Rename parhist to parplot and make it generic

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

4 files changed, 15 insertions, 8 deletions

diff --git a/R/llhist.R b/R/llhist.R
index 22e3aa08..e158495d 100644
--- a/R/llhist.R
+++ b/R/llhist.R
@@ -25,6 +25,7 @@ llhist <- function(object, breaks = "Sturges", lpos = "topleft", main = "",
     stop("llhist is only implemented for multistart.saem.mmkin objects")
   }
 
+  ll_orig <- logLik(attr(object, "orig"))
   ll <- stats::na.omit(sapply(object, llfunc))
 
   par(las = 1)
@@ -34,7 +35,7 @@ llhist <- function(object, breaks = "Sturges", lpos = "topleft", main = "",
 
   freq_factor <- h$counts[1] / h$density[1]
 
-  abline(v = logLik(attr(object, "orig")), col = 2)
+  abline(v = ll_orig, col = 2)
 
   legend(lpos, inset = c(0.05, 0.05), bty = "n",
     lty = 1, col = c(2),
diff --git a/R/multistart.R b/R/multistart.R
index 29ccdc44..14683c11 100644
--- a/R/multistart.R
+++ b/R/multistart.R
@@ -17,7 +17,7 @@
 #' @param x The multistart object to print
 #' @return A list of [saem.mmkin] objects, with class attributes
 #' 'multistart.saem.mmkin' and 'multistart'.
-#' @seealso [parhist], [llhist]
+#' @seealso [parplot], [llhist]
 #'
 #' @references Duchesne R, Guillemin A, Gandrillon O, Crauste F. Practical
 #' identifiability in the frame of nonlinear mixed effects models: the example
@@ -40,7 +40,7 @@
 #' f_mmkin <- mmkin("DFOP", dmta_ds, error_model = "tc", cores = 7, quiet = TRUE)
 #' f_saem_full <- saem(f_mmkin)
 #' f_saem_full_multi <- multistart(f_saem_full, n = 16, cores = 16)
-#' parhist(f_saem_full_multi, lpos = "bottomleft")
+#' parplot(f_saem_full_multi, lpos = "bottomleft")
 #' illparms(f_saem_full)
 #'
 #' f_saem_reduced <- update(f_saem_full, no_random_effect = "log_k2")
@@ -52,7 +52,7 @@
 #' cl <- makePSOCKcluster(12)
 #' clusterExport(cl, "f_mmkin")
 #' f_saem_reduced_multi <- multistart(f_saem_reduced, n = 16, cluster = cl)
-#' parhist(f_saem_reduced_multi, lpos = "topright")
+#' parplot(f_saem_reduced_multi, lpos = "topright")
 #' }
 multistart <- function(object, n = 50,
   cores = if (Sys.info()["sysname"] == "Windows") 1 else parallel::detectCores(),
diff --git a/R/parhist.R b/R/parplot.R
index 0f9c9964..627a4eb8 100644
--- a/R/parhist.R
+++ b/R/parplot.R
@@ -1,4 +1,4 @@
-#' Plot parameter distributions from multistart objects
+#' 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,
@@ -18,7 +18,13 @@
 #' @seealso [multistart]
 #' @importFrom stats median
 #' @export
-parhist <- function(object, llmin = -Inf, scale = c("best", "median"),
+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)
@@ -35,7 +41,7 @@ parhist <- function(object, llmin = -Inf, scale = c("best", "median"),
       else return(logLik(object$so))
     }
   } else {
-    stop("parhist is only implemented for multistart.saem.mmkin objects")
+    stop("parplot is only implemented for multistart.saem.mmkin objects")
   }
   ll <- sapply(object, llfunc)
   selected <- which(ll > llmin)
diff --git a/R/saem.R b/R/saem.R
index cf67b8e1..090ed3bf 100644
--- a/R/saem.R
+++ b/R/saem.R
@@ -726,7 +726,7 @@ saemix_data <- function(object, covariates = NULL, verbose = FALSE, ...) {
 #' @param \dots Passed to [saemix::logLik.SaemixObject]
 #' @param method Passed to [saemix::logLik.SaemixObject]
 #' @export
-logLik.saem.mmkin <- function(object, ..., method = c("lin", "is", "gq")) {
+logLik.saem.mmkin <- function(object, ..., method = c("is", "lin", "gq")) {
   method <- match.arg(method)
   return(logLik(object$so, method = method))
 }