From 48c463680b51fa767b4cd7bd62865f192d0354ac Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Sat, 6 Feb 2021 18:30:32 +0100 Subject: Reintroduce interface to saemix Also after the upgrade from buster to bullseye of my local system, some test results for saemix have changed. --- docs/dev/reference/plot.mixed.mmkin.html | 8 ++++---- 1 file changed, 4 insertions(+), 4 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 55c411e7..601e1554 100644 --- a/docs/dev/reference/plot.mixed.mmkin.html +++ b/docs/dev/reference/plot.mixed.mmkin.html @@ -72,7 +72,7 @@ mkin - 0.9.50.4 + 1.0.1.9000 @@ -161,7 +161,7 @@ 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.legend = 0.02 + 0.07 * nrow.legend, rel.height.bottom = 1.1, pch_ds = 1:length(i), col_ds = pch_ds + 1, @@ -283,10 +283,10 @@ corresponding model prediction lines for the different datasets.

f_saem <- saem(f, transformations = "saemix")
#> Running main SAEM algorithm -#> [1] "Mon Dec 21 05:58:23 2020" +#> [1] "Sat Feb 6 18:29:17 2021" #> .... #> Minimisation finished -#> [1] "Mon Dec 21 05:58:30 2020"
plot(f_saem) +#> [1] "Sat Feb 6 18:29:23 2021"
plot(f_saem)
# We can overlay the two variants if we generate predictions pred_nlme <- mkinpredict(dfop_sfo, -- cgit v1.2.1 From 3dde3b95f1db925c89cd04d19f95c6fc9f68f473 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Sat, 13 Feb 2021 12:40:44 +0100 Subject: Update docs --- docs/dev/reference/plot.mixed.mmkin.html | 6 +++--- 1 file changed, 3 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 601e1554..ef169074 100644 --- a/docs/dev/reference/plot.mixed.mmkin.html +++ b/docs/dev/reference/plot.mixed.mmkin.html @@ -72,7 +72,7 @@ mkin - 1.0.1.9000 + 1.0.2.9000
@@ -283,10 +283,10 @@ corresponding model prediction lines for the different datasets.

f_saem <- saem(f, transformations = "saemix")
#> Running main SAEM algorithm -#> [1] "Sat Feb 6 18:29:17 2021" +#> [1] "Sat Feb 13 12:33:07 2021" #> .... #> Minimisation finished -#> [1] "Sat Feb 6 18:29:23 2021"
plot(f_saem) +#> [1] "Sat Feb 13 12:33:13 2021"
plot(f_saem)
# We can overlay the two variants if we generate predictions pred_nlme <- mkinpredict(dfop_sfo, -- cgit v1.2.1 From b9be19af5e3085216d0cd5af439332f631fa8b92 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 15 Feb 2021 17:36:12 +0100 Subject: Fully rebuild docs, rerun tests and check --- docs/dev/reference/plot.mixed.mmkin.html | 6 +++--- 1 file changed, 3 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 ef169074..630e95a3 100644 --- a/docs/dev/reference/plot.mixed.mmkin.html +++ b/docs/dev/reference/plot.mixed.mmkin.html @@ -72,7 +72,7 @@ mkin - 1.0.2.9000 + 1.0.3.9000
@@ -283,10 +283,10 @@ corresponding model prediction lines for the different datasets.

f_saem <- saem(f, transformations = "saemix")
#> Running main SAEM algorithm -#> [1] "Sat Feb 13 12:33:07 2021" +#> [1] "Mon Feb 15 17:12:17 2021" #> .... #> Minimisation finished -#> [1] "Sat Feb 13 12:33:13 2021"
plot(f_saem) +#> [1] "Mon Feb 15 17:12:24 2021"
plot(f_saem)
# We can overlay the two variants if we generate predictions pred_nlme <- mkinpredict(dfop_sfo, -- cgit v1.2.1 From c73b2f30ec836c949885784ab576e814eb8070a9 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 9 Mar 2021 17:35:47 +0100 Subject: Some improvements for borderline cases - fit_with_errors for saem() - test_log_parms for mean_degparms() and saem() --- docs/dev/reference/plot.mixed.mmkin.html | 6 +++--- 1 file changed, 3 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 630e95a3..36796580 100644 --- a/docs/dev/reference/plot.mixed.mmkin.html +++ b/docs/dev/reference/plot.mixed.mmkin.html @@ -72,7 +72,7 @@ mkin - 1.0.3.9000 + 1.0.4.9000
@@ -283,10 +283,10 @@ corresponding model prediction lines for the different datasets.

f_saem <- saem(f, transformations = "saemix")
#> Running main SAEM algorithm -#> [1] "Mon Feb 15 17:12:17 2021" +#> [1] "Tue Mar 9 17:34:35 2021" #> .... #> Minimisation finished -#> [1] "Mon Feb 15 17:12:24 2021"
plot(f_saem) +#> [1] "Tue Mar 9 17:34:42 2021"
plot(f_saem)
# We can overlay the two variants if we generate predictions pred_nlme <- mkinpredict(dfop_sfo, -- cgit v1.2.1 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 From 0b754ffa91b9496bdd2f892cf3ca2bd887028dea Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 27 Jul 2021 18:22:01 +0200 Subject: Fix dimethenamid vignette problems and update docs --- docs/dev/reference/plot.mixed.mmkin.html | 6 +++--- 1 file changed, 3 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 a4222991..7f3faa90 100644 --- a/docs/dev/reference/plot.mixed.mmkin.html +++ b/docs/dev/reference/plot.mixed.mmkin.html @@ -72,7 +72,7 @@ mkin - 1.0.5 + 1.1.0
@@ -296,10 +296,10 @@ corresponding model prediction lines for the different datasets.

