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/news/index.html | 211 ++++++++++++++++++++++++++--------------------- 1 file changed, 116 insertions(+), 95 deletions(-) (limited to 'docs/dev/news/index.html') diff --git a/docs/dev/news/index.html b/docs/dev/news/index.html index c3597efe..998917f2 100644 --- a/docs/dev/news/index.html +++ b/docs/dev/news/index.html @@ -71,7 +71,7 @@ mkin - 0.9.50.4 + 1.0.1.9000 @@ -141,13 +141,36 @@ Source: NEWS.md -
-

-mkin 0.9.50.4 (unreleased) Unreleased +
+

+mkin 1.0.1.9000 Unreleased

-
+
    +

  • Switch to a versioning scheme where the fourth version component indicates development versions

    • +

  • Reintroduce the interface to the current development version of saemix, in particular:

    • +

  • ‘saemix_model’ and ‘saemix_data’: Helper functions to set up nonlinear mixed-effects models for mmkin row objects

    • +

  • ‘saem’: generic function to fit saemix models using ‘saemix_model’ and ‘saemix_data’, with a generator ‘saem.mmkin’, summary and plot methods

    • +
+
+
+

+mkin 1.0.1 Unreleased +

+
    +

  • ‘confint.mmkin’, ‘nlme.mmkin’, ‘transform_odeparms’: Fix example code in dontrun sections that failed with current defaults

    • +

  • ‘logLik.mkinfit’: Improve example code to avoid warnings and show convenient syntax

    • +

  • ‘mkinresplot’: Re-add Katrin Lindenberger as coauthor who was accidentally removed long ago

    • +

  • Remove tests relying on non-convergence of the FOMC fit to the FOCUS A dataset as this is platform dependent (revealed by the new additional tests on CRAN, thanks!)

    • +

  • Increase test tolerance for some parameter comparisons that also proved to be platform dependent

    • +
+
+
+

+mkin 1.0.0 2021-02-03 +

+

-General new features

+General

@@ -163,18 +188,14 @@ Mixed-effects models
-
+

-mkin 0.9.50.3 (2020-10-08) 2020-10-08 +mkin 0.9.50.3 (2020-10-08) 2020-10-08

  • ‘parms’: Add a method for mmkin objects

    • @@ -188,18 +209,18 @@

  • ‘endpoints’: Back-calculate DT50 value from DT90 also for the biphasic models DFOP, HS and SFORB

-
+

-mkin 0.9.50.2 (2020-05-12) 2020-05-12 +mkin 0.9.50.2 (2020-05-12) 2020-05-12

  • Increase tolerance for a platform specific test results on the Solaris test machine on CRAN

  • Updates and corrections (using the spelling package) to the documentation

-
+

-mkin 0.9.50.1 (2020-05-11) 2020-05-11 +mkin 0.9.50.1 (2020-05-11) 2020-05-11

  • Support SFORB with formation fractions

    • @@ -207,17 +228,17 @@

  • Improve performance by a) avoiding expensive calls in the cost function like merge() and data.frame(), and b) by implementing analytical solutions for SFO-SFO and DFOP-SFO

-
+

-mkin 0.9.49.11 (2020-04-20) 2020-04-20 +mkin 0.9.49.11 (2020-04-20) 2020-04-20

  • Increase a test tolerance to make it pass on all CRAN check machines
-
+

-mkin 0.9.49.10 (2020-04-18) 2020-04-18 +mkin 0.9.49.10 (2020-04-18) 2020-04-18

  • ‘nlme.mmkin’: An nlme method for mmkin row objects and an associated S3 class with print, plot, anova and endpoint methods

    • @@ -228,18 +249,18 @@

  • ‘summary.mkinfit’: Add AIC, BIC and log likelihood to the summary

-
+

-mkin 0.9.49.9 (2020-03-31) 2020-03-31 +mkin 0.9.49.9 (2020-03-31) 2020-03-31

  • ‘mkinmod’: Use pkgbuild::has_compiler instead of Sys.which(‘gcc’), as the latter will often fail even if Rtools are installed

  • ‘mkinds’: Use roxygen for documenting fields and methods of this R6 class

-
+

-mkin 0.9.49.8 (2020-01-09) 2020-01-09 +mkin 0.9.49.8 (2020-01-09) 2020-01-09

  • ‘aw’: Generic function for calculating Akaike weights, methods for mkinfit objects and mmkin columns

    • @@ -249,18 +270,18 @@

  • ‘confint.mkinfit’: Make the quadratic approximation the default, as the likelihood profiling takes a lot of time, especially if the fit has more than three parameters

-
+

-mkin 0.9.49.7 (2019-11-01) 2019-11-02 +mkin 0.9.49.7 (2019-11-01) 2019-11-02

  • Fix a bug introduced in 0.9.49.6 that occurred if the direct optimisation yielded a higher likelihood than the three-step optimisation in the d_3 algorithm, which caused the fitted parameters of the three-step optimisation to be returned instead of the parameters of the direct optimisation

  • Add a ‘nobs’ method for mkinfit objects, enabling the default ‘BIC’ method from the stats package. Also, add a ‘BIC’ method for mmkin column objects.

-
+

-mkin 0.9.49.6 (2019-10-31) 2019-10-31 +mkin 0.9.49.6 (2019-10-31) 2019-10-31

  • Implement a likelihood ratio test as a method for ‘lrtest’ from the lmtest package

    • @@ -278,9 +299,9 @@

  • Support summarizing ‘mkinfit’ objects generated with versions < 0.9.49.5

-
+

-mkin 0.9.49.5 (2019-07-04) 2019-07-04 +mkin 0.9.49.5 (2019-07-04) 2019-07-04

  • Several algorithms for minimization of the negative log-likelihood for non-constant error models (two-component and variance by variable). In the case the error model is constant variance, least squares is used as this is more stable. The default algorithm ‘d_3’ tries direct minimization and a three-step procedure, and returns the model with the highest likelihood.

    • @@ -297,9 +318,9 @@

  • Add example datasets obtained from risk assessment reports published by the European Food Safety Agency.

-
+

-mkin 0.9.48.1 (2019-03-04) 2019-03-04 +mkin 0.9.48.1 (2019-03-04) 2019-03-04

  • Add the function ‘logLik.mkinfit’ which makes it possible to calculate an AIC for mkinfit objects

    • @@ -314,9 +335,9 @@

  • ‘nafta’: Add evaluations according to the NAFTA guidance

-
+

-mkin 0.9.47.5 (2018-09-14) 2018-09-14 +mkin 0.9.47.5 (2018-09-14) 2018-09-14

  • Make the two-component error model stop in cases where it is inadequate to avoid nls crashes on windows

    • @@ -324,27 +345,27 @@

  • Exclude more example code from testing on CRAN to avoid NOTES from long execution times

-
+

-mkin 0.9.47.3 Unreleased +mkin 0.9.47.3 Unreleased

  • ‘mkinfit’: Improve fitting the error model for reweight.method = ‘tc’. Add ‘manual’ to possible arguments for ‘weight’

  • Test that FOCUS_2006_C can be evaluated with DFOP and reweight.method = ‘tc’

-
+

-mkin 0.9.47.2 (2018-07-19) 2018-07-19 +mkin 0.9.47.2 (2018-07-19) 2018-07-19

  • ‘sigma_twocomp’: Rename ‘sigma_rl’ to ‘sigma_twocomp’ as the Rocke and Lorenzato model assumes lognormal distribution for large y. Correct references to the Rocke and Lorenzato model accordingly.

