From d28ce9f8ad6f9573e403ebd8eb637ecd5e5b0e02 Mon Sep 17 00:00:00 2001
From: Johannes Ranke
Date: Mon, 21 Dec 2020 06:02:10 +0100
Subject: plot.mixed: Possibility to overlay predictions
---
docs/dev/pkgdown.yml | 2 +-
docs/dev/reference/Rplot001.png | Bin 1011 -> 19395 bytes
docs/dev/reference/plot.mixed.mmkin-3.png | Bin 163488 -> 163536 bytes
docs/dev/reference/plot.mixed.mmkin-4.png | Bin 0 -> 166687 bytes
docs/dev/reference/plot.mixed.mmkin.html | 23 +++++++++---
docs/dev/reference/saem.html | 57 +++++++++++++++---------------
6 files changed, 47 insertions(+), 35 deletions(-)
create mode 100644 docs/dev/reference/plot.mixed.mmkin-4.png
(limited to 'docs')
diff --git a/docs/dev/pkgdown.yml b/docs/dev/pkgdown.yml
index b3124589..85a358df 100644
--- a/docs/dev/pkgdown.yml
+++ b/docs/dev/pkgdown.yml
@@ -10,7 +10,7 @@ articles:
web_only/NAFTA_examples: NAFTA_examples.html
web_only/benchmarks: benchmarks.html
web_only/compiled_models: compiled_models.html
-last_built: 2020-12-19T11:24Z
+last_built: 2020-12-21T04:57Z
urls:
reference: https://pkgdown.jrwb.de/mkin/reference
article: https://pkgdown.jrwb.de/mkin/articles
diff --git a/docs/dev/reference/Rplot001.png b/docs/dev/reference/Rplot001.png
index 17a35806..bca41e2c 100644
Binary files a/docs/dev/reference/Rplot001.png and b/docs/dev/reference/Rplot001.png differ
diff --git a/docs/dev/reference/plot.mixed.mmkin-3.png b/docs/dev/reference/plot.mixed.mmkin-3.png
index 3055c0c9..5e00afe6 100644
Binary files a/docs/dev/reference/plot.mixed.mmkin-3.png and b/docs/dev/reference/plot.mixed.mmkin-3.png differ
diff --git a/docs/dev/reference/plot.mixed.mmkin-4.png b/docs/dev/reference/plot.mixed.mmkin-4.png
new file mode 100644
index 00000000..6a5f3b9c
Binary files /dev/null and b/docs/dev/reference/plot.mixed.mmkin-4.png differ
diff --git a/docs/dev/reference/plot.mixed.mmkin.html b/docs/dev/reference/plot.mixed.mmkin.html
index 90ba9184..55c411e7 100644
--- a/docs/dev/reference/plot.mixed.mmkin.html
+++ b/docs/dev/reference/plot.mixed.mmkin.html
@@ -121,7 +121,7 @@
-
-
+
@@ -156,6 +156,7 @@
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)),
@@ -204,6 +205,11 @@ variables in the model.
solution_type |
@@ -260,36 +267,33 @@ using mmkin.
state.ini = c(parent = 100), fixed_initials = "parent", quiet = TRUE)
f_saem_p0_fixed <- saem(f_mmkin_parent_p0_fixed)
#> Running main SAEM algorithm
-#> [1] "Wed Dec 16 18:27:30 2020"
+#> [1] "Mon Dec 21 05:58:33 2020"
#> ....
#> Minimisation finished
-#> [1] "Wed Dec 16 18:27:31 2020"
+#> [1] "Mon Dec 21 05:58:34 2020"
#> Running main SAEM algorithm
-#> [1] "Wed Dec 16 18:27:33 2020"
+#> [1] "Mon Dec 21 05:58:36 2020"
#> ....
#> Minimisation finished
-#> [1] "Wed Dec 16 18:27:35 2020"
f_saem_fomc <- saem(f_mmkin_parent["FOMC", ])
+#> [1] "Mon Dec 21 05:58:37 2020"
f_saem_fomc <- saem(f_mmkin_parent["FOMC", ])
#> Running main SAEM algorithm
-#> [1] "Wed Dec 16 18:27:35 2020"
+#> [1] "Mon Dec 21 05:58:38 2020"
#> ....
