From 95178837d3f91e84837628446b5fd468179af2b9 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 4 Jun 2019 15:09:28 +0200 Subject: Additional algorithm "d_c", more tests, docs The new algorithm tries direct optimization of the likelihood, as well as a three step procedure. In this way, we consistently get the model with the highest likelihood for SFO, DFOP and HS for all 12 new test datasets. --- docs/reference/AIC.mmkin.html | 4 +- docs/reference/CAKE_export.html | 4 +- docs/reference/DFOP.solution-1.png | Bin 19459 -> 19369 bytes docs/reference/DFOP.solution.html | 4 +- docs/reference/Extract.mmkin.html | 4 +- docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html | 4 +- docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html | 4 +- docs/reference/FOCUS_2006_HS_ref_A_to_F.html | 4 +- docs/reference/FOCUS_2006_SFO_ref_A_to_F.html | 4 +- docs/reference/FOCUS_2006_datasets.html | 4 +- docs/reference/FOMC.solution-1.png | Bin 18710 -> 18630 bytes docs/reference/FOMC.solution.html | 4 +- docs/reference/HS.solution-1.png | Bin 18994 -> 18893 bytes docs/reference/HS.solution.html | 4 +- docs/reference/IORE.solution-1.png | Bin 18751 -> 18668 bytes docs/reference/IORE.solution.html | 4 +- docs/reference/NAFTA_SOP_2015-1.png | Bin 41438 -> 41379 bytes docs/reference/NAFTA_SOP_2015.html | 4 +- docs/reference/NAFTA_SOP_Attachment-1.png | Bin 42265 -> 42204 bytes docs/reference/NAFTA_SOP_Attachment.html | 4 +- docs/reference/SFO.solution-1.png | Bin 18757 -> 18661 bytes docs/reference/SFO.solution.html | 4 +- docs/reference/SFORB.solution-1.png | Bin 20255 -> 20190 bytes docs/reference/SFORB.solution.html | 4 +- docs/reference/add_err-1.png | Bin 89826 -> 89500 bytes docs/reference/add_err-2.png | Bin 51200 -> 51024 bytes docs/reference/add_err-3.png | Bin 52617 -> 52523 bytes docs/reference/add_err.html | 4 +- docs/reference/endpoints.html | 4 +- docs/reference/experimental_data_for_UBA-1.png | Bin 0 -> 92900 bytes docs/reference/experimental_data_for_UBA.html | 223 +++++++++++++++++++++++++ docs/reference/geometric_mean.html | 4 +- docs/reference/ilr.html | 4 +- docs/reference/index.html | 16 +- docs/reference/logLik.mkinfit.html | 4 +- docs/reference/logistic.solution-1.png | Bin 63411 -> 63262 bytes docs/reference/logistic.solution-2.png | Bin 29229 -> 29139 bytes docs/reference/logistic.solution.html | 4 +- docs/reference/max_twa_parent.html | 4 +- docs/reference/mccall81_245T-1.png | Bin 58660 -> 58349 bytes docs/reference/mccall81_245T.html | 4 +- docs/reference/mkin_long_to_wide.html | 4 +- docs/reference/mkin_wide_to_long.html | 4 +- docs/reference/mkinds.html | 4 +- docs/reference/mkinerrmin.html | 4 +- docs/reference/mkinerrplot-1.png | Bin 35936 -> 35440 bytes docs/reference/mkinerrplot.html | 4 +- docs/reference/mkinfit.html | 205 +++++++++++++---------- docs/reference/mkinmod.html | 6 +- docs/reference/mkinparplot-1.png | Bin 16549 -> 16467 bytes docs/reference/mkinparplot.html | 4 +- docs/reference/mkinplot.html | 4 +- docs/reference/mkinpredict.html | 10 +- docs/reference/mkinresplot-1.png | Bin 14892 -> 14863 bytes docs/reference/mkinresplot.html | 4 +- docs/reference/mkinsub.html | 4 +- docs/reference/mmkin-1.png | Bin 97607 -> 97412 bytes docs/reference/mmkin-2.png | Bin 88226 -> 88000 bytes docs/reference/mmkin-3.png | Bin 85737 -> 85371 bytes docs/reference/mmkin-4.png | Bin 63315 -> 62975 bytes docs/reference/mmkin-5.png | Bin 57623 -> 57465 bytes docs/reference/mmkin.html | 8 +- docs/reference/nafta-1.png | Bin 41438 -> 41379 bytes docs/reference/nafta.html | 4 +- docs/reference/plot.mkinfit-1.png | Bin 45207 -> 45157 bytes docs/reference/plot.mkinfit-2.png | Bin 52884 -> 52842 bytes docs/reference/plot.mkinfit-3.png | Bin 51737 -> 51545 bytes docs/reference/plot.mkinfit-4.png | Bin 43712 -> 43670 bytes docs/reference/plot.mkinfit-5.png | Bin 59934 -> 59560 bytes docs/reference/plot.mkinfit-6.png | Bin 65811 -> 65273 bytes docs/reference/plot.mkinfit.html | 10 +- docs/reference/plot.mmkin-1.png | Bin 34389 -> 34273 bytes docs/reference/plot.mmkin-2.png | Bin 34725 -> 34629 bytes docs/reference/plot.mmkin-3.png | Bin 25445 -> 25550 bytes docs/reference/plot.mmkin-4.png | Bin 37126 -> 38129 bytes docs/reference/plot.mmkin.html | 8 +- docs/reference/plot.nafta.html | 4 +- docs/reference/print.mkinds.html | 4 +- docs/reference/print.mkinmod.html | 4 +- docs/reference/print.nafta.html | 4 +- docs/reference/schaefer07_complex_case-1.png | Bin 55662 -> 55626 bytes docs/reference/schaefer07_complex_case.html | 4 +- docs/reference/sigma_twocomp.html | 4 +- docs/reference/summary.mkinfit.html | 10 +- docs/reference/synthetic_data_for_UBA.html | 11 +- docs/reference/test_data_from_UBA_2014-1.png | Bin 53388 -> 53086 bytes docs/reference/test_data_from_UBA_2014-2.png | Bin 69105 -> 68670 bytes docs/reference/test_data_from_UBA_2014.html | 4 +- docs/reference/transform_odeparms.html | 4 +- 89 files changed, 474 insertions(+), 201 deletions(-) create mode 100644 docs/reference/experimental_data_for_UBA-1.png create mode 100644 docs/reference/experimental_data_for_UBA.html (limited to 'docs/reference') diff --git a/docs/reference/AIC.mmkin.html b/docs/reference/AIC.mmkin.html index c797567c..a5626847 100644 --- a/docs/reference/AIC.mmkin.html +++ b/docs/reference/AIC.mmkin.html @@ -64,7 +64,7 @@ mkin - 0.9.49.4 + 0.9.49.5 @@ -201,7 +201,7 @@
-

Site built with pkgdown 1.3.0.9000.

+

Site built with pkgdown 1.3.0.

diff --git a/docs/reference/CAKE_export.html b/docs/reference/CAKE_export.html index e4ed9cda..5db220ee 100644 --- a/docs/reference/CAKE_export.html +++ b/docs/reference/CAKE_export.html @@ -64,7 +64,7 @@ mkin - 0.9.49.4 + 0.9.49.5 @@ -232,7 +232,7 @@
-

Site built with pkgdown 1.3.0.9000.

+

Site built with pkgdown 1.3.0.

diff --git a/docs/reference/DFOP.solution-1.png b/docs/reference/DFOP.solution-1.png index 0fbc1da1..a2d75ccc 100644 Binary files a/docs/reference/DFOP.solution-1.png and b/docs/reference/DFOP.solution-1.png differ diff --git a/docs/reference/DFOP.solution.html b/docs/reference/DFOP.solution.html index 335c3a80..edfa70d3 100644 --- a/docs/reference/DFOP.solution.html +++ b/docs/reference/DFOP.solution.html @@ -64,7 +64,7 @@ mkin - 0.9.49.4 + 0.9.49.5 @@ -199,7 +199,7 @@
-

Site built with pkgdown 1.3.0.9000.

+

Site built with pkgdown 1.3.0.

diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index 652dfee0..1d1da50e 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -63,7 +63,7 @@ mkin - 0.9.49.4 + 0.9.49.5 @@ -229,7 +229,7 @@
-

Site built with pkgdown 1.3.0.9000.

+

Site built with pkgdown 1.3.0.

diff --git a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html index 047a5f4d..b1165f1d 100644 --- a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html +++ b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html @@ -67,7 +67,7 @@ in this fit." /> mkin - 0.9.49.4 + 0.9.49.5 @@ -187,7 +187,7 @@ in this fit.