  • ‘mkinfit’: Use 1.1 as starting value for N parameter of IORE models to obtain convergence in more difficult cases. Show parameter names when ‘trace_parms’ is ‘TRUE’.

-
+

-mkin 0.9.47.1 (2018-02-06) 2018-02-06 +mkin 0.9.47.1 (2018-02-06) 2018-02-06

  • Skip some tests on CRAN and winbuilder to avoid timeouts

    • @@ -355,27 +376,27 @@

  • ‘summary.mkinfit’: Show versions of mkin and R used for fitting (not the ones used for the summary) if the fit was generated with mkin >= 0.9.47.1

-
+

-mkin 0.9.46.3 (2017-11-16) 2017-11-16 +mkin 0.9.46.3 (2017-11-16) 2017-11-16

  • README.md, vignettes/mkin.Rmd: URLs were updated

  • synthetic_data_for_UBA: Add the code used to generate the data in the interest of reproducibility

-
+

-mkin 0.9.46.2 (2017-10-10) 2017-10-10 +mkin 0.9.46.2 (2017-10-10) 2017-10-10

  • Converted the vignette FOCUS_Z from tex/pdf to markdown/html

  • DESCRIPTION: Add ORCID

-
+

-mkin 0.9.46.1 (2017-09-14) 2017-09-14 +mkin 0.9.46.1 (2017-09-14) 2017-09-14

  • plot.mkinfit: Fix scaling of residual plots for the case of separate plots for each observed variable

    • @@ -383,17 +404,17 @@

  • Documentation updates

-
+

-mkin 0.9.46 (2017-07-24) 2017-07-29 +mkin 0.9.46 (2017-07-24) 2017-07-29

  • Remove test_FOMC_ill-defined.R as it is too platform dependent
-
+

-mkin 0.9.45.2 (2017-07-24) 2017-07-22 +mkin 0.9.45.2 (2017-07-24) 2017-07-22

  • Rename twa to max_twa_parent to avoid conflict with twa from my pfm package

    • @@ -402,9 +423,9 @@

  • Switch from microbenchmark to rbenchmark as the former is not supported on all platforms

-
+

-mkin 0.9.45.1 (2016-12-20) Unreleased +mkin 0.9.45.1 (2016-12-20) Unreleased

@@ -414,9 +435,9 @@

-
+

-mkin 0.9.45 (2016-12-08) 2016-12-08 +mkin 0.9.45 (2016-12-08) 2016-12-08

@@ -428,9 +449,9 @@

-
+

-mkin 0.9.44 (2016-06-29) 2016-06-29 +mkin 0.9.44 (2016-06-29) 2016-06-29

@@ -440,9 +461,9 @@

-
+

-mkin 0.9.43 (2016-06-28) 2016-06-28 +mkin 0.9.43 (2016-06-28) 2016-06-28

@@ -479,9 +500,9 @@

-
+

-mkin 0.9.42 (2016-03-25) 2016-03-25 +mkin 0.9.42 (2016-03-25) 2016-03-25

@@ -500,9 +521,9 @@

-
+

-mkin 0.9-41 (2015-11-09) 2015-11-09 +mkin 0.9-41 (2015-11-09) 2015-11-09

@@ -523,9 +544,9 @@

-
+

-mkin 0.9-40 (2015-07-21) 2015-07-21 +mkin 0.9-40 (2015-07-21) 2015-07-21

@@ -544,9 +565,9 @@

-
+

-mkin 0.9-39 (2015-06-26) 2015-06-26 +mkin 0.9-39 (2015-06-26) 2015-06-26

@@ -565,9 +586,9 @@

-
+

-mkin 0.9-38 (2015-06-24) 2015-06-23 +mkin 0.9-38 (2015-06-24) 2015-06-23

@@ -586,9 +607,9 @@

-
+

-mkin 0.9-36 (2015-06-21) 2015-06-21 +mkin 0.9-36 (2015-06-21) 2015-06-21

@@ -608,9 +629,9 @@

-
+

-mkin 0.9-35 (2015-05-15) 2015-05-15 +mkin 0.9-35 (2015-05-15) 2015-05-15

@@ -640,9 +661,9 @@

-
+

-mkin 0.9-34 (2014-11-22) 2014-11-22 +mkin 0.9-34 (2014-11-22) 2014-11-22

@@ -662,9 +683,9 @@

-
+

-mkin 0.9-33 (2014-10-22) 2014-10-12 +mkin 0.9-33 (2014-10-22) 2014-10-12

@@ -695,9 +716,9 @@

-
+

-mkin 0.9-32 (2014-07-24) 2014-07-24 +mkin 0.9-32 (2014-07-24) 2014-07-24

@@ -705,7 +726,7 @@

  • The number of degrees of freedom is difficult to define in the case of ilr transformation of formation fractions. Now for each source compartment the number of ilr parameters (=number of optimised parameters) is divided by the number of pathways to metabolites (=number of affected data series) which leads to fractional degrees of freedom in some cases.

  • The default for the initial value for the first state value is now taken from the mean of the observations at time zero, if available.

    • -

  • The kinetic model can alternatively be specified with a shorthand name for parent only degradation models, e.g. SFO, or DFOP.

    • +

  • The kinetic model can alternatively be specified with a shorthand name for parent only degradation models, e.g. SFO, or DFOP.

  • Optimisation method, number of model evaluations and time elapsed during optimisation are given in the summary of mkinfit objects.

  • The maximum number of iterations in the optimisation algorithm can be specified using the argument maxit.modFit to the mkinfit function.

  • mkinfit gives a warning when the fit does not converge (does not apply to SANN method). This warning is included in the summary.

    • @@ -732,9 +753,9 @@

-
+

-mkin 0.9-31 (2014-07-14) 2014-07-14 +mkin 0.9-31 (2014-07-14) 2014-07-14

@@ -744,9 +765,9 @@

-
+

-mkin 0.9-30 (2014-07-11) 2014-07-11 +mkin 0.9-30 (2014-07-11) 2014-07-11

@@ -759,7 +780,7 @@

Major changes

    -

  • The original and the transformed parameters now have different names (e.g. k_parent and log_k_parent. They also differ in how many they are when we have formation fractions but no pathway to sink.

    • +

  • The original and the transformed parameters now have different names (e.g. k_parent and log_k_parent. They also differ in how many they are when we have formation fractions but no pathway to sink.

  • The order of some of the information blocks in print.summary.mkinfit.R() has been ordered in a more logical way.

