From a0192522fd79cced4e22e3e6096e4238b6ac2329 Mon Sep 17 00:00:00 2001
From: Johannes Ranke
Date: Wed, 16 Dec 2020 19:12:40 +0100
Subject: Add printout of d24 model and update docs
---
docs/dev/404.html | 2 +-
docs/dev/articles/index.html | 2 +-
docs/dev/authors.html | 2 +-
docs/dev/index.html | 2 +-
docs/dev/news/index.html | 2 +-
docs/dev/pkgdown.yml | 2 +-
docs/dev/reference/D24_2014.html | 20 +++++++++++++++++++-
docs/dev/reference/index.html | 2 +-
docs/dev/reference/saem.html | 41 ++++++++++++++++++++--------------------
9 files changed, 47 insertions(+), 28 deletions(-)
(limited to 'docs')
diff --git a/docs/dev/404.html b/docs/dev/404.html
index 8ca69469..bea38406 100644
--- a/docs/dev/404.html
+++ b/docs/dev/404.html
@@ -120,7 +120,7 @@
-
-
+
diff --git a/docs/dev/articles/index.html b/docs/dev/articles/index.html
index 81d49aa3..6daa6960 100644
--- a/docs/dev/articles/index.html
+++ b/docs/dev/articles/index.html
@@ -120,7 +120,7 @@
-
-
+
diff --git a/docs/dev/authors.html b/docs/dev/authors.html
index 681b964d..d592b39f 100644
--- a/docs/dev/authors.html
+++ b/docs/dev/authors.html
@@ -120,7 +120,7 @@
-
-
+
diff --git a/docs/dev/index.html b/docs/dev/index.html
index b1b64e6d..a4399963 100644
--- a/docs/dev/index.html
+++ b/docs/dev/index.html
@@ -87,7 +87,7 @@
-
-
+
diff --git a/docs/dev/news/index.html b/docs/dev/news/index.html
index 7059189d..e21de4c2 100644
--- a/docs/dev/news/index.html
+++ b/docs/dev/news/index.html
@@ -120,7 +120,7 @@
-
-
+
diff --git a/docs/dev/pkgdown.yml b/docs/dev/pkgdown.yml
index db10e692..a106449f 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: 2020-12-11T14:39Z
+last_built: 2020-12-16T17:28Z
urls:
reference: https://pkgdown.jrwb.de/mkin/reference
article: https://pkgdown.jrwb.de/mkin/articles
diff --git a/docs/dev/reference/D24_2014.html b/docs/dev/reference/D24_2014.html
index e4a3216d..5ebf664e 100644
--- a/docs/dev/reference/D24_2014.html
+++ b/docs/dev/reference/D24_2014.html
@@ -220,7 +220,25 @@ specific pieces of information in the comments.
#> 13 365 6.3#> Temporary DLL for differentials generated and loaded
+#> Temporary DLL for differentials generated and loaded
#> <mkindsg> holding 5 mkinds objects
+#> Title $title: Aerobic soil degradation data on 2,4-D from the EU assessment in 2014
+#> Occurrene of observed compounds $observed_n:
+#> D24 DCP DCA
+#> 5 4 4
+#> Meta information $meta:
+#> study usda_soil_type study_moisture_ref_type rel_moisture
+#> 1 Cohen 1991 Silt loam <NA> NA
+#> 2 Liu and Adelfinskaya 2011 Silt loam pF1 0.5
+#> 3 Liu and Adelfinskaya 2011 Loam pF1 0.5
+#> 4 Liu and Adelfinskaya 2011 Loam pF1 0.5
+#> 5 Liu and Adelfinskaya 2011 Loamy sand pF1 0.5
+#> temperature
+#> 1 25
+#> 2 20
+#> 3 20
+#> 4 20
+#> 5 20
#> Running main SAEM algorithm
-#> [1] "Fri Dec 11 15:37:47 2020"
+#> [1] "Wed Dec 16 18:27:30 2020"
#> ....