-

Site built with pkgdown 1.3.0.9000.

+

Site built with pkgdown 1.3.0.

diff --git a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html index cc3560ed..03a15a5a 100644 --- a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html @@ -67,7 +67,7 @@ in this fit." /> mkin - 0.9.49.4 + 0.9.49.5 @@ -186,7 +186,7 @@ in this fit.

-

Site built with pkgdown 1.3.0.9000.

+

Site built with pkgdown 1.3.0.

diff --git a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html index 5f6fc197..6046ec88 100644 --- a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html @@ -67,7 +67,7 @@ in this fit." /> mkin - 0.9.49.4 + 0.9.49.5 @@ -187,7 +187,7 @@ in this fit.

-

Site built with pkgdown 1.3.0.9000.

+

Site built with pkgdown 1.3.0.

diff --git a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html index 45d00237..278425f6 100644 --- a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html @@ -67,7 +67,7 @@ in this fit." /> mkin - 0.9.49.4 + 0.9.49.5 @@ -185,7 +185,7 @@ in this fit.

-

Site built with pkgdown 1.3.0.9000.

+

Site built with pkgdown 1.3.0.

diff --git a/docs/reference/FOCUS_2006_datasets.html b/docs/reference/FOCUS_2006_datasets.html index 2b060f47..0d29deb2 100644 --- a/docs/reference/FOCUS_2006_datasets.html +++ b/docs/reference/FOCUS_2006_datasets.html @@ -63,7 +63,7 @@ mkin - 0.9.49.4 + 0.9.49.5 @@ -183,7 +183,7 @@
-

Site built with pkgdown 1.3.0.9000.

+

Site built with pkgdown 1.3.0.

diff --git a/docs/reference/FOMC.solution-1.png b/docs/reference/FOMC.solution-1.png index 127f3085..aa41a253 100644 Binary files a/docs/reference/FOMC.solution-1.png and b/docs/reference/FOMC.solution-1.png differ diff --git a/docs/reference/FOMC.solution.html b/docs/reference/FOMC.solution.html index 90a4810c..69c0a9ef 100644 --- a/docs/reference/FOMC.solution.html +++ b/docs/reference/FOMC.solution.html @@ -67,7 +67,7 @@ The form given here differs slightly from the original reference by Gustafson mkin - 0.9.49.4 + 0.9.49.5 @@ -213,7 +213,7 @@ The form given here differs slightly from the original reference by Gustafson
-

Site built with pkgdown 1.3.0.9000.

+

Site built with pkgdown 1.3.0.

diff --git a/docs/reference/HS.solution-1.png b/docs/reference/HS.solution-1.png index 4dc42c31..ae056d9b 100644 Binary files a/docs/reference/HS.solution-1.png and b/docs/reference/HS.solution-1.png differ diff --git a/docs/reference/HS.solution.html b/docs/reference/HS.solution.html index 1365e23f..e14f80ec 100644 --- a/docs/reference/HS.solution.html +++ b/docs/reference/HS.solution.html @@ -64,7 +64,7 @@ mkin - 0.9.49.4 + 0.9.49.5 @@ -200,7 +200,7 @@
-

Site built with pkgdown 1.3.0.9000.

+

Site built with pkgdown 1.3.0.

diff --git a/docs/reference/IORE.solution-1.png b/docs/reference/IORE.solution-1.png index d8b6e8e3..00e28460 100644 Binary files a/docs/reference/IORE.solution-1.png and b/docs/reference/IORE.solution-1.png differ diff --git a/docs/reference/IORE.solution.html b/docs/reference/IORE.solution.html index c67c2a37..ca0db0bb 100644 --- a/docs/reference/IORE.solution.html +++ b/docs/reference/IORE.solution.html @@ -64,7 +64,7 @@ mkin - 0.9.49.4 + 0.9.49.5 @@ -214,7 +214,7 @@
-

Site built with pkgdown 1.3.0.9000.

+

Site built with pkgdown 1.3.0.

diff --git a/docs/reference/NAFTA_SOP_2015-1.png b/docs/reference/NAFTA_SOP_2015-1.png index bcf5d12c..9025f2bb 100644 Binary files a/docs/reference/NAFTA_SOP_2015-1.png and b/docs/reference/NAFTA_SOP_2015-1.png differ diff --git a/docs/reference/NAFTA_SOP_2015.html b/docs/reference/NAFTA_SOP_2015.html index 84341a17..5b4ac227 100644 --- a/docs/reference/NAFTA_SOP_2015.html +++ b/docs/reference/NAFTA_SOP_2015.html @@ -63,7 +63,7 @@ mkin - 0.9.49.4 + 0.9.49.5 @@ -214,7 +214,7 @@
-

Site built with pkgdown 1.3.0.9000.

+

Site built with pkgdown 1.3.0.

diff --git a/docs/reference/NAFTA_SOP_Attachment-1.png b/docs/reference/NAFTA_SOP_Attachment-1.png index a40cb689..19da6da7 100644 Binary files a/docs/reference/NAFTA_SOP_Attachment-1.png and b/docs/reference/NAFTA_SOP_Attachment-1.png differ diff --git a/docs/reference/NAFTA_SOP_Attachment.html b/docs/reference/NAFTA_SOP_Attachment.html index 76d91c40..1af62530 100644 --- a/docs/reference/NAFTA_SOP_Attachment.html +++ b/docs/reference/NAFTA_SOP_Attachment.html @@ -63,7 +63,7 @@ mkin - 0.9.49.4 + 0.9.49.5 @@ -211,7 +211,7 @@
-

Site built with pkgdown 1.3.0.9000.

+

Site built with pkgdown 1.3.0.

diff --git a/docs/reference/SFO.solution-1.png b/docs/reference/SFO.solution-1.png index 9e6bd786..b0b854bb 100644 Binary files a/docs/reference/SFO.solution-1.png and b/docs/reference/SFO.solution-1.png differ diff --git a/docs/reference/SFO.solution.html b/docs/reference/SFO.solution.html index 2eb3a9b0..483869c4 100644 --- a/docs/reference/SFO.solution.html +++ b/docs/reference/SFO.solution.html @@ -63,7 +63,7 @@ mkin - 0.9.49.4 + 0.9.49.5 @@ -188,7 +188,7 @@
-

Site built with pkgdown 1.3.0.9000.

+

Site built with pkgdown 1.3.0.

diff --git a/docs/reference/SFORB.solution-1.png b/docs/reference/SFORB.solution-1.png index 6739fe6b..cd58caec 100644 Binary files a/docs/reference/SFORB.solution-1.png and b/docs/reference/SFORB.solution-1.png differ diff --git a/docs/reference/SFORB.solution.html b/docs/reference/SFORB.solution.html index f2743fe4..b49700f8 100644 --- a/docs/reference/SFORB.solution.html +++ b/docs/reference/SFORB.solution.html @@ -67,7 +67,7 @@ mkin - 0.9.49.4 + 0.9.49.5 @@ -205,7 +205,7 @@
-

Site built with pkgdown 1.3.0.9000.

+

Site built with pkgdown 1.3.0.

diff --git a/docs/reference/add_err-1.png b/docs/reference/add_err-1.png index 61f00d9b..fb369053 100644 Binary files a/docs/reference/add_err-1.png and b/docs/reference/add_err-1.png differ diff --git a/docs/reference/add_err-2.png b/docs/reference/add_err-2.png index 2fab0ee4..df843300 100644 Binary files a/docs/reference/add_err-2.png and b/docs/reference/add_err-2.png differ diff --git a/docs/reference/add_err-3.png b/docs/reference/add_err-3.png index 06f877c2..298f2ebd 100644 Binary files a/docs/reference/add_err-3.png and b/docs/reference/add_err-3.png differ diff --git a/docs/reference/add_err.html b/docs/reference/add_err.html index 63aa358c..4ce43f9f 100644 --- a/docs/reference/add_err.html +++ b/docs/reference/add_err.html @@ -65,7 +65,7 @@ mkin - 0.9.49.4 + 0.9.49.5 @@ -253,7 +253,7 @@
-

Site built with pkgdown 1.3.0.9000.

+

Site built with pkgdown 1.3.0.

diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html index 5f419781..c180dce2 100644 --- a/docs/reference/endpoints.html +++ b/docs/reference/endpoints.html @@ -66,7 +66,7 @@ with the advantage that the SFORB model can also be used for metabolites." /> mkin - 0.9.49.4 + 0.9.49.5 @@ -194,7 +194,7 @@ with the advantage that the SFORB model can also be used for metabolites.

