From 3529f5ff498d7d054c7b1911ddfc4b242902b85d Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Wed, 28 Sep 2022 16:34:57 +0200
Subject: Fix handling of multistart fits with failures

---
 R/parms.R | 82 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 82 insertions(+)
 create mode 100644 R/parms.R

(limited to 'R/parms.R')

diff --git a/R/parms.R b/R/parms.R
new file mode 100644
index 00000000..bd4e479b
--- /dev/null
+++ b/R/parms.R
@@ -0,0 +1,82 @@
+#' Extract model parameters
+#'
+#' 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.
+#' @param \dots Not used
+#' @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)
+#' parms(fit)
+#' parms(fit, transformed = TRUE)
+#'
+#' # mmkin objects
+#' ds <- lapply(experimental_data_for_UBA_2019[6:10],
+#'  function(x) subset(x$data[c("name", "time", "value")]))
+#' names(ds) <- paste("Dataset", 6:10)
+#' \dontrun{
+#' fits <- mmkin(c("SFO", "FOMC", "DFOP"), ds, quiet = TRUE, cores = 1)
+#' parms(fits["SFO", ])
+#' parms(fits[, 2])
+#' parms(fits)
+#' parms(fits, transformed = TRUE)
+#' }
+#' @export
+parms <- function(object, ...)
+{
+  UseMethod("parms", object)
+}
+
+#' @param transformed Should the parameters be returned as used internally
+#' during the optimisation?
+#' @param errparms Should the error model parameters be returned
+#' in addition to the degradation parameters?
+#' @rdname parms
+#' @export
+parms.mkinfit <- function(object, transformed = FALSE, errparms = TRUE, ...)
+{
+  res <- if (transformed) object$par
+    else c(object$bparms.optim, object$errparms)
+  if (!errparms) {
+    res[setdiff(names(res), names(object$errparms))]
+  }
+  else return(res)
+}
+
+#' @rdname parms
+#' @export
+parms.mmkin <- function(object, transformed = FALSE, errparms = TRUE, ...)
+{
+  if (nrow(object) == 1) {
+    res <- sapply(object, parms, transformed = transformed,
+      errparms = errparms, ...)
+    colnames(res) <- colnames(object)
+  } else {
+    res <- list()
+    for (i in 1:nrow(object)) {
+      res[[i]] <- parms(object[i, ], transformed = transformed,
+        errparms = errparms, ...)
+    }
+    names(res) <- rownames(object)
+  }
+  return(res)
+}
+
+#' @param exclude_failed For [multistart] objects, should rows for failed fits
+#' be removed from the returned parameter matrix?
+#' @rdname parms
+#' @export
+parms.multistart <- function(object, exclude_failed = TRUE, ...) {
+  res <- t(sapply(object, parms))
+  successful <- which(!is.na(res[, 1]))
+  first_success <- successful[1]
+  colnames(res) <- names(parms(object[[first_success]]))
+  if (exclude_failed) res <- res[successful, ]
+  return(res)
+}
-- 
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