#> Minimisation finished
-#> [1] "Fri Dec 11 15:37:49 2020"
+#> [1] "Wed Dec 16 18:27:31 2020"
#> Running main SAEM algorithm
-#> [1] "Fri Dec 11 15:37:51 2020"
+#> [1] "Wed Dec 16 18:27:33 2020"
#> ....
#> Minimisation finished
-#> [1] "Fri Dec 11 15:37:52 2020"
f_saem_fomc <- saem(f_mmkin_parent["FOMC", ])
+#> [1] "Wed Dec 16 18:27:35 2020"
f_saem_fomc <- saem(f_mmkin_parent["FOMC", ])
#> Running main SAEM algorithm
-#> [1] "Fri Dec 11 15:37:52 2020"
+#> [1] "Wed Dec 16 18:27:35 2020"
#> ....
#> Minimisation finished
-#> [1] "Fri Dec 11 15:37:55 2020"
f_saem_dfop <- saem(f_mmkin_parent["DFOP", ])
+#> [1] "Wed Dec 16 18:27:37 2020"
f_saem_dfop <- saem(f_mmkin_parent["DFOP", ])
#> Running main SAEM algorithm
-#> [1] "Fri Dec 11 15:37:55 2020"
+#> [1] "Wed Dec 16 18:27:37 2020"
#> ....
#> Minimisation finished
-#> [1] "Fri Dec 11 15:37:58 2020"
+#> [1] "Wed Dec 16 18:27:40 2020"
#> Running main SAEM algorithm
-#> [1] "Fri Dec 11 15:38:01 2020"
+#> [1] "Wed Dec 16 18:27:43 2020"
#> ....
#> Minimisation finished
-#> [1] "Fri Dec 11 15:38:06 2020"
#> Likelihoods computed by importance sampling
#> AIC BIC
#> 1 467.7096 464.9757
#> 2 469.5208 466.3963
#> Running main SAEM algorithm
-#> [1] "Fri Dec 11 15:38:09 2020"
+#> [1] "Wed Dec 16 18:27:50 2020"
#> ....
#> Minimisation finished
-#> [1] "Fri Dec 11 15:38:14 2020"
f_saem_dfop_sfo <- saem(f_mmkin["DFOP-SFO", ])
+#> [1] "Wed Dec 16 18:27:55 2020"
f_saem_dfop_sfo <- saem(f_mmkin["DFOP-SFO", ])
#> Running main SAEM algorithm
-#> [1] "Fri Dec 11 15:38:15 2020"
+#> [1] "Wed Dec 16 18:27:56 2020"
#> ....
#> Minimisation finished
-#> [1] "Fri Dec 11 15:38:24 2020"
# We can use print, plot and summary methods to check the results
+#> [1] "Wed Dec 16 18:28:05 2020"
#> Kinetic nonlinear mixed-effects model fit by SAEM
#> Structural model:
@@ -375,6 +373,8 @@ 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
#>
@@ -400,11 +400,12 @@ using
mmkin.
#> SD.log_k2 1.90634 0.70934 3.1033
#> SD.g_qlogis 0.44771 -0.86417 1.7596
#> saemix version used for fitting: 3.1.9000
+
#>
+#> LL by is "-407.78 (df=13)"
#> 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: Fri Dec 11 15:38:25 2020
-#> Date of summary: Fri Dec 11 15:38:25 2020
+#> Date of fit: Wed Dec 16 18:28:06 2020
+#> Date of summary: Wed Dec 16 18:28:06 2020
#>
#> Equations:
#> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -419,7 +420,7 @@ using
mmkin.
#>
#> Model predictions using solution type analytical
#>
-#> Fitted in 10.096 s using 300, 100 iterations
+#> Fitted in 9.889 s using 300, 100 iterations
#>
#> Variance model: Constant variance
#>
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