-

Site built with pkgdown 1.3.0.9000.

+

Site built with pkgdown 1.3.0.

diff --git a/docs/reference/experimental_data_for_UBA-1.png b/docs/reference/experimental_data_for_UBA-1.png new file mode 100644 index 00000000..d3880fea Binary files /dev/null and b/docs/reference/experimental_data_for_UBA-1.png differ diff --git a/docs/reference/experimental_data_for_UBA.html b/docs/reference/experimental_data_for_UBA.html new file mode 100644 index 00000000..3e8d20ef --- /dev/null +++ b/docs/reference/experimental_data_for_UBA.html @@ -0,0 +1,223 @@ + + + + + + + + +Experimental datasets used for development and testing of error models — experimental_data_for_UBA_2019 • mkin + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+
+ + + +
+ +
+
+
+

Experimental datasets used for development and testing of error models

+ + +
+ +
+ +

The 12 datasets were extracted from active substance evaluation dossiers published + by EFSA. Kinetic evaluations shown for these datasets are intended to illustrate + and advance error model specifications. The fact that these data and some + results are shown here do not imply a license to use them in the context of + pesticide registrations, as the use of the data may be constrained by + data protection regulations.

+ +
+ + 
experimental_data_for_UBA_2019
+ +

Format

+ +

A list containing twelve datasets as an R6 class defined by mkinds, + each containing, among others, the following components

+
title

The name of the dataset, e.g. Soil 1

+
data

A data frame with the data in the form expected by mkinfit

+
+ +

Source

+ +

Ranke (2019) Documentation of results obtained for the error model expertise + written for the German Umweltbundesamt.

+ + +

Examples

+ 

+# Model definitions
+sfo_sfo <- mkinmod(
+  parent = mkinsub("SFO", to = "A1"),
+  A1 = mkinsub("SFO"),
+  use_of_ff = "max"
+)
#> Successfully compiled differential equation model from auto-generated C code.

+dfop_sfo <- mkinmod(
+  parent = mkinsub("DFOP", to = "A1"),
+  A1 = mkinsub("SFO"),
+  use_of_ff = "max"
+)
#> Successfully compiled differential equation model from auto-generated C code.

+sfo_sfo_sfo <- mkinmod(
+  parent = mkinsub("SFO", to = "A1"),
+  A1 = mkinsub("SFO", to = "A2"),
+  A2 = mkinsub("SFO"),
+  use_of_ff = "max"
+)
#> Successfully compiled differential equation model from auto-generated C code.

+dfop_sfo_sfo <- mkinmod(
+  parent = mkinsub("DFOP", to = "A1"),
+  A1 = mkinsub("SFO", to = "A2"),
+  A2 = mkinsub("SFO"),
+  use_of_ff = "max"
+)
#> Successfully compiled differential equation model from auto-generated C code.
d_1_2 <- lapply(experimental_data_for_UBA_2019[1:2], function(x) x$data)
+names(d_1_2) <- paste("Soil", 1:2)
+
+
+f_1_2_tc <- mmkin(list("DFOP-SFO-SFO" = dfop_sfo_sfo), d_1_2, error_model = "tc")
+
+plot(f_1_2_tc, resplot = "errmod")

+
+
+ +
+ +
+
+

Developed by Johannes Ranke.

+
+ +
+

Site built with pkgdown 1.3.0.

+
+
+
+ + + + + + diff --git a/docs/reference/geometric_mean.html b/docs/reference/geometric_mean.html index 908aa8cc..286b40d4 100644 --- a/docs/reference/geometric_mean.html +++ b/docs/reference/geometric_mean.html @@ -63,7 +63,7 @@ mkin - 0.9.49.4 + 0.9.49.5 @@ -174,7 +174,7 @@
-

Site built with pkgdown 1.3.0.9000.

+

Site built with pkgdown 1.3.0.

diff --git a/docs/reference/ilr.html b/docs/reference/ilr.html index 0a18d535..3eac2872 100644 --- a/docs/reference/ilr.html +++ b/docs/reference/ilr.html @@ -63,7 +63,7 @@ mkin - 0.9.49.4 + 0.9.49.5 @@ -196,7 +196,7 @@
-

Site built with pkgdown 1.3.0.9000.

+

Site built with pkgdown 1.3.0.

diff --git a/docs/reference/index.html b/docs/reference/index.html index 42028d60..c5ac0d72 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -60,7 +60,7 @@ mkin - 0.9.49.4 + 0.9.49.5 @@ -194,6 +194,12 @@

Function to plot the confidence intervals obtained using mkinfit

+ +

mkinerrplot()

+ +

Function to plot squared residuals and the error model for an mkin object

+ +

endpoints()

@@ -306,6 +312,12 @@

Synthetic datasets for one parent compound with two metabolites

+ +

experimental_data_for_UBA_2019

+ +

Experimental datasets used for development and testing of error models

+ +

test_data_from_UBA_2014

@@ -529,7 +541,7 @@
-

Site built with pkgdown 1.3.0.9000.

+

Site built with pkgdown 1.3.0.

diff --git a/docs/reference/logLik.mkinfit.html b/docs/reference/logLik.mkinfit.html index 0184d573..a6cf4867 100644 --- a/docs/reference/logLik.mkinfit.html +++ b/docs/reference/logLik.mkinfit.html @@ -69,7 +69,7 @@ The total number of estimated parameters returned with the value mkin - 0.9.49.4 + 0.9.49.5 @@ -205,7 +205,7 @@ The total number of estimated parameters returned with the value
-

Site built with pkgdown 1.3.0.9000.

+

Site built with pkgdown 1.3.0.

diff --git a/docs/reference/logistic.solution-1.png b/docs/reference/logistic.solution-1.png index 0aaa520b..b9fb891c 100644 Binary files a/docs/reference/logistic.solution-1.png and b/docs/reference/logistic.solution-1.png differ diff --git a/docs/reference/logistic.solution-2.png b/docs/reference/logistic.solution-2.png index d1831a46..752fd9d4 100644 Binary files a/docs/reference/logistic.solution-2.png and b/docs/reference/logistic.solution-2.png differ diff --git a/docs/reference/logistic.solution.html b/docs/reference/logistic.solution.html index 3b45b14f..cee169d2 100644 --- a/docs/reference/logistic.solution.html +++ b/docs/reference/logistic.solution.html @@ -64,7 +64,7 @@ mkin - 0.9.49.4 + 0.9.49.5 @@ -242,7 +242,7 @@
-

Site built with pkgdown 1.3.0.9000.

+

Site built with pkgdown 1.3.0.

diff --git a/docs/reference/max_twa_parent.html b/docs/reference/max_twa_parent.html index 33c5ee4f..ad19853d 100644 --- a/docs/reference/max_twa_parent.html +++ b/docs/reference/max_twa_parent.html @@ -67,7 +67,7 @@ guidance." /> mkin - 0.9.49.4 + 0.9.49.5 @@ -196,7 +196,7 @@ guidance.

-

Site built with pkgdown 1.3.0.9000.

+

Site built with pkgdown 1.3.0.

diff --git a/docs/reference/mccall81_245T-1.png b/docs/reference/mccall81_245T-1.png index 859f315a..b9a42571 100644 Binary files a/docs/reference/mccall81_245T-1.png and b/docs/reference/mccall81_245T-1.png differ diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index 1db9a9d9..1af77f6b 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -65,7 +65,7 @@ mkin - 0.9.49.4 + 0.9.49.5 @@ -237,7 +237,7 @@
-

Site built with pkgdown 1.3.0.9000.

+

Site built with pkgdown 1.3.0.

diff --git a/docs/reference/mkin_long_to_wide.html b/docs/reference/mkin_long_to_wide.html index 7d0ad2fc..6f0d5376 100644 --- a/docs/reference/mkin_long_to_wide.html +++ b/docs/reference/mkin_long_to_wide.html @@ -65,7 +65,7 @@ mkin - 0.9.49.4 + 0.9.49.5 @@ -208,7 +208,7 @@
-

Site built with pkgdown 1.3.0.9000.

+

Site built with pkgdown 1.3.0.

diff --git a/docs/reference/mkin_wide_to_long.html b/docs/reference/mkin_wide_to_long.html index 4fc0e2ed..869c4586 100644 --- a/docs/reference/mkin_wide_to_long.html +++ b/docs/reference/mkin_wide_to_long.html @@ -64,7 +64,7 @@ mkin - 0.9.49.4 + 0.9.49.5 @@ -186,7 +186,7 @@
-

Site built with pkgdown 1.3.0.9000.

