test_log_parms for plot.mixed.mmkin, roxygen run

6 files changed, 31 insertions, 6 deletions

diff --git a/NEWS.md b/NEWS.md
index 5d0ea69a..a91523bd 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -12,7 +12,9 @@
 
 - 'saem': generic function to fit saemix models using 'saemix_model' and 'saemix_data', with a generator 'saem.mmkin', summary and plot methods
 
-- 'mean_degparms': New argument 'test_log_parms' that makes the function only consider log-transformed parameters where the untransformed parameters pass the t-test for a certain confidence level. This can be used to check more plausible parameters for 'saem'
+- 'mean_degparms': New argument 'test_log_parms' that makes the function only consider log-transformed parameters where the untransformed parameters pass the t-test for a certain confidence level. This can be used to obtain more plausible starting parameters for 'saem'
+
+- 'plot.mixed.mmkin': Gains arguments 'test_log_parms' and 'conf.level'
 
 # mkin 1.0.4 (Unreleased)
 
diff --git a/R/mixed.mmkin.R b/R/mixed.mmkin.R
index 7aa5edd5..682a9a34 100644
--- a/R/mixed.mmkin.R
+++ b/R/mixed.mmkin.R
@@ -3,6 +3,8 @@
 #' @param object An [mmkin] row object
 #' @param method The method to be used
 #' @param \dots Currently not used
+#' @return An object of class 'mixed.mmkin' which has the observed data in a
+#'   single dataframe which is convenient for plotting
 #' @examples
 #' sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120)
 #' n_biphasic <- 8
@@ -54,7 +56,6 @@ mixed.mmkin <- function(object, method = c("none"), ...) {
   if (nrow(object) > 1) stop("Only row objects allowed")
 
   method <- match.arg(method)
-  if (method == "default") method = c("naive", "nlme")
 
   ds_names <- colnames(object)
   res <- list(mmkin = object, mkinmod = object[[1]]$mkinmod)
diff --git a/R/plot.mixed.mmkin.R b/R/plot.mixed.mmkin.R
index 21399496..f0682c10 100644
--- a/R/plot.mixed.mmkin.R
+++ b/R/plot.mixed.mmkin.R
@@ -10,6 +10,10 @@ utils::globalVariables("ds")
 #'   `resplot = "time"`.
 #' @param pred_over Named list of alternative predictions as obtained
 #'   from [mkinpredict] with a compatible [mkinmod].
+#' @param test_log_parms Passed to [mean_degparms] in the case of an
+#'   [mixed.mmkin] object
+#' @param conf.level Passed to [mean_degparms] in the case of an
+#'   [mixed.mmkin] object
 #' @param rel.height.legend The relative height of the legend shown on top
 #' @param rel.height.bottom The relative height of the bottom plot row
 #' @param ymax Vector of maximum y axis values
@@ -58,6 +62,8 @@ plot.mixed.mmkin <- function(x,
   xlim = range(x$data$time),
   resplot = c("predicted", "time"),
   pred_over = NULL,
+  test_log_parms = FALSE,
+  conf.level = 0.6,
   ymax = "auto", maxabs = "auto",
   ncol.legend = ifelse(length(i) <= 3, length(i) + 1, ifelse(length(i) <= 8, 3, 4)),
   nrow.legend = ceiling((length(i) + 1) / ncol.legend),
@@ -76,7 +82,7 @@ plot.mixed.mmkin <- function(x,
   backtransform = TRUE
 
   if (identical(class(x), "mixed.mmkin")) {
-    degparms_pop <- mean_degparms(x$mmkin)
+    degparms_pop <- mean_degparms(x$mmkin, test_log_parms = test_log_parms, conf.level = conf.level)
 
     degparms_tmp <- parms(x$mmkin, transformed = TRUE)
     degparms_i <- as.data.frame(t(degparms_tmp[setdiff(rownames(degparms_tmp), names(fit_1$errparms)), ]))
diff --git a/man/mixed.Rd b/man/mixed.Rd
index 8b00382d..95cae364 100644
--- a/man/mixed.Rd
+++ b/man/mixed.Rd
@@ -23,6 +23,10 @@ mixed(object, ...)
 
 \item{digits}{Number of digits to use for printing.}
 }
+\value{
+An object of class 'mixed.mmkin' which has the observed data in a
+single dataframe which is convenient for plotting
+}
 \description{
 Create a mixed effects model from an mmkin row object
 }
diff --git a/man/plot.mixed.mmkin.Rd b/man/plot.mixed.mmkin.Rd
index b1200729..bcab3e74 100644
--- a/man/plot.mixed.mmkin.Rd
+++ b/man/plot.mixed.mmkin.Rd
@@ -13,6 +13,8 @@
   xlim = range(x$data$time),
   resplot = c("predicted", "time"),
   pred_over = NULL,
+  test_log_parms = FALSE,
+  conf.level = 0.6,
   ymax = "auto",
   maxabs = "auto",
   ncol.legend = ifelse(length(i) <= 3, length(i) + 1, ifelse(length(i) <= 8, 3, 4)),
@@ -49,6 +51,12 @@ predicted values?}
 \item{pred_over}{Named list of alternative predictions as obtained
 from \link{mkinpredict} with a compatible \link{mkinmod}.}
 
+\item{test_log_parms}{Passed to \link{mean_degparms} in the case of an
+\link{mixed.mmkin} object}
+
+\item{conf.level}{Passed to \link{mean_degparms} in the case of an
+\link{mixed.mmkin} object}
+
 \item{ymax}{Vector of maximum y axis values}
 
 \item{maxabs}{Maximum absolute value of the residuals. This is used for the
diff --git a/man/saem.Rd b/man/saem.Rd
index 45f74e44..f462f405 100644
--- a/man/saem.Rd
+++ b/man/saem.Rd
@@ -17,8 +17,9 @@ saem(object, ...)
   test_log_parms = FALSE,
   conf.level = 0.6,
   solution_type = "auto",
-  control = list(displayProgress = FALSE, print = FALSE, save = FALSE, save.graphs =
-    FALSE),
+  nbiter.saemix = c(300, 100),
+  control = list(displayProgress = FALSE, print = FALSE, nbiter.saemix = nbiter.saemix,
+    save = FALSE, save.graphs = FALSE),
   fail_with_errors = TRUE,
   verbose = FALSE,
   quiet = FALSE,
@@ -65,7 +66,10 @@ for parameter that are tested if requested by 'test_log_parms'.}
 \item{solution_type}{Possibility to specify the solution type in case the
 automatic choice is not desired}
 
-\item{control}{Passed to \link[saemix:saemix]{saemix::saemix}}
+\item{nbiter.saemix}{Convenience option to increase the number of
+iterations}
+
+\item{control}{Passed to \link[saemix:saemix]{saemix::saemix}.}
 
 \item{fail_with_errors}{Should a failure to compute standard errors
 from the inverse of the Fisher Information Matrix be a failure?}