f_saem <- saem(f, transformations = "saemix")
#> Running main SAEM algorithm -#> [1] "Fri Jun 11 10:56:37 2021" +#> [1] "Tue Jul 27 16:30:50 2021" #> .... #> Minimisation finished -#> [1] "Fri Jun 11 10:56:44 2021"
plot(f_saem) +#> [1] "Tue Jul 27 16:30:58 2021"
plot(f_saem)
f_obs <- mmkin(list("DFOP-SFO" = dfop_sfo), ds, quiet = TRUE, error_model = "obs") f_nlmix <- nlmix(f_obs) -- cgit v1.2.1 From 137612045c23198f10d6e8612c32e266c2a6c00e Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 29 Jul 2021 12:17:56 +0200 Subject: Go back to 1.0.x version, update docs --- docs/dev/reference/plot.mixed.mmkin.html | 6 +++--- 1 file changed, 3 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 7f3faa90..8962ce1c 100644 --- a/docs/dev/reference/plot.mixed.mmkin.html +++ b/docs/dev/reference/plot.mixed.mmkin.html @@ -72,7 +72,7 @@ mkin - 1.1.0 + 1.0.5
@@ -296,10 +296,10 @@ corresponding model prediction lines for the different datasets.

f_saem <- saem(f, transformations = "saemix")
#> Running main SAEM algorithm -#> [1] "Tue Jul 27 16:30:50 2021" +#> [1] "Thu Jul 29 12:13:54 2021" #> .... #> Minimisation finished -#> [1] "Tue Jul 27 16:30:58 2021"
plot(f_saem) +#> [1] "Thu Jul 29 12:14:02 2021"
plot(f_saem)
f_obs <- mmkin(list("DFOP-SFO" = dfop_sfo), ds, quiet = TRUE, error_model = "obs") f_nlmix <- nlmix(f_obs) -- cgit v1.2.1 From 51fab94230e926cec690dc455964bd797a97b7c7 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 4 Aug 2021 16:37:52 +0200 Subject: Improve AIC table in vignette --- docs/dev/reference/plot.mixed.mmkin.html | 4 ++-- 1 file changed, 2 insertions(+), 2 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 8962ce1c..746a8640 100644 --- a/docs/dev/reference/plot.mixed.mmkin.html +++ b/docs/dev/reference/plot.mixed.mmkin.html @@ -296,10 +296,10 @@ corresponding model prediction lines for the different datasets.

f_saem <- saem(f, transformations = "saemix")
#> Running main SAEM algorithm -#> [1] "Thu Jul 29 12:13:54 2021" +#> [1] "Wed Aug 4 16:21:52 2021" #> .... #> Minimisation finished -#> [1] "Thu Jul 29 12:14:02 2021"
plot(f_saem) +#> [1] "Wed Aug 4 16:22:00 2021"
plot(f_saem)
f_obs <- mmkin(list("DFOP-SFO" = dfop_sfo), ds, quiet = TRUE, error_model = "obs") f_nlmix <- nlmix(f_obs) -- cgit v1.2.1 From c41381a961263c28d60976e68923157916c78b15 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 16 Sep 2021 15:31:13 +0200 Subject: Adapt and improve the dimethenamid vignette Adapt to the corrected data and unify control parameters for saemix and nlmixr with saem. Update docs --- docs/dev/reference/plot.mixed.mmkin.html | 6 +++--- 1 file changed, 3 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 746a8640..9f0eb965 100644 --- a/docs/dev/reference/plot.mixed.mmkin.html +++ b/docs/dev/reference/plot.mixed.mmkin.html @@ -72,7 +72,7 @@ mkin - 1.0.5 + 1.1.0
@@ -296,10 +296,10 @@ corresponding model prediction lines for the different datasets.

f_saem <- saem(f, transformations = "saemix")
#> Running main SAEM algorithm -#> [1] "Wed Aug 4 16:21:52 2021" +#> [1] "Thu Sep 16 14:34:31 2021" #> .... #> Minimisation finished -#> [1] "Wed Aug 4 16:22:00 2021"
plot(f_saem) +#> [1] "Thu Sep 16 14:34:38 2021"
plot(f_saem)
f_obs <- mmkin(list("DFOP-SFO" = dfop_sfo), ds, quiet = TRUE, error_model = "obs") f_nlmix <- nlmix(f_obs) -- cgit v1.2.1 From ff83d8b2ba623513d92ac90fac4a1b0ec98c2cb5 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 5 Oct 2021 17:33:52 +0200 Subject: Update docs --- docs/dev/reference/plot.mixed.mmkin.html | 10 +++------- 1 file changed, 3 insertions(+), 7 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 9f0eb965..69345b2f 100644 --- a/docs/dev/reference/plot.mixed.mmkin.html +++ b/docs/dev/reference/plot.mixed.mmkin.html @@ -295,12 +295,8 @@ corresponding model prediction lines for the different datasets.

plot(f_nlme)
f_saem <- saem(f, transformations = "saemix") -
#> Running main SAEM algorithm -#> [1] "Thu Sep 16 14:34:31 2021" -#> .... -#> Minimisation finished -#> [1] "Thu Sep 16 14:34:38 2021"
plot(f_saem) -
+
#> Error in saem(f, transformations = "saemix"): unused argument (transformations = "saemix")
plot(f_saem) +
#> Error in plot(f_saem): object 'f_saem' not found
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) @@ -311,7 +307,7 @@ corresponding model prediction lines for the different datasets.

c(parent = f_nlme$bparms.optim[[1]], A1 = 0), seq(0, 180, by = 0.2)) plot(f_saem, pred_over = list(nlme = pred_nlme)) -
# } +
#> Error in plot(f_saem, pred_over = list(nlme = pred_nlme)): object 'f_saem' not found
# }