From 2a521ab0a4b7d981a2042353e2c60b8a877489b8 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Fri, 16 Sep 2022 10:51:48 +0200
Subject: Improve docs and update pkgdown

---
 R/multistart.R    |  8 ++++----
 R/parms.mkinfit.R | 19 +++++++++----------
 2 files changed, 13 insertions(+), 14 deletions(-)

(limited to 'R')

diff --git a/R/multistart.R b/R/multistart.R
index 94292e82..52f279f0 100644
--- a/R/multistart.R
+++ b/R/multistart.R
@@ -15,7 +15,7 @@
 #' used?
 #' @param cores How many fits should be run in parallel?
 #' @param \dots Passed to the update function, or to the basic plotting
-#' function in the case of the graphical function.
+#' function in the case of the graphical functions.
 #' @param x The multistart object to print
 #' @param breaks Passed to [hist]
 #' @param main title of the plot
@@ -66,7 +66,7 @@ parms.multistart <- function(object, ...) {
 #' @rdname multistart
 #' @importFrom stats median
 #' @export
-parhist <- function(object, lpos = "topleft", ...) {
+parhist <- function(object, lpos = "topleft", main = "", ...) {
   orig <- attr(object, "orig")
   orig_parms <- parms(orig)
   start_parms <- orig$mean_dp_start
@@ -79,7 +79,7 @@ parhist <- function(object, lpos = "topleft", ...) {
   start_scaled_parms[names(start_parms)] <-
     start_parms / median_parms[names(start_parms)]
 
-  boxplot(all_scaled_parms, log = "y", ...)
+  boxplot(all_scaled_parms, log = "y", main = main, ...)
   points(orig_scaled_parms, col = 2, cex = 2)
   points(start_scaled_parms, col = 3, cex = 3)
   legend(lpos, inset = c(0.05, 0.05), bty = "n",
@@ -93,7 +93,7 @@ parhist <- function(object, lpos = "topleft", ...) {
 #' @rdname multistart
 #' @importFrom KernSmooth bkde
 #' @export
-llhist <- function(object, breaks = "Sturges", main = "", lpos = "topleft", ...) {
+llhist <- function(object, breaks = "Sturges", lpos = "topleft", main = "", ...) {
   ll <- sapply(object, logLik)
   kde <- KernSmooth::bkde(ll)
   h <- hist(ll, freq = TRUE,
diff --git a/R/parms.mkinfit.R b/R/parms.mkinfit.R
index 31ca05bc..83766355 100644
--- a/R/parms.mkinfit.R
+++ b/R/parms.mkinfit.R
@@ -1,16 +1,15 @@
-#' Extract model parameters from mkinfit models
+#' Extract model parameters
 #'
-#' This function always returns degradation model parameters as well as error
-#' model parameters, in order to avoid working with a fitted model without
-#' considering the error structure that was assumed for the fit.
+#' This function returns degradation model parameters as well as error
+#' model parameters per default, in order to avoid working with a fitted model
+#' without considering the error structure that was assumed for the fit.
 #'
-#' @param object A fitted model object. Methods are implemented for
-#'  [mkinfit()] objects and for [mmkin()] objects.
+#' @param object A fitted model object.
 #' @param \dots Not used
-#' @return For mkinfit objects, a numeric vector of fitted model parameters.
-#' For mmkin row objects, a matrix with the parameters with a row for each
-#' dataset. If the mmkin object has more than one row, a list of such matrices
-#' is returned.
+#' @return Depending on the object, a numeric vector of fitted model parameters,
+#' a matrix (e.g. for mmkin row objects), or a list of matrices (e.g. for
+#' mmkin objects with more than one row).
+#' @seealso [saem], [multistart]
 #' @examples
 #' # mkinfit objects
 #' fit <- mkinfit("SFO", FOCUS_2006_C, quiet = TRUE)
-- 
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