From 6d6dc7d53bf99b088af3488588574afc832fb7fe Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Fri, 19 Mar 2021 11:22:07 +0100
Subject: test_log_parms for plot.mixed.mmkin, roxygen run

---
 man/mixed.Rd            |  4 ++++
 man/plot.mixed.mmkin.Rd |  8 ++++++++
 man/saem.Rd             | 10 +++++++---
 3 files changed, 19 insertions(+), 3 deletions(-)

(limited to 'man')

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?}
-- 
cgit v1.2.1