@@ -776,9 +797,9 @@
-
+

-mkin 0.9-29 (2014-06-27) 2014-06-27 +mkin 0.9-29 (2014-06-27) 2014-06-27

  • R/mkinresplot.R: Make it possible to specify xlim

    • @@ -786,9 +807,9 @@

  • R/endpoints.R, man/endpoints.Rd: Calculate additional (pseudo)-DT50 values for FOMC, DFOP, HS and SFORB. Avoid calculation of formation fractions from rate constants when they are directly fitted

-
+

-mkin 0.9-28 (2014-05-20) 2014-05-20 +mkin 0.9-28 (2014-05-20) 2014-05-20

  • Do not backtransform confidence intervals for formation fractions if more than one compound is formed, as such parameters only define the pathways as a set

    • @@ -796,9 +817,9 @@

  • Correct ‘isotropic’ into ‘isometric’ for the ilr transformation

-
+

-mkin 0.9-27 (2014-05-10) 2014-05-10 +mkin 0.9-27 (2014-05-10) 2014-05-10

  • Fork the GUI into a separate package gmkin

    • @@ -820,9 +841,9 @@

  • Add gmkin workspace datasets FOCUS_2006_gmkin and FOCUS_2006_Z_gmkin

-
+

-mkin 0.9-24 (2013-11-06) 2013-11-06 +mkin 0.9-24 (2013-11-06) 2013-11-06

  • Bugfix re-enabling the fixing of any combination of initial values for state variables

    • @@ -830,9 +851,9 @@

  • Backtransform fixed ODE parameters for the summary

-
+

-mkin 0.9-22 (2013-10-26) 2013-10-26 +mkin 0.9-22 (2013-10-26) 2013-10-26

  • Get rid of the optimisation step in mkinerrmin - this was unnecessary. Thanks to KinGUII for the inspiration - actually this is equation 6-2 in FOCUS kinetics p. 91 that I had overlooked originally

    • -- cgit v1.2.3 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/404.html | 2 +- docs/dev/articles/index.html | 2 +- docs/dev/authors.html | 2 +- docs/dev/index.html | 2 +- docs/dev/news/index.html | 18 ++++++++++---- docs/dev/pkgdown.yml | 2 +- docs/dev/reference/endpoints.html | 2 +- docs/dev/reference/index.html | 2 +- docs/dev/reference/plot.mixed.mmkin.html | 6 ++--- docs/dev/reference/saem.html | 38 +++++++++++++++--------------- docs/dev/reference/summary.saem.mmkin.html | 14 +++++------ 11 files changed, 49 insertions(+), 41 deletions(-) (limited to 'docs/dev/news/index.html') diff --git a/docs/dev/404.html b/docs/dev/404.html index 5f29faf2..ea547a2a 100644 --- a/docs/dev/404.html +++ b/docs/dev/404.html @@ -71,7 +71,7 @@ mkin - 1.0.1.9000 + 1.0.2.9000
diff --git a/docs/dev/articles/index.html b/docs/dev/articles/index.html index 441d49c0..57d0c0eb 100644 --- a/docs/dev/articles/index.html +++ b/docs/dev/articles/index.html @@ -71,7 +71,7 @@ mkin - 1.0.1.9000 + 1.0.2.9000
diff --git a/docs/dev/authors.html b/docs/dev/authors.html index 9641eec0..8ffb9f97 100644 --- a/docs/dev/authors.html +++ b/docs/dev/authors.html @@ -71,7 +71,7 @@ mkin - 1.0.1.9000 + 1.0.2.9000
diff --git a/docs/dev/index.html b/docs/dev/index.html index 8888633d..ff9b201f 100644 --- a/docs/dev/index.html +++ b/docs/dev/index.html @@ -38,7 +38,7 @@ mkin - 1.0.1.9000 + 1.0.2.9000
diff --git a/docs/dev/news/index.html b/docs/dev/news/index.html index 998917f2..eab75984 100644 --- a/docs/dev/news/index.html +++ b/docs/dev/news/index.html @@ -71,7 +71,7 @@ mkin - 1.0.1.9000 + 1.0.2.9000
@@ -141,9 +141,9 @@ Source: NEWS.md
-
-

-mkin 1.0.1.9000 Unreleased +
+

+mkin 1.0.2.9000 Unreleased

  • Switch to a versioning scheme where the fourth version component indicates development versions

    • @@ -151,10 +151,18 @@

  • ‘saemix_model’ and ‘saemix_data’: Helper functions to set up nonlinear mixed-effects models for mmkin row objects

  • ‘saem’: generic function to fit saemix models using ‘saemix_model’ and ‘saemix_data’, with a generator ‘saem.mmkin’, summary and plot methods

+
+
+

+mkin 1.0.2 Unreleased +

+
    +
  • ‘mkinfit’: Keep model names stored in ‘mkinmod’ objects, avoiding their loss in ‘gmkin’
    • +

-mkin 1.0.1 Unreleased +mkin 1.0.1 2021-02-10

  • ‘confint.mmkin’, ‘nlme.mmkin’, ‘transform_odeparms’: Fix example code in dontrun sections that failed with current defaults

    • diff --git a/docs/dev/pkgdown.yml b/docs/dev/pkgdown.yml index f9b16e29..8921a1e4 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: 2021-02-06T17:26Z +last_built: 2021-02-13T11:32Z urls: reference: https://pkgdown.jrwb.de/mkin/reference article: https://pkgdown.jrwb.de/mkin/articles diff --git a/docs/dev/reference/endpoints.html b/docs/dev/reference/endpoints.html index a13e11a7..301b454f 100644 --- a/docs/dev/reference/endpoints.html +++ b/docs/dev/reference/endpoints.html @@ -78,7 +78,7 @@ advantage that the SFORB model can also be used for metabolites." /> mkin - 1.0.1.9000 + 1.0.2.9000
diff --git a/docs/dev/reference/index.html b/docs/dev/reference/index.html index 7e98aa50..b52ecb22 100644 --- a/docs/dev/reference/index.html +++ b/docs/dev/reference/index.html @@ -71,7 +71,7 @@ mkin - 1.0.1.9000 + 1.0.2.9000

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, diff --git a/docs/dev/reference/saem.html b/docs/dev/reference/saem.html index 4578db2a..02483bec 100644 --- a/docs/dev/reference/saem.html +++ b/docs/dev/reference/saem.html @@ -74,7 +74,7 @@ Expectation Maximisation algorithm (SAEM)." /> mkin - 1.0.1.9000 + 1.0.2.9000
@@ -261,27 +261,27 @@ 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] "Sat Feb 6 18:29:26 2021" +#> [1] "Sat Feb 13 12:33:16 2021" #> .... #> Minimisation finished -#> [1] "Sat Feb 6 18:29:27 2021"
+#> [1] "Sat Feb 13 12:33:18 2021"
f_mmkin_parent <- mmkin(c("SFO", "FOMC", "DFOP"), ds, quiet = TRUE) f_saem_sfo <- saem(f_mmkin_parent["SFO", ])
#> Running main SAEM algorithm -#> [1] "Sat Feb 6 18:29:28 2021" +#> [1] "Sat Feb 13 12:33:19 2021" #> .... #> Minimisation finished -#> [1] "Sat Feb 6 18:29:30 2021"
f_saem_fomc <- saem(f_mmkin_parent["FOMC", ]) +#> [1] "Sat Feb 13 12:33:20 2021"
f_saem_fomc <- saem(f_mmkin_parent["FOMC", ])
#> Running main SAEM algorithm -#> [1] "Sat Feb 6 18:29:30 2021" +#> [1] "Sat Feb 13 12:33:20 2021" #> .... #> Minimisation finished -#> [1] "Sat Feb 6 18:29:32 2021"
f_saem_dfop <- saem(f_mmkin_parent["DFOP", ]) +#> [1] "Sat Feb 13 12:33:22 2021"
f_saem_dfop <- saem(f_mmkin_parent["DFOP", ])
#> Running main SAEM algorithm -#> [1] "Sat Feb 6 18:29:32 2021" +#> [1] "Sat Feb 13 12:33:23 2021" #> .... #> Minimisation finished -#> [1] "Sat Feb 6 18:29:35 2021"
+#> [1] "Sat Feb 13 12:33:25 2021"
# The returned saem.mmkin object contains an SaemixObject, therefore we can use # functions from saemix library(saemix) @@ -324,10 +324,10 @@ 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] "Sat Feb 6 18:29:37 2021" +#> [1] "Sat Feb 13 12:33:28 2021" #> .... #> Minimisation finished -#> [1] "Sat Feb 6 18:29:42 2021"
compare.saemix(list(f_saem_fomc$so, f_saem_fomc_tc$so)) +#> [1] "Sat Feb 13 12:33:32 2021"
compare.saemix(list(f_saem_fomc$so, f_saem_fomc_tc$so))
#> Error in compare.saemix(list(f_saem_fomc$so, f_saem_fomc_tc$so)): 'compare.saemix' requires at least two models.
sfo_sfo <- mkinmod(parent = mkinsub("SFO", "A1"), A1 = mkinsub("SFO")) @@ -346,15 +346,15 @@ using mmkin.