+

Site built with pkgdown 1.3.0.

diff --git a/docs/reference/mkinds.html b/docs/reference/mkinds.html index 2c01be70..89f40abf 100644 --- a/docs/reference/mkinds.html +++ b/docs/reference/mkinds.html @@ -63,7 +63,7 @@ mkin - 0.9.49.4 + 0.9.49.5 @@ -176,7 +176,7 @@ in order to be compatible with mkinfit

-

Site built with pkgdown 1.3.0.9000.

+

Site built with pkgdown 1.3.0.

diff --git a/docs/reference/mkinerrmin.html b/docs/reference/mkinerrmin.html index 3ebea1e4..8fd09215 100644 --- a/docs/reference/mkinerrmin.html +++ b/docs/reference/mkinerrmin.html @@ -64,7 +64,7 @@ chi-squared test as defined in the FOCUS kinetics report from 2006." /> mkin - 0.9.49.4 + 0.9.49.5 @@ -211,7 +211,7 @@ chi-squared test as defined in the FOCUS kinetics report from 2006.

-

Site built with pkgdown 1.3.0.9000.

+

Site built with pkgdown 1.3.0.

diff --git a/docs/reference/mkinerrplot-1.png b/docs/reference/mkinerrplot-1.png index 9c663646..476edc49 100644 Binary files a/docs/reference/mkinerrplot-1.png and b/docs/reference/mkinerrplot-1.png differ diff --git a/docs/reference/mkinerrplot.html b/docs/reference/mkinerrplot.html index 66da40b5..a0201963 100644 --- a/docs/reference/mkinerrplot.html +++ b/docs/reference/mkinerrplot.html @@ -68,7 +68,7 @@ mkin - 0.9.49.4 + 0.9.49.5 @@ -238,7 +238,7 @@
-

Site built with pkgdown 1.3.0.9000.

+

Site built with pkgdown 1.3.0.

diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index bfca44fc..8cabcb21 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -71,7 +71,7 @@ Per default, parameters in the kinetic models are internally transformed in mkin - 0.9.49.4 + 0.9.49.5 @@ -163,6 +163,8 @@ Per default, parameters in the kinetic models are internally transformed in quiet = FALSE, atol = 1e-8, rtol = 1e-10, n.outtimes = 100, error_model = c("const", "obs", "tc"), + error_model_algorithm = c("d_3", "direct", "twostep", "threestep", "fourstep", "IRLS"), + reweight.tol = 1e-8, reweight.max.iter = 10, trace_parms = FALSE, ...)

Arguments

@@ -321,6 +323,41 @@ Per default, parameters in the kinetic models are internally transformed in errors follow a lognormal distribution for large values, not a normal distribution as assumed by this method.

+ + error_model_algorithm +

If the error model is "const", the error model algorithm is ignored, + because no special algorithm is needed and unweighted (also known as + ordinary) least squares fitting can be applied.

+

The default algorithm "d_3" will directly minimize the negative + log-likelihood and - independently - also use the three step algorithm + described below. The fit with the higher likelihood is returned.

+

The algorithm "direct" will directly minimize the negative + log-likelihood.

+

The algorithm "twostep" will minimize the negative log-likelihood + after an initial unweighted leas squares optimisation step.

+

The algorithm "threestep" starts with unweighted least squares, + then optimizes only the error model using the degradation model + parameters found, and then minimizes the negative log-likelihood + with free degradation and error model parameters.

+

The algorithm "fourstep" starts with unweighted least squares, + then optimizes only the error model using the degradation model + parameters found, then optimizes the degradation model again + with fixed error model parameters, and finally minimizes the negative + log-likelihood with free degradation and error model parameters.

+

The algorithm "IRLS" starts with unweighted least squares, + and then iterates optimization of the error model parameters and subsequent + optimization of the degradation model using those error model parameters, + until the error model parameters converge.

+ + + reweight.tol +

Tolerance for the convergence criterion calculated from the error model + parameters in IRLS fits.

+ + + reweight.max.iter +

Maximum number of iterations in IRLS fits.

+ trace_parms

Should a trace of the parameter values be listed?

@@ -360,17 +397,17 @@ Per default, parameters in the kinetic models are internally transformed in

Examples

# Use shorthand notation for parent only degradation
 fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
-summary(fit)
#> mkin version used for fitting:    0.9.49.4 
+summary(fit)
#> mkin version used for fitting:    0.9.49.5 
 #> R version used for fitting:       3.6.0 
-#> Date of fit:     Wed May  8 20:50:50 2019 
-#> Date of summary: Wed May  8 20:50:50 2019 
+#> Date of fit:     Tue Jun  4 15:01:15 2019 
+#> Date of summary: Tue Jun  4 15:01:15 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 #> 
 #> Model predictions using solution type analytical 
 #> 
-#> Fitted using 222 model solutions performed in 0.456 s
+#> Fitted using 222 model solutions performed in 0.461 s
 #> 
 #> Error model:
 #> Constant variance 
@@ -443,7 +480,7 @@ Per default, parameters in the kinetic models are internally transformed in
   m1 = mkinsub("SFO"))
#> Successfully compiled differential equation model from auto-generated C code.
# Fit the model to the FOCUS example dataset D using defaults
 print(system.time(fit <- mkinfit(SFO_SFO, FOCUS_2006_D,
                            solution_type = "eigen", quiet = TRUE)))
#> Warning: Observations with value of zero were removed from the data
#>        User      System verstrichen 
-#>       1.488       0.000       1.488 
coef(fit)
#> NULL
endpoints(fit)
#> $ff
+#>       1.521       0.000       1.526 
coef(fit)
#> NULL
endpoints(fit)
#> $ff
 #> parent_sink   parent_m1     m1_sink 
 #>    0.485524    0.514476    1.000000 
 #> 
@@ -515,7 +552,7 @@ Per default, parameters in the kinetic models are internally transformed in
 #> Sum of squared residuals at call 126: 371.2134
 #> Sum of squared residuals at call 135: 371.2134
 #> Negative log-likelihood at call 145: 97.22429
#> Optimisation successfully terminated.
#>        User      System verstrichen 
-#>       1.086       0.000       1.087 
coef(fit.deSolve)
#> NULL
endpoints(fit.deSolve)
#> $ff
+#>       1.093       0.000       1.093 
coef(fit.deSolve)
#> NULL
endpoints(fit.deSolve)
#> $ff
 #> parent_sink   parent_m1     m1_sink 
 #>    0.485524    0.514476    1.000000 
 #> 
@@ -545,10 +582,10 @@ Per default, parameters in the kinetic models are internally transformed in
 fit.SFORB_SFO <- mkinfit(SFORB_SFO, FOCUS_2006_D, parms.ini = fit.SFORB$bparms.ode, quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data

