From d28ce9f8ad6f9573e403ebd8eb637ecd5e5b0e02 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Mon, 21 Dec 2020 06:02:10 +0100
Subject: plot.mixed: Possibility to overlay predictions

---
 man/plot.mixed.mmkin.Rd | 13 ++++++++++++-
 man/saem.Rd             |  5 +++++
 2 files changed, 17 insertions(+), 1 deletion(-)

(limited to 'man')

diff --git a/man/plot.mixed.mmkin.Rd b/man/plot.mixed.mmkin.Rd
index b90a4b3a..c7b2344f 100644
--- a/man/plot.mixed.mmkin.Rd
+++ b/man/plot.mixed.mmkin.Rd
@@ -12,6 +12,7 @@
   xlab = "Time",
   xlim = range(x$data$time),
   resplot = c("predicted", "time"),
+  pred_over = NULL,
   ymax = "auto",
   maxabs = "auto",
   ncol.legend = ifelse(length(i) <= 3, length(i) + 1, ifelse(length(i) <= 8, 3, 4)),
@@ -45,6 +46,9 @@ variables in the model.}
 \item{resplot}{Should the residuals plotted against time or against
 predicted values?}
 
+\item{pred_over}{Named list of alternative predictions as obtained
+from \link{mkinpredict} with a compatible \link{mkinmod}.}
+
 \item{ymax}{Vector of maximum y axis values}
 
 \item{maxabs}{Maximum absolute value of the residuals. This is used for the
@@ -90,8 +94,15 @@ plot(f[, 3:4], standardized = TRUE)
 f_nlme <- nlme(f, control = list(pnlsMaxIter = 120, tolerance = 1e-3))
 plot(f_nlme)
 
-f_saem <- saem(f)
+f_saem <- saem(f, transformations = "saemix")
 plot(f_saem)
+
+# We can overlay the two variants if we generate predictions
+pred_nlme <- mkinpredict(dfop_sfo,
+  f_nlme$bparms.optim[-1],
+  c(parent = f_nlme$bparms.optim[[1]], A1 = 0),
+  seq(0, 180, by = 0.2))
+plot(f_saem, pred_over = list(nlme = pred_nlme))
 }
 }
 \author{
diff --git a/man/saem.Rd b/man/saem.Rd
index dba948bb..775a8e7b 100644
--- a/man/saem.Rd
+++ b/man/saem.Rd
@@ -13,6 +13,7 @@ saem(object, ...)
 \method{saem}{mmkin}(
   object,
   transformations = c("mkin", "saemix"),
+  degparms_start = numeric(),
   solution_type = "auto",
   control = list(displayProgress = FALSE, print = FALSE, save = FALSE, save.graphs =
     FALSE),
@@ -28,6 +29,7 @@ saemix_model(
   object,
   solution_type = "auto",
   transformations = c("mkin", "saemix"),
+  degparms_start = numeric(),
   verbose = FALSE,
   ...
 )
@@ -46,6 +48,9 @@ are done in 'saemix' for the supported cases. Currently this is only
 supported in cases where the initial concentration of the parent is not fixed,
 SFO or DFOP is used for the parent and there is either no metabolite or one.}
 
+\item{degparms_start}{Parameter values given as a named numeric vector will
+be used to override the starting values obtained from the 'mmkin' object.}
+
 \item{solution_type}{Possibility to specify the solution type in case the
 automatic choice is not desired}
 
-- 
cgit v1.2.1