# four minutes f_saem_sfo_sfo <- saem(f_mmkin["SFO-SFO", ])
#> Running main SAEM algorithm -#> [1] "Sat Feb 6 18:29:44 2021" +#> [1] "Sat Feb 13 12:33:35 2021" #> .... #> Minimisation finished -#> [1] "Sat Feb 6 18:29:48 2021"
f_saem_dfop_sfo <- saem(f_mmkin["DFOP-SFO", ]) +#> [1] "Sat Feb 13 12:33:39 2021"
f_saem_dfop_sfo <- saem(f_mmkin["DFOP-SFO", ])
#> Running main SAEM algorithm -#> [1] "Sat Feb 6 18:29:49 2021" +#> [1] "Sat Feb 13 12:33:40 2021" #> .... #> Minimisation finished -#> [1] "Sat Feb 6 18:29:57 2021"
# We can use print, plot and summary methods to check the results +#> [1] "Sat Feb 13 12:33:48 2021"
# We can use print, plot and summary methods to check the results print(f_saem_dfop_sfo)
#> Kinetic nonlinear mixed-effects model fit by SAEM #> Structural model: @@ -395,10 +395,10 @@ using mmkin.

#> SD.g_qlogis 0.44771 -0.86417 1.7596
plot(f_saem_dfop_sfo)
summary(f_saem_dfop_sfo, data = TRUE)
#> saemix version used for fitting: 3.1.9000 -#> mkin version used for pre-fitting: 1.0.1.9000 +#> mkin version used for pre-fitting: 1.0.2.9000 #> R version used for fitting: 4.0.3 -#> Date of fit: Sat Feb 6 18:29:57 2021 -#> Date of summary: Sat Feb 6 18:29:58 2021 +#> Date of fit: Sat Feb 13 12:33:48 2021 +#> Date of summary: Sat Feb 13 12:33:48 2021 #> #> Equations: #> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -413,7 +413,7 @@ using mmkin.

#> #> Model predictions using solution type analytical #> -#> Fitted in 8.539 s using 300, 100 iterations +#> Fitted in 8.875 s using 300, 100 iterations #> #> Variance model: Constant variance #> diff --git a/docs/dev/reference/summary.saem.mmkin.html b/docs/dev/reference/summary.saem.mmkin.html index 93e1365d..81054813 100644 --- a/docs/dev/reference/summary.saem.mmkin.html +++ b/docs/dev/reference/summary.saem.mmkin.html @@ -76,7 +76,7 @@ endpoints such as formation fractions and DT50 values. Optionally mkin - 1.0.1.9000 + 1.0.2.9000
@@ -260,15 +260,15 @@ saemix authors for the parts inherited from saemix.

quiet = TRUE, error_model = "tc", cores = 5) f_saem_dfop_sfo <- saem(f_mmkin_dfop_sfo)
#> Running main SAEM algorithm -#> [1] "Sat Feb 6 18:30:00 2021" +#> [1] "Sat Feb 13 12:33:52 2021" #> .... #> Minimisation finished -#> [1] "Sat Feb 6 18:30:11 2021"
summary(f_saem_dfop_sfo, data = TRUE) +#> [1] "Sat Feb 13 12:34:03 2021"
summary(f_saem_dfop_sfo, data = TRUE)
#> saemix version used for fitting: 3.1.9000 -#> mkin version used for pre-fitting: 1.0.1.9000 +#> mkin version used for pre-fitting: 1.0.2.9000 #> R version used for fitting: 4.0.3 -#> Date of fit: Sat Feb 6 18:30:12 2021 -#> Date of summary: Sat Feb 6 18:30:12 2021 +#> Date of fit: Sat Feb 13 12:34:04 2021 +#> Date of summary: Sat Feb 13 12:34:04 2021 #> #> Equations: #> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -283,7 +283,7 @@ saemix authors for the parts inherited from saemix.

#> #> Model predictions using solution type analytical #> -#> Fitted in 11.769 s using 300, 100 iterations +#> Fitted in 11.899 s using 300, 100 iterations #> #> Variance model: Two-component variance function #> -- cgit v1.2.3 From c4f327e62f19c0a3fc77a538f7cf0c2c619019d8 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Sat, 13 Feb 2021 13:27:09 +0100 Subject: Update static docs --- docs/dev/news/index.html | 20 +++++++++++++++----- docs/dev/pkgdown.yml | 2 +- 2 files changed, 16 insertions(+), 6 deletions(-) (limited to 'docs/dev/news/index.html') diff --git a/docs/dev/news/index.html b/docs/dev/news/index.html index eab75984..1421edf4 100644 --- a/docs/dev/news/index.html +++ b/docs/dev/news/index.html @@ -145,12 +145,22 @@

mkin 1.0.2.9000 Unreleased

+
+

+General

+
    +
  • Switch to a versioning scheme where the fourth version component indicates development versions
    • +
+
+
+

+Mixed-effects models

    -

  • Switch to a versioning scheme where the fourth version component indicates development versions

  • Reintroduce the interface to the current development version of saemix, in particular:

  • ‘saemix_model’ and ‘saemix_data’: Helper functions to set up nonlinear mixed-effects models for mmkin row objects

  • ‘saem’: generic function to fit saemix models using ‘saemix_model’ and ‘saemix_data’, with a generator ‘saem.mmkin’, summary and plot methods

+

@@ -176,9 +186,9 @@

mkin 1.0.0 2021-02-03

-
+

-General

+General

  • ‘mkinmod’ models gain arguments ‘name’ and ‘dll_dir’ which, in conjunction with a current version of the ‘inline’ package, make it possible to still use the DLL used for fast ODE solutions with ‘deSolve’ after saving and restoring the ‘mkinmod’ object.

