From c29e27b9bf5f5361db44e28b06da7b8a1e636e85 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Sat, 9 Apr 2022 06:21:23 +0200
Subject: Improvements to mean_degparms() and plot.mixed.mmkin()

- New argument 'default_log_parms' for mean_degparms()
- 'plot.mixed.mmkin': Pass the frame argument also to residual plots,
  take the 'default_log_parms' argument for 'mean_degparms' used for
  constructing approximate population curves, plot population curve last
  to avoid that it is covered by data
---
 man/dimethenamid_2018.Rd | 10 +++++++---
 man/mean_degparms.Rd     | 12 +++++++++++-
 man/plot.mixed.mmkin.Rd  |  4 ++++
 3 files changed, 22 insertions(+), 4 deletions(-)

(limited to 'man')

diff --git a/man/dimethenamid_2018.Rd b/man/dimethenamid_2018.Rd
index 6c28ab7b..20d2dc1b 100644
--- a/man/dimethenamid_2018.Rd
+++ b/man/dimethenamid_2018.Rd
@@ -62,12 +62,16 @@ plot(mixed(dmta_sfo_sfo3p_tc), test_log_parms = FALSE)
 # look more plausible, but the truth is likely to be in
 # between these variants
 plot(mixed(dmta_sfo_sfo3p_tc), test_log_parms = TRUE)
-# Therefore we use nonlinear mixed-effects models
+# We can also specify a default value for the failing
+# log parameters, to mimic FOCUS guidance
+plot(mixed(dmta_sfo_sfo3p_tc), test_log_parms = TRUE,
+  default_log_parms = log(2)/1000)
+# As these attempts are not satisfying, we use nonlinear mixed-effects models
 # f_dmta_nlme_tc <- nlme(dmta_sfo_sfo3p_tc)
 # nlme reaches maxIter = 50 without convergence
 f_dmta_saem_tc <- saem(dmta_sfo_sfo3p_tc)
 # I am commenting out the convergence plot as rendering them
-# with pkgdown fails (at least without further tweaks to the 
+# with pkgdown fails (at least without further tweaks to the
 # graphics device used)
 #saemix::plot(f_dmta_saem_tc$so, plot.type = "convergence")
 summary(f_dmta_saem_tc)
@@ -78,7 +82,7 @@ summary(f_dmta_saem_tc)
 #   covariance.model = diag(c(0, rep(1, 7))))
 # saemix::plot(f_dmta_saem_tc_2$so, plot.type = "convergence")
 # This does not perform better judged by AIC and BIC
-saemix::compare.saemix(f_dmta_saem_tc$so, f_dmta_saem_tc_2$so)
+# saemix::compare.saemix(f_dmta_saem_tc$so, f_dmta_saem_tc_2$so)
 }
 }
 \keyword{datasets}
diff --git a/man/mean_degparms.Rd b/man/mean_degparms.Rd
index 5e2b4b0f..bc986d35 100644
--- a/man/mean_degparms.Rd
+++ b/man/mean_degparms.Rd
@@ -4,7 +4,13 @@
 \alias{mean_degparms}
 \title{Calculate mean degradation parameters for an mmkin row object}
 \usage{
-mean_degparms(object, random = FALSE, test_log_parms = FALSE, conf.level = 0.6)
+mean_degparms(
+  object,
+  random = FALSE,
+  test_log_parms = FALSE,
+  conf.level = 0.6,
+  default_log_parms = NA
+)
 }
 \arguments{
 \item{object}{An mmkin row object containing several fits of the same model to different datasets}
@@ -17,6 +23,10 @@ rate constants) pass the t-test for significant difference from zero.}
 
 \item{conf.level}{Possibility to adjust the required confidence level
 for parameter that are tested if requested by 'test_log_parms'.}
+
+\item{default_log_parms}{If set to a numeric value, this is used
+as a default value for the tested log parameters that failed the
+t-test.}
 }
 \value{
 If random is FALSE (default), a named vector containing mean values
diff --git a/man/plot.mixed.mmkin.Rd b/man/plot.mixed.mmkin.Rd
index d87ca22c..33b4a67f 100644
--- a/man/plot.mixed.mmkin.Rd
+++ b/man/plot.mixed.mmkin.Rd
@@ -15,6 +15,7 @@
   pred_over = NULL,
   test_log_parms = FALSE,
   conf.level = 0.6,
+  default_log_parms = NA,
   ymax = "auto",
   maxabs = "auto",
   ncol.legend = ifelse(length(i) <= 3, length(i) + 1, ifelse(length(i) <= 8, 3, 4)),
@@ -57,6 +58,9 @@ from \link{mkinpredict} with a compatible \link{mkinmod}.}
 \item{conf.level}{Passed to \link{mean_degparms} in the case of an
 \link{mixed.mmkin} object}
 
+\item{default_log_parms}{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
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