 
# Weighted fits, including IRLS
 SFO_SFO.ff <- mkinmod(parent = mkinsub("SFO", "m1"),
-                      m1 = mkinsub("SFO"), use_of_ff = "max")
#> Successfully compiled differential equation model from auto-generated C code.
f.noweight <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
summary(f.noweight)
#> mkin version used for fitting:    0.9.49.4 
+                      m1 = mkinsub("SFO"), use_of_ff = "max")
#> Successfully compiled differential equation model from auto-generated C code.
f.noweight <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
summary(f.noweight)
#> mkin version used for fitting:    0.9.49.5 
 #> R version used for fitting:       3.6.0 
-#> Date of fit:     Wed May  8 20:51:06 2019 
-#> Date of summary: Wed May  8 20:51:06 2019 
+#> Date of fit:     Tue Jun  4 15:01:31 2019 
+#> Date of summary: Tue Jun  4 15:01:31 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -556,7 +593,7 @@ Per default, parameters in the kinetic models are internally transformed in
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted using 421 model solutions performed in 1.082 s
+#> Fitted using 421 model solutions performed in 1.096 s
 #> 
 #> Error model:
 #> Constant variance 
@@ -663,10 +700,10 @@ Per default, parameters in the kinetic models are internally transformed in
 #>   100       m1    31.04  31.98163 -9.416e-01
 #>   100       m1    33.13  31.98163  1.148e+00
 #>   120       m1    25.15  28.78984 -3.640e+00
-#>   120       m1    33.31  28.78984  4.520e+00
f.obs <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, error_model = "obs", quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
summary(f.obs)
#> mkin version used for fitting:    0.9.49.4 
+#>   120       m1    33.31  28.78984  4.520e+00
f.obs <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, error_model = "obs", quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
summary(f.obs)
#> mkin version used for fitting:    0.9.49.5 
 #> R version used for fitting:       3.6.0 
-#> Date of fit:     Wed May  8 20:51:08 2019 
-#> Date of summary: Wed May  8 20:51:08 2019 
+#> Date of fit:     Tue Jun  4 15:01:34 2019 
+#> Date of summary: Tue Jun  4 15:01:34 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -674,19 +711,19 @@ Per default, parameters in the kinetic models are internally transformed in
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted using 758 model solutions performed in 1.971 s
+#> Fitted using 979 model solutions performed in 2.603 s
 #> 
 #> Error model:
 #> Variance unique to each observed variable 
 #> 
 #> Starting values for parameters to be optimised:
-#>                   value   type
-#> parent_0       100.7500  state
-#> k_parent         0.1000 deparm
-#> k_m1             0.1001 deparm
-#> f_parent_to_m1   0.5000 deparm
-#> sigma_parent     3.0000  error
-#> sigma_m1         3.0000  error
+#>                     value   type
+#> parent_0       100.750000  state
+#> k_parent         0.100000 deparm
+#> k_m1             0.100100 deparm
+#> f_parent_to_m1   0.500000 deparm
+#> sigma_parent     3.398909  error
+#> sigma_m1         2.857157  error
 #> 
 #> Starting values for the transformed parameters actually optimised:
 #>                     value lower upper
@@ -694,8 +731,8 @@ Per default, parameters in the kinetic models are internally transformed in
 #> log_k_parent    -2.302585  -Inf   Inf
 #> log_k_m1        -2.301586  -Inf   Inf
 #> f_parent_ilr_1   0.000000  -Inf   Inf
-#> sigma_parent     3.000000     0   Inf
-#> sigma_m1         3.000000     0   Inf
+#> sigma_parent     3.398909     0   Inf
+#> sigma_m1         2.857157     0   Inf
 #> 
 #> Fixed parameter values:
 #>      value  type
@@ -715,14 +752,14 @@ Per default, parameters in the kinetic models are internally transformed in
 #> parent_0        1.00000      0.51078 -0.19133       -0.59997     0.035670
 #> log_k_parent    0.51078      1.00000 -0.37458       -0.59239     0.069833
 #> log_k_m1       -0.19133     -0.37458  1.00000        0.74398    -0.026158
-#> f_parent_ilr_1 -0.59997     -0.59239  0.74398        1.00000    -0.041368
+#> f_parent_ilr_1 -0.59997     -0.59239  0.74398        1.00000    -0.041369
 #> sigma_parent    0.03567      0.06983 -0.02616       -0.04137     1.000000
-#> sigma_m1       -0.03385     -0.06627  0.02482        0.03925    -0.004628
+#> sigma_m1       -0.03385     -0.06627  0.02482        0.03926    -0.004628
 #>                 sigma_m1
 #> parent_0       -0.033847
 #> log_k_parent   -0.066265
-#> log_k_m1        0.024821
-#> f_parent_ilr_1  0.039255
+#> log_k_m1        0.024823
+#> f_parent_ilr_1  0.039256
 #> sigma_parent   -0.004628
 #> sigma_m1        1.000000
 #> 
@@ -786,17 +823,17 @@ Per default, parameters in the kinetic models are internally transformed in
 #>    21       m1    46.44  41.65115  4.789e+00
 #>    35       m1    41.22  43.29465 -2.075e+00
 #>    35       m1    37.95  43.29465 -5.345e+00
-#>    50       m1    41.19  41.19948 -9.481e-03
+#>    50       m1    41.19  41.19948 -9.479e-03
 #>    50       m1    40.01  41.19948 -1.189e+00
-#>    75       m1    40.09  36.44036  3.650e+00
-#>    75       m1    33.85  36.44036 -2.590e+00
-#>   100       m1    31.04  31.98774 -9.477e-01
-#>   100       m1    33.13  31.98774  1.142e+00
-#>   120       m1    25.15  28.80430 -3.654e+00
-#>   120       m1    33.31  28.80430  4.506e+00
f.tc <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, error_model = "tc", quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
summary(f.tc)
#> mkin version used for fitting:    0.9.49.4 
+#>    75       m1    40.09  36.44035  3.650e+00
+#>    75       m1    33.85  36.44035 -2.590e+00
+#>   100       m1    31.04  31.98773 -9.477e-01
+#>   100       m1    33.13  31.98773  1.142e+00
+#>   120       m1    25.15  28.80429 -3.654e+00
+#>   120       m1    33.31  28.80429  4.506e+00
f.tc <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, error_model = "tc", quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
summary(f.tc)
#> mkin version used for fitting:    0.9.49.5 
 #> R version used for fitting:       3.6.0 
-#> Date of fit:     Wed May  8 20:51:11 2019 
-#> Date of summary: Wed May  8 20:51:11 2019 
+#> Date of fit:     Tue Jun  4 15:01:43 2019 
+#> Date of summary: Tue Jun  4 15:01:43 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -804,28 +841,28 @@ Per default, parameters in the kinetic models are internally transformed in
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted using 821 model solutions performed in 3.29 s
+#> Fitted using 2289 model solutions performed in 9.499 s
 #> 
 #> Error model:
 #> Two-component variance function 
 #> 
 #> Starting values for parameters to be optimised:
-#>                   value   type
-#> parent_0       100.7500  state
-#> k_parent         0.1000 deparm
-#> k_m1             0.1001 deparm
-#> f_parent_to_m1   0.5000 deparm
-#> sigma_low        0.1000  error
-#> rsd_high         0.1000  error
+#>                       value   type
+#> parent_0       1.007500e+02  state
+#> k_parent       1.000000e-01 deparm
+#> k_m1           1.001000e-01 deparm
+#> f_parent_to_m1 5.000000e-01 deparm
+#> sigma_low      5.641148e-03  error
+#> rsd_high       8.430766e-02  error
 #> 
 #> Starting values for the transformed parameters actually optimised:
-#>                     value lower upper
-#> parent_0       100.750000  -Inf   Inf
-#> log_k_parent    -2.302585  -Inf   Inf
-#> log_k_m1        -2.301586  -Inf   Inf
-#> f_parent_ilr_1   0.000000  -Inf   Inf
-#> sigma_low        0.100000     0   Inf
-#> rsd_high         0.100000     0   Inf
+#>                        value lower upper
+#> parent_0       100.750000000  -Inf   Inf
+#> log_k_parent    -2.302585093  -Inf   Inf
+#> log_k_m1        -2.301585593  -Inf   Inf
+#> f_parent_ilr_1   0.000000000  -Inf   Inf
+#> sigma_low        0.005641148     0   Inf
+#> rsd_high         0.084307660     0   Inf
 #> 
 #> Fixed parameter values:
 #>      value  type
@@ -856,7 +893,7 @@ Per default, parameters in the kinetic models are internally transformed in
 #>                 Estimate  t value    Pr(>t)     Lower     Upper
 #> parent_0       1.007e+02  38.4300 1.180e-28 95.400000 1.061e+02
 #> k_parent       1.006e-01 112.8000 1.718e-43  0.098760 1.024e-01
-#> k_m1           5.167e-03  10.9500 1.172e-12  0.004290 6.223e-03
+#> k_m1           5.167e-03  10.9500 1.171e-12  0.004290 6.223e-03
 #> f_parent_to_m1 5.084e-01  26.0100 2.146e-23  0.468600 5.481e-01
 #> sigma_low      3.050e-03   0.6314 2.661e-01 -0.006786 1.289e-02
 #> rsd_high       7.928e-02   8.4170 6.418e-10  0.060100 9.847e-02
@@ -879,18 +916,18 @@ Per default, parameters in the kinetic models are internally transformed in
 #> 
 #> Data:
 #>  time variable observed predicted   residual
-#>     0   parent    99.46 100.73433  -1.274329
-#>     0   parent   102.04 100.73433   1.305671
-#>     1   parent    93.50  91.09750   2.402495
-#>     1   parent    92.50  91.09750   1.402495
-#>     3   parent    63.23  74.50140 -11.271403
-#>     3   parent    68.99  74.50140  -5.511403
-#>     7   parent    52.32  49.82880   2.491205
-#>     7   parent    55.13  49.82880   5.301205
-#>    14   parent    27.27  24.64809   2.621909
-#>    14   parent    26.64  24.64809   1.991909
-#>    21   parent    11.50  12.19231  -0.692315
-#>    21   parent    11.64  12.19231  -0.552315
+#>     0   parent    99.46 100.73434  -1.274339
+#>     0   parent   102.04 100.73434   1.305661
+#>     1   parent    93.50  91.09751   2.402486
+#>     1   parent    92.50  91.09751   1.402486
+#>     3   parent    63.23  74.50141 -11.271410
+#>     3   parent    68.99  74.50141  -5.511410
+#>     7   parent    52.32  49.82880   2.491201
+#>     7   parent    55.13  49.82880   5.301201
+#>    14   parent    27.27  24.64809   2.621908
+#>    14   parent    26.64  24.64809   1.991908
+#>    21   parent    11.50  12.19232  -0.692315
+#>    21   parent    11.64  12.19232  -0.552315
 #>    35   parent     2.85   2.98327  -0.133266
 #>    35   parent     2.91   2.98327  -0.073266
 #>    50   parent     0.69   0.66013   0.029874
@@ -899,24 +936,24 @@ Per default, parameters in the kinetic models are internally transformed in
 #>    75   parent     0.06   0.05344   0.006562
 #>     1       m1     4.84   4.88645  -0.046451
 #>     1       m1     5.64   4.88645   0.753549
-#>     3       m1    12.91  13.22867  -0.318668
-#>     3       m1    12.96  13.22867  -0.268668
-#>     7       m1    22.97  25.36416  -2.394164
-#>     7       m1    24.47  25.36416  -0.894164
-#>    14       m1    41.69  37.00974   4.680265
-#>    14       m1    33.21  37.00974  -3.799735
-#>    21       m1    44.37  41.90133   2.468670
-#>    21       m1    46.44  41.90133   4.538670
-#>    35       m1    41.22  43.45691  -2.236914
-#>    35       m1    37.95  43.45691  -5.506914
-#>    50       m1    41.19  41.34199  -0.151988
-#>    50       m1    40.01  41.34199  -1.331988
-#>    75       m1    40.09  36.61471   3.475290
-#>    75       m1    33.85  36.61471  -2.764710
-#>   100       m1    31.04  32.20083  -1.160830
-#>   100       m1    33.13  32.20083   0.929170
-#>   120       m1    25.15  29.04131  -3.891312
-#>   120       m1    33.31  29.04131   4.268688