  • ‘mkindsg’ R6 class for groups of ‘mkinds’ datasets with metadata

    • @@ -191,9 +201,9 @@

  • ‘plot.mkinfit’: Change default ylab from “Observed” to “Residue”. Pass xlab to residual plot if show_residuals is TRUE.

-
+

-Mixed-effects models

+Mixed-effects models

  • ‘mixed.mmkin’ New container for mmkin objects for plotting with the ‘plot.mixed.mmkin’ method

  • ‘plot.mixed.mmkin’ method used for ‘nlme.mmkin’ inheriting from ‘mixed.mmkin’ (currently virtual)

    • diff --git a/docs/dev/pkgdown.yml b/docs/dev/pkgdown.yml index 2e984557..c74efaf7 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: 2021-02-13T12:16Z +last_built: 2021-02-13T12:27Z urls: reference: https://pkgdown.jrwb.de/mkin/reference article: https://pkgdown.jrwb.de/mkin/articles -- cgit v1.2.3 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 --- GNUmakefile | 2 +- build.log | 3 +- check.log | 4 +- docs/dev/404.html | 2 +- docs/dev/articles/FOCUS_D.html | 23 +-- .../accessible-code-block-0.0.1/empty-anchor.js | 15 ++ .../articles/FOCUS_D_files/figure-html/plot-1.png | Bin 81432 -> 79176 bytes .../FOCUS_D_files/header-attrs-2.6/header-attrs.js | 12 ++ 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create mode 100644 docs/dev/articles/web_only/benchmarks_files/accessible-code-block-0.0.1/empty-anchor.js create mode 100644 docs/dev/articles/web_only/benchmarks_files/header-attrs-2.6/header-attrs.js create mode 100644 docs/dev/articles/web_only/compiled_models_files/accessible-code-block-0.0.1/empty-anchor.js create mode 100644 docs/dev/articles/web_only/compiled_models_files/header-attrs-2.6/header-attrs.js (limited to 'docs/dev/news/index.html') diff --git a/GNUmakefile b/GNUmakefile index 8604d3b3..d7c68ebf 100644 --- a/GNUmakefile +++ b/GNUmakefile @@ -112,7 +112,7 @@ pd: roxygen "$(RBIN)/Rscript" -e "pkgdown::build_site(run_dont_run = TRUE, lazy = TRUE)" git add -A -pd_release: roxygen +pd_all: roxygen "$(RBIN)/Rscript" -e "pkgdown::build_site(run_dont_run = TRUE)" git add -A diff --git a/build.log b/build.log index 293831aa..d50a4860 100644 --- a/build.log +++ b/build.log @@ -6,4 +6,5 @@ * creating vignettes ... OK * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories -* building ‘mkin_1.0.2.9000.tar.gz’ +* building ‘mkin_1.0.3.9000.tar.gz’ + diff --git a/check.log b/check.log index 2a4d87ad..ac59f6af 100644 --- a/check.log +++ b/check.log @@ -5,12 +5,12 @@ * using options ‘--no-tests --as-cran’ * checking for file ‘mkin/DESCRIPTION’ ... OK * checking extension type ... Package -* this is package ‘mkin’ version ‘1.0.2.9000’ +* this is package ‘mkin’ version ‘1.0.3.9000’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... NOTE Maintainer: ‘Johannes Ranke ’ -Version contains large components (1.0.2.9000) +Version contains large components (1.0.3.9000) Unknown, possibly mis-spelled, fields in DESCRIPTION: ‘Remotes’ diff --git a/docs/dev/404.html b/docs/dev/404.html index ea547a2a..f9e51aa3 100644 --- a/docs/dev/404.html +++ b/docs/dev/404.html @@ -71,7 +71,7 @@ mkin - 1.0.2.9000 + 1.0.3.9000
diff --git a/docs/dev/articles/FOCUS_D.html b/docs/dev/articles/FOCUS_D.html index dd86f677..a35a255a 100644 --- a/docs/dev/articles/FOCUS_D.html +++ b/docs/dev/articles/FOCUS_D.html @@ -32,7 +32,7 @@ mkin - 0.9.50.4 + 1.0.3.9000
@@ -81,7 +81,7 @@
diff --git a/docs/dev/reference/DFOP.solution.html b/docs/dev/reference/DFOP.solution.html index 22b28732..3ee660f2 100644 --- a/docs/dev/reference/DFOP.solution.html +++ b/docs/dev/reference/DFOP.solution.html @@ -73,7 +73,7 @@ two exponential decline functions." /> mkin - 0.9.50.4 + 1.0.3.9000
@@ -122,7 +122,7 @@ two exponential decline functions." />
  • - +
    • diff --git a/docs/dev/reference/Extract.mmkin.html b/docs/dev/reference/Extract.mmkin.html index 0c02355f..8381337a 100644 --- a/docs/dev/reference/Extract.mmkin.html +++ b/docs/dev/reference/Extract.mmkin.html @@ -72,7 +72,7 @@ mkin - 0.9.50.4 + 1.0.3.9000
@@ -121,7 +121,7 @@
  • - +
    • @@ -220,7 +220,7 @@ either a list of mkinfit objects or a single mkinfit object.