#> Minimisation finished
-#> [1] "Wed Dec 16 18:27:37 2020"
f_saem_dfop <- saem(f_mmkin_parent["DFOP", ])
+#> [1] "Mon Dec 21 05:58:40 2020"
f_saem_dfop <- saem(f_mmkin_parent["DFOP", ])
#> Running main SAEM algorithm
-#> [1] "Wed Dec 16 18:27:37 2020"
+#> [1] "Mon Dec 21 05:58:40 2020"
#> ....
#> Minimisation finished
-#> [1] "Wed Dec 16 18:27:40 2020"
+#> [1] "Mon Dec 21 05:58:43 2020"
#> Package saemix, version 3.1.9000
#> please direct bugs, questions and feedback to emmanuelle.comets@inserm.fr
#> Likelihoods computed by importance sampling
#> AIC BIC
-#> 1 624.2484 622.2956
-#> 2 467.7096 464.9757
-#> 3 495.4373 491.9222
#> Error in compare.saemix(list(f_saem_sfo$so, f_saem_fomc$so, f_saem_dfop$so)): 'compare.saemix' requires at least two models.
#> Plotting convergence plots
#> Plotting individual fits
#> Simulating data using nsim = 1000 simulated datasets
@@ -326,13 +330,11 @@ using
mmkin.
f_mmkin_parent_tc <- update(f_mmkin_parent, error_model
= "tc")
f_saem_fomc_tc <- saem(f_mmkin_parent_tc["FOMC",
])
#> Running main SAEM algorithm
-#> [1] "Wed Dec 16 18:27:43 2020"
+#> [1] "Mon Dec 21 05:58:46 2020"
#> ....
#> Minimisation finished
-#> [1] "Wed Dec 16 18:27:48 2020"
#> Likelihoods computed by importance sampling
#> AIC BIC
-#> 1 467.7096 464.9757
-#> 2 469.5208 466.3963
+#> [1] "Mon Dec 21 05:58:51 2020"
#> Error in compare.saemix(list(f_saem_fomc$so, f_saem_fomc_tc$so)): 'compare.saemix' requires at least two models.
#> Temporary DLL for differentials generated and loaded
#> Running main SAEM algorithm
-#> [1] "Wed Dec 16 18:27:50 2020"
+#> [1] "Mon Dec 21 05:58:53 2020"
#> ....
#> Minimisation finished
-#> [1] "Wed Dec 16 18:27:55 2020"
f_saem_dfop_sfo <- saem(f_mmkin["DFOP-SFO", ])
+#> [1] "Mon Dec 21 05:58:58 2020"
f_saem_dfop_sfo <- saem(f_mmkin["DFOP-SFO", ])
#> Running main SAEM algorithm
-#> [1] "Wed Dec 16 18:27:56 2020"
+#> [1] "Mon Dec 21 05:58:59 2020"
#> ....
#> Minimisation finished
-#> [1] "Wed Dec 16 18:28:05 2020"
# We can use print, plot and summary methods to check the results
+#> [1] "Mon Dec 21 05:59:08 2020"
#> Kinetic nonlinear mixed-effects model fit by SAEM
#> Structural model:
@@ -373,8 +375,6 @@ using
mmkin.
#> 170 observations of 2 variable(s) grouped in 5 datasets
#>
#> Likelihood computed by importance sampling
-#>
-#> LL by is "-407.78 (df=13)"
#> AIC BIC logLik
#> 841.6 836.5 -407.8
#>
@@ -400,12 +400,11 @@ using
mmkin.
#> SD.log_k2 1.90634 0.70934 3.1033
#> SD.g_qlogis 0.44771 -0.86417 1.7596
#>
-#> LL by is "-407.78 (df=13)"
#> saemix version used for fitting: 3.1.9000
+
#> saemix version used for fitting: 3.1.9000
#> mkin version used for pre-fitting: 0.9.50.4
#> R version used for fitting: 4.0.3
-#> Date of fit: Wed Dec 16 18:28:06 2020
-#> Date of summary: Wed Dec 16 18:28:06 2020
+#> Date of fit: Mon Dec 21 05:59:09 2020
+#> Date of summary: Mon Dec 21 05:59:09 2020
#>
#> Equations:
#> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -420,7 +419,7 @@ using
mmkin.
#>
#> Model predictions using solution type analytical
#>
-#> Fitted in 9.889 s using 300, 100 iterations
+#> Fitted in 9.836 s using 300, 100 iterations
#>
#> Variance model: Constant variance
#>
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