 
 #' @rdname parplot
 #' @export
-parplot.multistart.saem.mmkin <- function(object, llmin = -Inf, scale = c("best", "median"),
+parplot.multistart.saem.mmkin <- function(object, llmin = -Inf, llquant = NA,
+  scale = c("best", "median"),
   lpos = "bottomleft", main = "", ...)
 {
   oldpar <- par(no.readonly = TRUE)
@@ -48,6 +52,10 @@ parplot.multistart.saem.mmkin <- function(object, llmin = -Inf, scale = c("best"
     stop("parplot is only implemented for multistart.saem.mmkin objects")
   }
   ll <- sapply(object, llfunc)
+  if (!is.na(llquant[1])) {
+    if (llmin != -Inf) warning("Overriding 'llmin' because 'llquant' was specified")
+    llmin <- quantile(ll, 1 - llquant)
+  }
   selected <- which(ll > llmin)
   selected_parms <- all_parms[selected, ]
 
@@ -110,7 +118,7 @@ parplot.multistart.saem.mmkin <- function(object, llmin = -Inf, scale = c("best"
   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",
+      "Original start",
+      "Original results",
       "Multistart runs"))
 }
-- 
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