+#>     3       m1    12.91  13.22867  -0.318669
+#>     3       m1    12.96  13.22867  -0.268669
+#>     7       m1    22.97  25.36417  -2.394166
+#>     7       m1    24.47  25.36417  -0.894166
+#>    14       m1    41.69  37.00974   4.680263
+#>    14       m1    33.21  37.00974  -3.799737
+#>    21       m1    44.37  41.90133   2.468669
+#>    21       m1    46.44  41.90133   4.538669
+#>    35       m1    41.22  43.45691  -2.236913
+#>    35       m1    37.95  43.45691  -5.506913
+#>    50       m1    41.19  41.34199  -0.151985
+#>    50       m1    40.01  41.34199  -1.331985
+#>    75       m1    40.09  36.61471   3.475295
+#>    75       m1    33.85  36.61471  -2.764705
+#>   100       m1    31.04  32.20082  -1.160823
+#>   100       m1    33.13  32.20082   0.929177
+#>   120       m1    25.15  29.04130  -3.891304
+#>   120       m1    33.31  29.04130   4.268696
-

Site built with pkgdown 1.3.0.9000.

+

Site built with pkgdown 1.3.0.

diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index 51be5465..2c5f056e 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -68,7 +68,7 @@ For the definition of model types and their parameters, the equations given mkin - 0.9.49.4 + 0.9.49.5 @@ -234,7 +234,7 @@ For the definition of model types and their parameters, the equations given SFO_SFO <- mkinmod( parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"), verbose = TRUE)
#> Compilation argument: -#> /usr/lib/R/bin/R CMD SHLIB file4bbd307f8763.c 2> file4bbd307f8763.c.err.txt +#> /usr/lib/R/bin/R CMD SHLIB filebbe6b539c4f.c 2> filebbe6b539c4f.c.err.txt #> Program source: #> 1: #include <R.h> #> 2: @@ -291,7 +291,7 @@ For the definition of model types and their parameters, the equations given
-

Site built with pkgdown 1.3.0.9000.

+

Site built with pkgdown 1.3.0.

diff --git a/docs/reference/mkinparplot-1.png b/docs/reference/mkinparplot-1.png index 65918d53..d4259579 100644 Binary files a/docs/reference/mkinparplot-1.png and b/docs/reference/mkinparplot-1.png differ diff --git a/docs/reference/mkinparplot.html b/docs/reference/mkinparplot.html index 8cfb9374..71fd6245 100644 --- a/docs/reference/mkinparplot.html +++ b/docs/reference/mkinparplot.html @@ -64,7 +64,7 @@ mkin - 0.9.49.4 + 0.9.49.5 @@ -177,7 +177,7 @@
-

Site built with pkgdown 1.3.0.9000.

+

Site built with pkgdown 1.3.0.

diff --git a/docs/reference/mkinplot.html b/docs/reference/mkinplot.html index 0c8ee269..5ac632c8 100644 --- a/docs/reference/mkinplot.html +++ b/docs/reference/mkinplot.html @@ -63,7 +63,7 @@ mkin - 0.9.49.4 + 0.9.49.5 @@ -172,7 +172,7 @@
-

Site built with pkgdown 1.3.0.9000.

+

Site built with pkgdown 1.3.0.

diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index 8e2e307b..f339b26a 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -65,7 +65,7 @@ mkin - 0.9.49.4 + 0.9.49.5 @@ -328,17 +328,17 @@ c(parent = 100, m1 = 0), seq(0, 20, by = 0.1), solution_type = "eigen")[201,]))
#> time parent m1 #> 201 20 4.978707 27.46227
#> User System verstrichen -#> 0.003 0.000 0.004
system.time( +#> 0.003 0.000 0.003
system.time( print(mkinpredict(SFO_SFO, c(k_parent_m1 = 0.05, k_parent_sink = 0.1, k_m1_sink = 0.01), c(parent = 100, m1 = 0), seq(0, 20, by = 0.1), solution_type = "deSolve")[201,]))
#> time parent m1 #> 201 20 4.978707 27.46227
#> User System verstrichen -#> 0.002 0.000 0.001
system.time( +#> 0.002 0.000 0.002
system.time( print(mkinpredict(SFO_SFO, c(k_parent_m1 = 0.05, k_parent_sink = 0.1, k_m1_sink = 0.01), c(parent = 100, m1 = 0), seq(0, 20, by = 0.1), solution_type = "deSolve", use_compiled = FALSE)[201,]))
#> time parent m1 #> 201 20 4.978707 27.46227
#> User System verstrichen -#> 0.021 0.000 0.021
+#> 0.021 0.000 0.022
# Predict from a fitted model f <- mkinfit(SFO_SFO, FOCUS_2006_C)
#> Ordinary least squares optimisation
#> Sum of squared residuals at call 1: 552.5739 #> Sum of squared residuals at call 3: 552.5739 @@ -397,7 +397,7 @@
-

Site built with pkgdown 1.3.0.9000.

+

Site built with pkgdown 1.3.0.

diff --git a/docs/reference/mkinresplot-1.png b/docs/reference/mkinresplot-1.png index 344561de..d29181c3 100644 Binary files a/docs/reference/mkinresplot-1.png and b/docs/reference/mkinresplot-1.png differ diff --git a/docs/reference/mkinresplot.html b/docs/reference/mkinresplot.html index ab3b35b4..45722db4 100644 --- a/docs/reference/mkinresplot.html +++ b/docs/reference/mkinresplot.html @@ -66,7 +66,7 @@ mkin - 0.9.49.4 + 0.9.49.5 @@ -224,7 +224,7 @@
-

Site built with pkgdown 1.3.0.9000.

+

Site built with pkgdown 1.3.0.

diff --git a/docs/reference/mkinsub.html b/docs/reference/mkinsub.html index b87ceca4..4d81f639 100644 --- a/docs/reference/mkinsub.html +++ b/docs/reference/mkinsub.html @@ -64,7 +64,7 @@ mkin - 0.9.49.4 + 0.9.49.5 @@ -203,7 +203,7 @@
-

Site built with pkgdown 1.3.0.9000.