    )
#> $par #> parent_0 log_alpha log_beta sigma -#> 99.666193 2.549849 5.050586 1.890202 +#> 99.666192 2.549850 5.050586 1.890202 #> #> $objective #> [1] 28.58291 diff --git a/docs/dev/reference/FOCUS_2006_DFOP_ref_A_to_B.html b/docs/dev/reference/FOCUS_2006_DFOP_ref_A_to_B.html index 16d12378..a188430d 100644 --- a/docs/dev/reference/FOCUS_2006_DFOP_ref_A_to_B.html +++ b/docs/dev/reference/FOCUS_2006_DFOP_ref_A_to_B.html @@ -76,7 +76,7 @@ in this fit." /> mkin - 0.9.50.4 + 1.0.3.9000
@@ -125,7 +125,7 @@ in this fit." />
  • - +
    • diff --git a/docs/dev/reference/FOCUS_2006_FOMC_ref_A_to_F.html b/docs/dev/reference/FOCUS_2006_FOMC_ref_A_to_F.html index 6b8a6119..0bee1c16 100644 --- a/docs/dev/reference/FOCUS_2006_FOMC_ref_A_to_F.html +++ b/docs/dev/reference/FOCUS_2006_FOMC_ref_A_to_F.html @@ -76,7 +76,7 @@ in this fit." /> mkin - 0.9.50.4 + 1.0.3.9000
@@ -125,7 +125,7 @@ in this fit." />
  • - +
    • diff --git a/docs/dev/reference/FOCUS_2006_HS_ref_A_to_F.html b/docs/dev/reference/FOCUS_2006_HS_ref_A_to_F.html index 076a66c6..460fdf0d 100644 --- a/docs/dev/reference/FOCUS_2006_HS_ref_A_to_F.html +++ b/docs/dev/reference/FOCUS_2006_HS_ref_A_to_F.html @@ -76,7 +76,7 @@ in this fit." /> mkin - 0.9.50.4 + 1.0.3.9000
@@ -125,7 +125,7 @@ in this fit." />
  • - +
    • diff --git a/docs/dev/reference/FOCUS_2006_SFO_ref_A_to_F.html b/docs/dev/reference/FOCUS_2006_SFO_ref_A_to_F.html index 08f1d416..c1a5fdff 100644 --- a/docs/dev/reference/FOCUS_2006_SFO_ref_A_to_F.html +++ b/docs/dev/reference/FOCUS_2006_SFO_ref_A_to_F.html @@ -76,7 +76,7 @@ in this fit." /> mkin - 0.9.50.4 + 1.0.3.9000
@@ -125,7 +125,7 @@ in this fit." />
  • - +
    • diff --git a/docs/dev/reference/FOCUS_2006_datasets.html b/docs/dev/reference/FOCUS_2006_datasets.html index df4651f8..fb3a8f17 100644 --- a/docs/dev/reference/FOCUS_2006_datasets.html +++ b/docs/dev/reference/FOCUS_2006_datasets.html @@ -72,7 +72,7 @@ mkin - 0.9.50.4 + 1.0.3.9000
@@ -121,7 +121,7 @@
  • - +
    • diff --git a/docs/dev/reference/FOMC.solution.html b/docs/dev/reference/FOMC.solution.html index ed5c4d21..1a5124e0 100644 --- a/docs/dev/reference/FOMC.solution.html +++ b/docs/dev/reference/FOMC.solution.html @@ -73,7 +73,7 @@ a decreasing rate constant." /> mkin - 0.9.50.4 + 1.0.3.9000
@@ -122,7 +122,7 @@ a decreasing rate constant." />
  • - +
    • diff --git a/docs/dev/reference/HS.solution.html b/docs/dev/reference/HS.solution.html index 8cf5c7f9..1b79e8b6 100644 --- a/docs/dev/reference/HS.solution.html +++ b/docs/dev/reference/HS.solution.html @@ -73,7 +73,7 @@ between them." /> mkin - 0.9.50.4 + 1.0.3.9000
@@ -122,7 +122,7 @@ between them." />
  • - +
    • diff --git a/docs/dev/reference/IORE.solution.html b/docs/dev/reference/IORE.solution.html index 29d615dc..bc17319e 100644 --- a/docs/dev/reference/IORE.solution.html +++ b/docs/dev/reference/IORE.solution.html @@ -73,7 +73,7 @@ a concentration dependent rate constant." /> mkin - 0.9.50.4 + 1.0.3.9000
@@ -122,7 +122,7 @@ a concentration dependent rate constant." />
  • - +
    • diff --git a/docs/dev/reference/NAFTA_SOP_2015-1.png b/docs/dev/reference/NAFTA_SOP_2015-1.png index 4d823d77..4f0d7833 100644 Binary files a/docs/dev/reference/NAFTA_SOP_2015-1.png and b/docs/dev/reference/NAFTA_SOP_2015-1.png differ diff --git a/docs/dev/reference/NAFTA_SOP_2015.html b/docs/dev/reference/NAFTA_SOP_2015.html index 4243faba..fb65fec8 100644 --- a/docs/dev/reference/NAFTA_SOP_2015.html +++ b/docs/dev/reference/NAFTA_SOP_2015.html @@ -72,7 +72,7 @@ mkin - 0.9.50.4 + 1.0.3.9000
@@ -121,7 +121,7 @@
  • - +
    • diff --git a/docs/dev/reference/NAFTA_SOP_Attachment-1.png b/docs/dev/reference/NAFTA_SOP_Attachment-1.png index 6eb10cde..9417685e 100644 Binary files a/docs/dev/reference/NAFTA_SOP_Attachment-1.png and b/docs/dev/reference/NAFTA_SOP_Attachment-1.png differ diff --git a/docs/dev/reference/NAFTA_SOP_Attachment.html b/docs/dev/reference/NAFTA_SOP_Attachment.html index de984984..311a7c61 100644 --- a/docs/dev/reference/NAFTA_SOP_Attachment.html +++ b/docs/dev/reference/NAFTA_SOP_Attachment.html @@ -72,7 +72,7 @@ mkin - 0.9.50.4 + 1.0.3.9000
@@ -121,7 +121,7 @@
  • - +
    • @@ -193,7 +193,7 @@ #> Estimate Pr(>t) Lower Upper #> parent_0 9.99e+01 1.41e-26 98.8116 101.0810 #> k1 2.67e-02 5.05e-06 0.0243 0.0295 -#> k2 2.42e-12 5.00e-01 0.0000 Inf +#> k2 2.26e-12 5.00e-01 0.0000 Inf #> g 6.47e-01 3.67e-06 0.6248 0.6677 #> sigma 1.27e+00 8.91e-06 0.8395 1.6929 #> @@ -202,7 +202,7 @@ #> DT50 DT90 DT50_rep #> SFO 67.7 2.25e+02 6.77e+01 #> IORE 58.2 1.07e+03 3.22e+02 -#> DFOP 55.5 5.22e+11 2.86e+11 +#> DFOP 55.5 5.59e+11 3.07e+11 #> #> Representative half-life: #> [1] 321.51
plot(nafta_att_p5a) diff --git a/docs/dev/reference/Rplot001.png b/docs/dev/reference/Rplot001.png index 17a35806..7f498242 100644 Binary files a/docs/dev/reference/Rplot001.png and b/docs/dev/reference/Rplot001.png differ diff --git a/docs/dev/reference/Rplot002.png b/docs/dev/reference/Rplot002.png index 9b97a634..54c31a3f 100644 Binary files a/docs/dev/reference/Rplot002.png and b/docs/dev/reference/Rplot002.png differ diff --git a/docs/dev/reference/Rplot006.png b/docs/dev/reference/Rplot006.png index 730a7481..81525882 100644 Binary files a/docs/dev/reference/Rplot006.png and b/docs/dev/reference/Rplot006.png differ diff --git a/docs/dev/reference/Rplot007.png b/docs/dev/reference/Rplot007.png index fce3b6ee..10b7455a 100644 Binary files a/docs/dev/reference/Rplot007.png and b/docs/dev/reference/Rplot007.png differ diff --git a/docs/dev/reference/SFO.solution.html b/docs/dev/reference/SFO.solution.html index b3e7ef9a..43c434c6 100644 --- a/docs/dev/reference/SFO.solution.html +++ b/docs/dev/reference/SFO.solution.html @@ -72,7 +72,7 @@ mkin - 0.9.50.4 + 1.0.3.9000
@@ -121,7 +121,7 @@
  • - +
