saemix.mmkin and nlme.mmkin inherit from mixed.mmkin

With a plot method. The class mixed.mmkin is currently only a virtual
class created to unify the plotting method.

3 files changed, 12 insertions, 34 deletions

diff --git a/man/nlme.mmkin.Rd b/man/nlme.mmkin.Rd
index 85bd74f6..9526a427 100644
--- a/man/nlme.mmkin.Rd
+++ b/man/nlme.mmkin.Rd
@@ -66,8 +66,8 @@ parameters taken from the mmkin object are used}
 \item{object}{An nlme.mmkin object to update}
 }
 \value{
-Upon success, a fitted nlme.mmkin object, which is an nlme object
-with additional elements
+Upon success, a fitted 'nlme.mmkin' object, which is an nlme object
+with additional elements. It also inherits from 'mixed.mmkin'.
 }
 \description{
 This functions sets up a nonlinear mixed effects model for an mmkin row
@@ -150,5 +150,6 @@ endpoints(f_nlme_dfop)
 }
 }
 \seealso{
-\code{\link[=nlme_function]{nlme_function()}}
+\code{\link[=nlme_function]{nlme_function()}}, \link{plot.mixed.mmkin}, \link{summary.nlme.mmkin},
+\link{parms.nlme.mmkin}
 }
diff --git a/man/plot_mixed.Rd b/man/plot.mixed.mmkin.Rd
index d3cee7c9..66e79f09 100644
--- a/man/plot_mixed.Rd
+++ b/man/plot.mixed.mmkin.Rd
@@ -1,33 +1,10 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/plot_mixed.R
-\name{plot_mixed}
-\alias{plot_mixed}
-\alias{plot.saem.mmkin}
-\alias{plot.nlme.mmkin}
+% Please edit documentation in R/plot.mixed.mmkin.R
+\name{plot.mixed.mmkin}
+\alias{plot.mixed.mmkin}
 \title{Plot predictions from a fitted nonlinear mixed model obtained via an mmkin row object}
 \usage{
-\method{plot}{saem.mmkin}(
-  x,
-  i = 1:ncol(x$mmkin),
-  obs_vars = names(x$mkinmod$map),
-  standardized = TRUE,
-  xlab = "Time",
-  xlim = range(x$data$time),
-  resplot = c("predicted", "time"),
-  ymax = "auto",
-  maxabs = "auto",
-  ncol.legend = ifelse(length(i) <= 3, length(i) + 1, ifelse(length(i) <= 8, 3, 4)),
-  nrow.legend = ceiling((length(i) + 1)/ncol.legend),
-  rel.height.legend = 0.03 + 0.08 * nrow.legend,
-  rel.height.bottom = 1.1,
-  pch_ds = 1:length(i),
-  col_ds = pch_ds + 1,
-  lty_ds = col_ds,
-  frame = TRUE,
-  ...
-)
-
-\method{plot}{nlme.mmkin}(
+\method{plot}{mixed.mmkin}(
   x,
   i = 1:ncol(x$mmkin),
   obs_vars = names(x$mkinmod$map),
@@ -93,7 +70,7 @@ corresponding model prediction lines for the different datasets.}
 \item{...}{Further arguments passed to \code{\link{plot}}.}
 }
 \value{
-The functions are called for their side effect.
+The function is called for its side effect.
 }
 \description{
 Plot predictions from a fitted nonlinear mixed model obtained via an mmkin row object
@@ -108,7 +85,6 @@ dfop_sfo <- mkinmod(parent = mkinsub("DFOP", "A1"),
 f <- mmkin(list("DFOP-SFO" = dfop_sfo), ds, quiet = TRUE)
 plot(f[, 3:4], standardized = TRUE)
 
-library(nlme)
 # For this fit we need to increase pnlsMaxiter, and we increase the
 # tolerance in order to speed up the fit for this example evaluation
 f_nlme <- nlme(f, control = list(pnlsMaxIter = 120, tolerance = 1e-3))
diff --git a/man/saem.Rd b/man/saem.Rd
index 56b54fbf..17f777c4 100644
--- a/man/saem.Rd
+++ b/man/saem.Rd
@@ -44,7 +44,8 @@ by the saemix function?}
 }
 \value{
 An S3 object of class 'saem.mmkin', containing the fitted
-\link[saemix:SaemixObject-class]{saemix::SaemixObject} as a list component named 'so'.
+\link[saemix:SaemixObject-class]{saemix::SaemixObject} as a list component named 'so'. The
+object also inherits from 'mixed.mmkin'.
 
 An \link[saemix:SaemixModel-class]{saemix::SaemixModel} object.
 
@@ -114,5 +115,5 @@ summary(f_saem_dfop_sfo, data = FALSE)
 }
 }
 \seealso{
-\link{summary.saem.mmkin}
+\link{summary.saem.mmkin} \link{plot.mixed.mmkin}
 }