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-rw-r--r--man/dimethenamid_2018.Rd10
-rw-r--r--man/mean_degparms.Rd12
-rw-r--r--man/plot.mixed.mmkin.Rd4
3 files changed, 22 insertions, 4 deletions
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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