    • diff --git a/docs/dev/reference/SFORB.solution.html b/docs/dev/reference/SFORB.solution.html index 9310212f..807fbe5c 100644 --- a/docs/dev/reference/SFORB.solution.html +++ b/docs/dev/reference/SFORB.solution.html @@ -76,7 +76,7 @@ and no substance in the bound fraction." /> mkin - 0.9.50.4 + 1.0.3.9000
@@ -125,7 +125,7 @@ and no substance in the bound fraction." />
  • - +
    • diff --git a/docs/dev/reference/add_err-1.png b/docs/dev/reference/add_err-1.png index d2ce797f..9ba106db 100644 Binary files a/docs/dev/reference/add_err-1.png and b/docs/dev/reference/add_err-1.png differ diff --git a/docs/dev/reference/add_err-2.png b/docs/dev/reference/add_err-2.png index ac220c9e..3088c40e 100644 Binary files a/docs/dev/reference/add_err-2.png and b/docs/dev/reference/add_err-2.png differ diff --git a/docs/dev/reference/add_err-3.png b/docs/dev/reference/add_err-3.png index 40465b71..493a761a 100644 Binary files a/docs/dev/reference/add_err-3.png and b/docs/dev/reference/add_err-3.png differ diff --git a/docs/dev/reference/add_err.html b/docs/dev/reference/add_err.html index 6ea30515..b94cef29 100644 --- a/docs/dev/reference/add_err.html +++ b/docs/dev/reference/add_err.html @@ -74,7 +74,7 @@ may depend on the predicted value and is specified as a standard deviation." /> mkin - 0.9.50.4 + 1.0.3.9000
@@ -123,7 +123,7 @@ may depend on the predicted value and is specified as a standard deviation." />
  • - +
    • diff --git a/docs/dev/reference/aw.html b/docs/dev/reference/aw.html index ef808dd8..3b06f2a6 100644 --- a/docs/dev/reference/aw.html +++ b/docs/dev/reference/aw.html @@ -74,7 +74,7 @@ by Burnham and Anderson (2004)." /> mkin - 0.9.50.4 + 1.0.3.9000
@@ -123,7 +123,7 @@ by Burnham and Anderson (2004)." />
  • - +
    • diff --git a/docs/dev/reference/confint.mkinfit.html b/docs/dev/reference/confint.mkinfit.html index 89bb3d89..2237a539 100644 --- a/docs/dev/reference/confint.mkinfit.html +++ b/docs/dev/reference/confint.mkinfit.html @@ -79,7 +79,7 @@ method of Venzon and Moolgavkar (1988)." /> mkin - 1.0.1.9000 + 1.0.3.9000
@@ -285,13 +285,13 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, f_d_1 <- mkinfit(SFO_SFO, subset(FOCUS_2006_D, value != 0), quiet = TRUE) system.time(ci_profile <- confint(f_d_1, method = "profile", cores = 1, quiet = TRUE))
#> user system elapsed -#> 4.258 0.916 3.889
# Using more cores does not save much time here, as parent_0 takes up most of the time +#> 4.295 1.008 3.959
# Using more cores does not save much time here, as parent_0 takes up most of the time # If we additionally exclude parent_0 (the confidence of which is often of # minor interest), we get a nice performance improvement if we use at least 4 cores system.time(ci_profile_no_parent_0 <- confint(f_d_1, method = "profile", c("k_parent_sink", "k_parent_m1", "k_m1_sink", "sigma"), cores = n_cores))
#> Profiling the likelihood
#> user system elapsed -#> 1.459 0.088 0.907
ci_profile +#> 1.451 0.126 0.923
ci_profile
#> 2.5% 97.5% #> parent_0 96.456003640 1.027703e+02 #> k_parent_sink 0.040762501 5.549764e-02 diff --git a/docs/dev/reference/create_deg_func.html b/docs/dev/reference/create_deg_func.html index 4945d157..65a682bb 100644 --- a/docs/dev/reference/create_deg_func.html +++ b/docs/dev/reference/create_deg_func.html @@ -72,7 +72,7 @@ mkin - 0.9.50.4 + 1.0.3.9000
@@ -121,7 +121,7 @@
  • - +
    • @@ -181,8 +181,8 @@ deSolve = mkinfit(SFO_SFO, FOCUS_D, solution_type = "deSolve", quiet = TRUE), replications = 2)
#> Loading required package: rbenchmark
#> test replications elapsed relative user.self sys.self user.child -#> 1 analytical 2 0.396 1.000 0.395 0 0 -#> 2 deSolve 2 0.694 1.753 0.693 0 0 +#> 1 analytical 2 0.396 1.00 0.396 0 0 +#> 2 deSolve 2 0.709 1.79 0.707 0 0 #> sys.child #> 1 0 #> 2 0
DFOP_SFO <- mkinmod( @@ -193,8 +193,8 @@ deSolve = mkinfit(DFOP_SFO, FOCUS_D, solution_type = "deSolve", quiet = TRUE), replications = 2)
#> test replications elapsed relative user.self sys.self user.child -#> 1 analytical 2 0.838 1.000 0.838 0.001 0 -#> 2 deSolve 2 1.573 1.877 1.572 0.000 0 +#> 1 analytical 2 0.844 1.000 0.844 0 0 +#> 2 deSolve 2 1.624 1.924 1.624 0 0 #> sys.child #> 1 0 #> 2 0
# } diff --git a/docs/dev/reference/dimethenamid_2018.html b/docs/dev/reference/dimethenamid_2018.html index 21dea623..a06599df 100644 --- a/docs/dev/reference/dimethenamid_2018.html +++ b/docs/dev/reference/dimethenamid_2018.html @@ -77,7 +77,7 @@ constrained by data protection regulations." /> mkin - 0.9.50.4 + 1.0.3.9000
diff --git a/docs/dev/reference/endpoints.html b/docs/dev/reference/endpoints.html index 301b454f..c9912f9c 100644 --- a/docs/dev/reference/endpoints.html +++ b/docs/dev/reference/endpoints.html @@ -78,7 +78,7 @@ advantage that the SFORB model can also be used for metabolites." /> mkin - 1.0.2.9000 + 1.0.3.9000
diff --git a/docs/dev/reference/experimental_data_for_UBA-1.png b/docs/dev/reference/experimental_data_for_UBA-1.png index 24cb54c5..33946ded 100644 Binary files a/docs/dev/reference/experimental_data_for_UBA-1.png and b/docs/dev/reference/experimental_data_for_UBA-1.png differ diff --git a/docs/dev/reference/experimental_data_for_UBA.html b/docs/dev/reference/experimental_data_for_UBA.html index 78e57fb0..9904370f 100644 --- a/docs/dev/reference/experimental_data_for_UBA.html +++ b/docs/dev/reference/experimental_data_for_UBA.html @@ -100,7 +100,7 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl mkin - 0.9.50.4 + 1.0.3.9000
@@ -149,7 +149,7 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl
  • - +
    • diff --git a/docs/dev/reference/f_time_norm_focus.html b/docs/dev/reference/f_time_norm_focus.html index 3421043d..852e00a0 100644 --- a/docs/dev/reference/f_time_norm_focus.html +++ b/docs/dev/reference/f_time_norm_focus.html @@ -73,7 +73,7 @@ in Appendix 8 to the FOCUS kinetics guidance (FOCUS 2014, p. 369)." /> mkin - 0.9.50.4 + 1.0.3.9000
