From 0c9b2f0e3c8ce65cb790c9e048476784cbbea070 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 11 Jun 2021 11:14:45 +0200 Subject: Finished 'summary.nlmixr.mmkin', checks, docs --- docs/dev/reference/plot.mixed.mmkin.html | 23 ++++++++++++++++++++--- 1 file changed, 20 insertions(+), 3 deletions(-) (limited to 'docs/dev/reference/plot.mixed.mmkin.html') diff --git a/docs/dev/reference/plot.mixed.mmkin.html b/docs/dev/reference/plot.mixed.mmkin.html index 36796580..a4222991 100644 --- a/docs/dev/reference/plot.mixed.mmkin.html +++ b/docs/dev/reference/plot.mixed.mmkin.html @@ -72,7 +72,7 @@ mkin - 1.0.4.9000 + 1.0.5 @@ -157,6 +157,8 @@ 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)), @@ -210,6 +212,16 @@ predicted values?

pred_over

Named list of alternative predictions as obtained from mkinpredict with a compatible mkinmod.

+ + + test_log_parms +

Passed to mean_degparms in the case of an +mixed.mmkin object

+ + + conf.level +

Passed to mean_degparms in the case of an +mixed.mmkin object

ymax @@ -278,16 +290,21 @@ corresponding model prediction lines for the different datasets.

# For this fit we need to increase pnlsMaxiter, and we increase the # tolerance in order to speed up the fit for this example evaluation +# It still takes 20 seconds to run f_nlme <- nlme(f, control = list(pnlsMaxIter = 120, tolerance = 1e-3)) plot(f_nlme)
f_saem <- saem(f, transformations = "saemix")
#> Running main SAEM algorithm -#> [1] "Tue Mar 9 17:34:35 2021" +#> [1] "Fri Jun 11 10:56:37 2021" #> .... #> Minimisation finished -#> [1] "Tue Mar 9 17:34:42 2021"
plot(f_saem) +#> [1] "Fri Jun 11 10:56:44 2021"
plot(f_saem)
+f_obs <- mmkin(list("DFOP-SFO" = dfop_sfo), ds, quiet = TRUE, error_model = "obs") +f_nlmix <- nlmix(f_obs) +
#> Error in nlmix(f_obs): could not find function "nlmix"
plot(f_nlmix) +
#> Error in plot(f_nlmix): object 'f_nlmix' not found
# We can overlay the two variants if we generate predictions pred_nlme <- mkinpredict(dfop_sfo, f_nlme$bparms.optim[-1], -- cgit v1.2.1