+

Site built with pkgdown 1.3.0.

diff --git a/docs/reference/mmkin-1.png b/docs/reference/mmkin-1.png index 9d86a2df..328cec9b 100644 Binary files a/docs/reference/mmkin-1.png and b/docs/reference/mmkin-1.png differ diff --git a/docs/reference/mmkin-2.png b/docs/reference/mmkin-2.png index 59d293d5..5e264309 100644 Binary files a/docs/reference/mmkin-2.png and b/docs/reference/mmkin-2.png differ diff --git a/docs/reference/mmkin-3.png b/docs/reference/mmkin-3.png index a947ac65..0a58a86b 100644 Binary files a/docs/reference/mmkin-3.png and b/docs/reference/mmkin-3.png differ diff --git a/docs/reference/mmkin-4.png b/docs/reference/mmkin-4.png index 89048ea3..9d8c0931 100644 Binary files a/docs/reference/mmkin-4.png and b/docs/reference/mmkin-4.png differ diff --git a/docs/reference/mmkin-5.png b/docs/reference/mmkin-5.png index 0c81649c..29206932 100644 Binary files a/docs/reference/mmkin-5.png and b/docs/reference/mmkin-5.png differ diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index 3e297eb3..a830646f 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -64,7 +64,7 @@ mkin - 0.9.49.4 + 0.9.49.5 @@ -194,8 +194,8 @@ time_1 <- system.time(fits.4 <- mmkin(models, datasets, cores = 1, quiet = TRUE)) time_default
#> User System verstrichen -#> 0.048 0.024 5.085
time_1
#> User System verstrichen -#> 19.074 0.004 19.089
+#> 0.046 0.032 5.094
time_1
#> User System verstrichen +#> 19.798 0.004 19.814
endpoints(fits.0[["SFO_lin", 2]])
#> $ff #> parent_M1 parent_sink M1_M2 M1_sink #> 0.7340481 0.2659519 0.7505684 0.2494316 @@ -240,7 +240,7 @@
-

Site built with pkgdown 1.3.0.9000.

+

Site built with pkgdown 1.3.0.

diff --git a/docs/reference/nafta-1.png b/docs/reference/nafta-1.png index bcf5d12c..9025f2bb 100644 Binary files a/docs/reference/nafta-1.png and b/docs/reference/nafta-1.png differ diff --git a/docs/reference/nafta.html b/docs/reference/nafta.html index a9ee2f76..e0c3c0e2 100644 --- a/docs/reference/nafta.html +++ b/docs/reference/nafta.html @@ -65,7 +65,7 @@ mkin - 0.9.49.4 + 0.9.49.5 @@ -244,7 +244,7 @@
-

Site built with pkgdown 1.3.0.9000.

+

Site built with pkgdown 1.3.0.

diff --git a/docs/reference/plot.mkinfit-1.png b/docs/reference/plot.mkinfit-1.png index f70e9e31..0fe3c263 100644 Binary files a/docs/reference/plot.mkinfit-1.png and b/docs/reference/plot.mkinfit-1.png differ diff --git a/docs/reference/plot.mkinfit-2.png b/docs/reference/plot.mkinfit-2.png index 6facce0f..84bec348 100644 Binary files a/docs/reference/plot.mkinfit-2.png and b/docs/reference/plot.mkinfit-2.png differ diff --git a/docs/reference/plot.mkinfit-3.png b/docs/reference/plot.mkinfit-3.png index b53b3134..557046da 100644 Binary files a/docs/reference/plot.mkinfit-3.png and b/docs/reference/plot.mkinfit-3.png differ diff --git a/docs/reference/plot.mkinfit-4.png b/docs/reference/plot.mkinfit-4.png index 70a936ee..60203c3d 100644 Binary files a/docs/reference/plot.mkinfit-4.png and b/docs/reference/plot.mkinfit-4.png differ diff --git a/docs/reference/plot.mkinfit-5.png b/docs/reference/plot.mkinfit-5.png index 2e208996..36fcff6a 100644 Binary files a/docs/reference/plot.mkinfit-5.png and b/docs/reference/plot.mkinfit-5.png differ diff --git a/docs/reference/plot.mkinfit-6.png b/docs/reference/plot.mkinfit-6.png index 1da876b4..ad2ffa8c 100644 Binary files a/docs/reference/plot.mkinfit-6.png and b/docs/reference/plot.mkinfit-6.png differ diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html index 7bfc17f6..5cab42fd 100644 --- a/docs/reference/plot.mkinfit.html +++ b/docs/reference/plot.mkinfit.html @@ -68,7 +68,7 @@ If the current plot device is a tikz device, mkin - 0.9.49.4 + 0.9.49.5 @@ -269,9 +269,9 @@ plot_sep(fit, sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE, …

Examples

- 
# One parent compound, one metabolite, both single first order, path from
-# parent to sink included
-SFO_SFO <- mkinmod(parent = mkinsub("SFO", "m1", full = "Parent"),
+    
# One parent compound, one metabolite, both single first order, path from
+# parent to sink included
+
SFO_SFO <- mkinmod(parent = mkinsub("SFO", "m1", full = "Parent"),
                    m1 = mkinsub("SFO", full = "Metabolite M1" ))
#> Successfully compiled differential equation model from auto-generated C code.
fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE, error_model = "tc")
#> Warning: Observations with value of zero were removed from the data
plot(fit)
plot(fit, show_residuals = TRUE)
plot(fit, show_errplot = TRUE)

 # Show the observed variables separately
 plot(fit, sep_obs = TRUE, lpos = c("topright", "bottomright"))

@@ -306,7 +306,7 @@ plot_sep(fit, sep_obs = TRUE,  show_residuals = TRUE, show_errmin = TRUE, …
 

 
 

-  
Site built with pkgdown 1.3.0.9000.

+  
Site built with pkgdown 1.3.0.

 

       
    

diff --git a/docs/reference/plot.mmkin-1.png b/docs/reference/plot.mmkin-1.png
index 03d334f7..8cf969c9 100644
Binary files a/docs/reference/plot.mmkin-1.png and b/docs/reference/plot.mmkin-1.png differ
diff --git a/docs/reference/plot.mmkin-2.png b/docs/reference/plot.mmkin-2.png
index 25ed01cc..45d67b55 100644
Binary files a/docs/reference/plot.mmkin-2.png and b/docs/reference/plot.mmkin-2.png differ
diff --git a/docs/reference/plot.mmkin-3.png b/docs/reference/plot.mmkin-3.png
index 7f32afe2..47cd7eec 100644
Binary files a/docs/reference/plot.mmkin-3.png and b/docs/reference/plot.mmkin-3.png differ
diff --git a/docs/reference/plot.mmkin-4.png b/docs/reference/plot.mmkin-4.png
index b03dffb2..44037bb4 100644
Binary files a/docs/reference/plot.mmkin-4.png and b/docs/reference/plot.mmkin-4.png differ
diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html
index 3037ca24..0b626d1b 100644
--- a/docs/reference/plot.mmkin.html
+++ b/docs/reference/plot.mmkin.html
@@ -67,7 +67,7 @@ If the current plot device is a tikz device,
       
       
         mkin
-        0.9.49.4
+        0.9.49.5
       
     
 
@@ -197,8 +197,8 @@ If the current plot device is a tikz device,
     
  
  # Only use one core not to offend CRAN checks
   fits <- mmkin(c("FOMC", "HS"),
                 list("FOCUS B" = FOCUS_2006_B, "FOCUS C" = FOCUS_2006_C), # named list for titles
-                cores = 1, quiet = TRUE, error_model = "tc")
-  plot(fits[, "FOCUS C"])
  plot(fits["FOMC", ])

+                cores = 1, quiet = TRUE, error_model = "tc")
#> Warning: Optimisation did not converge:
+#> iteration limit reached without convergence (10)
  plot(fits[, "FOCUS C"])
  plot(fits["FOMC", ])

   # We can also plot a single fit, if we like the way plot.mmkin works, but then the plot
   # height should be smaller than the plot width (this is not possible for the html pages
   # generated by pkgdown, as far as I know).
@@ -227,7 +227,7 @@ If the current plot device is a tikz device,
 

 
 

-  
Site built with pkgdown 1.3.0.9000.

+  
Site built with pkgdown 1.3.0.

 

       
    
diff --git a/docs/reference/plot.nafta.html b/docs/reference/plot.nafta.html
index 1aa4485a..fdc6e0ac 100644
--- a/docs/reference/plot.nafta.html
+++ b/docs/reference/plot.nafta.html
@@ -67,7 +67,7 @@
       
       
         mkin
-        0.9.49.4
+        0.9.49.5
       
     
 
@@ -187,7 +187,7 @@ plot(x, legend = FALSE, main = "auto", …)

 
 
 

-  
Site built with pkgdown 1.3.0.9000.

+  
Site built with pkgdown 1.3.0.

 

       
    
diff --git a/docs/reference/print.mkinds.html b/docs/reference/print.mkinds.html
index 2cc112aa..7c401533 100644
--- a/docs/reference/print.mkinds.html
+++ b/docs/reference/print.mkinds.html
@@ -63,7 +63,7 @@
       
       
         mkin
-        0.9.49.4
+        0.9.49.5
       
     
 
@@ -165,7 +165,7 @@
 
 
 

-  
Site built with pkgdown 1.3.0.9000.

+  
Site built with pkgdown 1.3.0.

 

       
    
diff --git a/docs/reference/print.mkinmod.html b/docs/reference/print.mkinmod.html
index d09b629e..4ca7631b 100644
--- a/docs/reference/print.mkinmod.html
+++ b/docs/reference/print.mkinmod.html
@@ -63,7 +63,7 @@
       
       
         mkin
-        0.9.49.4
+        0.9.49.5
       
     
 
@@ -186,7 +186,7 @@
 
 
 

-  
Site built with pkgdown 1.3.0.9000.

+  
Site built with pkgdown 1.3.0.

 

       
    
diff --git a/docs/reference/print.nafta.html b/docs/reference/print.nafta.html
index 28847afe..10afb77d 100644
--- a/docs/reference/print.nafta.html
+++ b/docs/reference/print.nafta.html
@@ -65,7 +65,7 @@
       
       
         mkin
-        0.9.49.4
+        0.9.49.5
       
     
 
@@ -177,7 +177,7 @@
 
 
 

-  
Site built with pkgdown 1.3.0.9000.

+  
Site built with pkgdown 1.3.0.

 

       
    
diff --git a/docs/reference/schaefer07_complex_case-1.png b/docs/reference/schaefer07_complex_case-1.png
index 49967dc9..34356613 100644
Binary files a/docs/reference/schaefer07_complex_case-1.png and b/docs/reference/schaefer07_complex_case-1.png differ
diff --git a/docs/reference/schaefer07_complex_case.html b/docs/reference/schaefer07_complex_case.html
index 09f6d1e2..50e07d37 100644
--- a/docs/reference/schaefer07_complex_case.html
+++ b/docs/reference/schaefer07_complex_case.html
@@ -65,7 +65,7 @@
       
       
         mkin
-        0.9.49.4
+        0.9.49.5
       
     
 
@@ -216,7 +216,7 @@
 
 
 

-  
Site built with pkgdown 1.3.0.9000.

+  
Site built with pkgdown 1.3.0.

 

       
    
diff --git a/docs/reference/sigma_twocomp.html b/docs/reference/sigma_twocomp.html
index 265c7d1f..b73b81f4 100644
--- a/docs/reference/sigma_twocomp.html
+++ b/docs/reference/sigma_twocomp.html
@@ -68,7 +68,7 @@ This is the error model used for example by Werner et al. (1978). The model
       
       
         mkin
-        0.9.49.4
+        0.9.49.5
       
     
 
@@ -195,7 +195,7 @@ This is the error model used for example by Werner et al. (1978). The model
 
 
 

-  
Site built with pkgdown 1.3.0.9000.

+  
Site built with pkgdown 1.3.0.

 

       
    
diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html
index b3151da1..ffe1edb1 100644
--- a/docs/reference/summary.mkinfit.html
+++ b/docs/reference/summary.mkinfit.html
@@ -66,7 +66,7 @@
       
       
         mkin
-        0.9.49.4
+        0.9.49.5
       
     
 
@@ -209,10 +209,10 @@
     
 
     
Examples

-    
  summary(mkinfit(mkinmod(parent = mkinsub("SFO")), FOCUS_2006_A, quiet = TRUE))
#> mkin version used for fitting:    0.9.49.4 
+    
  summary(mkinfit(mkinmod(parent = mkinsub("SFO")), FOCUS_2006_A, quiet = TRUE))
#> mkin version used for fitting:    0.9.49.5 
 #> R version used for fitting:       3.6.0 
-#> Date of fit:     Wed May  8 20:52:12 2019 
-#> Date of summary: Wed May  8 20:52:12 2019 
+#> Date of fit:     Tue Jun  4 15:03:02 2019 
+#> Date of summary: Tue Jun  4 15:03:02 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent_sink * parent
@@ -307,7 +307,7 @@
 

 
 

-  
Site built with pkgdown 1.3.0.9000.

+  
Site built with pkgdown 1.3.0.

 

       
    

diff --git a/docs/reference/synthetic_data_for_UBA.html b/docs/reference/synthetic_data_for_UBA.html
index 2c2623e4..4a7ca728 100644
--- a/docs/reference/synthetic_data_for_UBA.html
+++ b/docs/reference/synthetic_data_for_UBA.html
@@ -40,7 +40,7 @@ Variance component 'a' is based on a normal distribution with standard deviation
  Variance component 'c' is based on the error model from Rocke and Lorenzato (1995), with the
  minimum standard deviation (for small y values) of 0.5, and a proportionality constant of 0.07
  for the increase of the standard deviation with y. Note that this is a simplified version
- of the error model proposed by Rocke and Lorenzato (1995), as in their model the error of the 
+ of the error model proposed by Rocke and Lorenzato (1995), as in their model the error of the
  measured values approximates lognormal distribution for high values, whereas we are using
  normally distributed error components all along.
 Initial concentrations for metabolites and all values where adding the variance component resulted
@@ -78,7 +78,7 @@ Compare also the code in the example section to see the degradation models." />
       
       
         mkin
-        0.9.49.4
+        0.9.49.5
       
     
 
@@ -151,7 +151,7 @@ Compare also the code in the example section to see the degradation models." />
  Variance component 'c' is based on the error model from Rocke and Lorenzato (1995), with the
  minimum standard deviation (for small y values) of 0.5, and a proportionality constant of 0.07
  for the increase of the standard deviation with y. Note that this is a simplified version
- of the error model proposed by Rocke and Lorenzato (1995), as in their model the error of the 
+ of the error model proposed by Rocke and Lorenzato (1995), as in their model the error of the
  measured values approximates lognormal distribution for high values, whereas we are using
  normally distributed error components all along.

 
Initial concentrations for metabolites and all values where adding the variance component resulted
@@ -253,7 +253,8 @@ add_err = function(d, sdfunc, LOD = 0.1, reps = 2, seed = 123456789)
   return(d_NA)
 }
 
-# The following is the two-component model of Rocke and Lorenzato (1995)
+# The following is the simplified version of the two-component model of Rocke
+# and Lorenzato (1995)
 sdfunc_twocomp = function(value, sd_low, rsd_high) {
   sqrt(sd_low^2 + value^2 * rsd_high^2)
 }
@@ -304,7 +305,7 @@ summary(fit)
 
 
 

-  
Site built with pkgdown 1.3.0.9000.

+  
Site built with pkgdown 1.3.0.

 

       
    
diff --git a/docs/reference/test_data_from_UBA_2014-1.png b/docs/reference/test_data_from_UBA_2014-1.png
index a9aeea21..fc05f896 100644
Binary files a/docs/reference/test_data_from_UBA_2014-1.png and b/docs/reference/test_data_from_UBA_2014-1.png differ
diff --git a/docs/reference/test_data_from_UBA_2014-2.png b/docs/reference/test_data_from_UBA_2014-2.png
index f6c91bff..b0dfdd5a 100644
Binary files a/docs/reference/test_data_from_UBA_2014-2.png and b/docs/reference/test_data_from_UBA_2014-2.png differ
diff --git a/docs/reference/test_data_from_UBA_2014.html b/docs/reference/test_data_from_UBA_2014.html
index bc988340..e40d320f 100644
--- a/docs/reference/test_data_from_UBA_2014.html
+++ b/docs/reference/test_data_from_UBA_2014.html
@@ -64,7 +64,7 @@
       
       
         mkin
-        0.9.49.4
+        0.9.49.5
       
     
 
@@ -231,7 +231,7 @@
 
 
 

-  
Site built with pkgdown 1.3.0.9000.

+  
Site built with pkgdown 1.3.0.

 

       
    
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html
index 7e05480e..bf134334 100644
--- a/docs/reference/transform_odeparms.html
+++ b/docs/reference/transform_odeparms.html
@@ -71,7 +71,7 @@ The transformation of sets of formation fractions is fragile, as it supposes
       
       
         mkin
-        0.9.49.4
+        0.9.49.5
       
     
 
@@ -293,7 +293,7 @@ The transformation of sets of formation fractions is fragile, as it supposes
 
 
 

-  
Site built with pkgdown 1.3.0.9000.

+  
Site built with pkgdown 1.3.0.

 

       
    
-- 
cgit v1.2.1