diff --git a/docs/dev/reference/focus_soil_moisture.html b/docs/dev/reference/focus_soil_moisture.html index c46fd69a..0e6fea28 100644 --- a/docs/dev/reference/focus_soil_moisture.html +++ b/docs/dev/reference/focus_soil_moisture.html @@ -73,7 +73,7 @@ corresponds to pF2, MWHC to pF 1 and 1/3 bar to pF 2.5." /> mkin - 0.9.50.4 + 1.0.3.9000
@@ -122,7 +122,7 @@ corresponds to pF2, MWHC to pF 1 and 1/3 bar to pF 2.5." />
  • - +
    • diff --git a/docs/dev/reference/get_deg_func.html b/docs/dev/reference/get_deg_func.html index a266bf5f..fb661085 100644 --- a/docs/dev/reference/get_deg_func.html +++ b/docs/dev/reference/get_deg_func.html @@ -72,7 +72,7 @@ mkin - 0.9.50.4 + 1.0.3.9000
@@ -121,7 +121,7 @@
  • - +
    • diff --git a/docs/dev/reference/ilr.html b/docs/dev/reference/ilr.html index 98e51211..452647d6 100644 --- a/docs/dev/reference/ilr.html +++ b/docs/dev/reference/ilr.html @@ -73,7 +73,7 @@ transformations." /> mkin - 0.9.50.4 + 1.0.3.9000
@@ -122,7 +122,7 @@ transformations." />
  • - +
    • diff --git a/docs/dev/reference/index.html b/docs/dev/reference/index.html index b52ecb22..03a21517 100644 --- a/docs/dev/reference/index.html +++ b/docs/dev/reference/index.html @@ -71,7 +71,7 @@ mkin - 1.0.2.9000 + 1.0.3.9000
diff --git a/docs/dev/reference/loftest-1.png b/docs/dev/reference/loftest-1.png index 6b918fec..d6006ecc 100644 Binary files a/docs/dev/reference/loftest-1.png and b/docs/dev/reference/loftest-1.png differ diff --git a/docs/dev/reference/loftest-2.png b/docs/dev/reference/loftest-2.png index 60874bd3..4d0dc551 100644 Binary files a/docs/dev/reference/loftest-2.png and b/docs/dev/reference/loftest-2.png differ diff --git a/docs/dev/reference/loftest-3.png b/docs/dev/reference/loftest-3.png index 4837e7f2..6afd084b 100644 Binary files a/docs/dev/reference/loftest-3.png and b/docs/dev/reference/loftest-3.png differ diff --git a/docs/dev/reference/loftest-4.png b/docs/dev/reference/loftest-4.png index 9c18ac30..f94eede1 100644 Binary files a/docs/dev/reference/loftest-4.png and b/docs/dev/reference/loftest-4.png differ diff --git a/docs/dev/reference/loftest-5.png b/docs/dev/reference/loftest-5.png index 11f2bda7..43460a65 100644 Binary files a/docs/dev/reference/loftest-5.png and b/docs/dev/reference/loftest-5.png differ diff --git a/docs/dev/reference/loftest.html b/docs/dev/reference/loftest.html index abbbd3b9..9dbd547d 100644 --- a/docs/dev/reference/loftest.html +++ b/docs/dev/reference/loftest.html @@ -75,7 +75,7 @@ lrtest.default from the lmtest package." /> mkin - 0.9.50.4 + 1.0.3.9000
@@ -124,7 +124,7 @@ lrtest.default from the lmtest package." />
  • - +
    • diff --git a/docs/dev/reference/logLik.mkinfit.html b/docs/dev/reference/logLik.mkinfit.html index 82c0654f..3e9452c6 100644 --- a/docs/dev/reference/logLik.mkinfit.html +++ b/docs/dev/reference/logLik.mkinfit.html @@ -76,7 +76,7 @@ the error model." /> mkin - 1.0.1.9000 + 1.0.3.9000
diff --git a/docs/dev/reference/logistic.solution-2.png b/docs/dev/reference/logistic.solution-2.png index 764996df..73e6436d 100644 Binary files a/docs/dev/reference/logistic.solution-2.png and b/docs/dev/reference/logistic.solution-2.png differ diff --git a/docs/dev/reference/logistic.solution.html b/docs/dev/reference/logistic.solution.html index 950e8a8e..ab68c99e 100644 --- a/docs/dev/reference/logistic.solution.html +++ b/docs/dev/reference/logistic.solution.html @@ -73,7 +73,7 @@ an increasing rate constant, supposedly caused by microbial growth" /> mkin - 0.9.50.4 + 1.0.3.9000
@@ -122,7 +122,7 @@ an increasing rate constant, supposedly caused by microbial growth" />
  • - +
    • @@ -240,10 +240,10 @@ Version 1.1, 18 December 2014 plot_sep(m)
summary(m)$bpar
#> Estimate se_notrans t value Pr(>t) Lower -#> parent_0 1.057896e+02 1.9023449703 55.610119 3.768361e-16 1.016451e+02 -#> kmax 6.398190e-02 0.0143201031 4.467978 3.841829e-04 3.929235e-02 +#> parent_0 1.057896e+02 1.9023449590 55.610120 3.768360e-16 1.016451e+02 +#> kmax 6.398190e-02 0.0143201029 4.467978 3.841828e-04 3.929235e-02 #> k0 1.612775e-04 0.0005866813 0.274898 3.940351e-01 5.846688e-08 -#> r 2.263946e-01 0.1718110715 1.317695 1.061044e-01 4.335843e-02 +#> r 2.263946e-01 0.1718110662 1.317695 1.061043e-01 4.335843e-02 #> sigma 5.332935e+00 0.9145907310 5.830952 4.036926e-05 3.340213e+00 #> Upper #> parent_0 109.9341588 diff --git a/docs/dev/reference/lrtest.mkinfit.html b/docs/dev/reference/lrtest.mkinfit.html index b76ebc87..f2d8472e 100644 --- a/docs/dev/reference/lrtest.mkinfit.html +++ b/docs/dev/reference/lrtest.mkinfit.html @@ -76,7 +76,7 @@ and can be expressed by fixing the parameters of the other." /> mkin - 0.9.50.4 + 1.0.3.9000
@@ -125,7 +125,7 @@ and can be expressed by fixing the parameters of the other." />
  • - +
    • diff --git a/docs/dev/reference/max_twa_parent.html b/docs/dev/reference/max_twa_parent.html index 25f745e9..a358568a 100644 --- a/docs/dev/reference/max_twa_parent.html +++ b/docs/dev/reference/max_twa_parent.html @@ -78,7 +78,7 @@ soil section of the FOCUS guidance." /> mkin - 0.9.50.4 + 1.0.3.9000
@@ -127,7 +127,7 @@ soil section of the FOCUS guidance." />
@@ -181,30 +181,30 @@ fit.1 <- mkinfit(SFO_SFO_SFO, subset(mccall81_245T, soil == "Commerce"), quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
summary(fit.1)$bpar
#> Estimate se_notrans t value Pr(>t) -#> T245_0 1.038550e+02 2.1847074888 47.537272 4.472189e-18 +#> T245_0 1.038550e+02 2.1847074945 47.537272 4.472189e-18 #> k_T245 4.337042e-02 0.0018983965 22.845818 2.276911e-13 -#> k_phenol 4.050581e-01 0.2986993400 1.356073 9.756988e-02 -#> k_anisole 6.678742e-03 0.0008021439 8.326114 2.623176e-07 -#> f_T245_to_phenol 6.227599e-01 0.3985340295 1.562627 6.949412e-02 -#> f_phenol_to_anisole 1.000000e+00 0.6718439378 1.488441 7.867787e-02 -#> sigma 2.514628e+00 0.4907558750 5.123989 6.233156e-05 +#> k_phenol 4.050581e-01 0.2986993563 1.356073 9.756989e-02 +#> k_anisole 6.678742e-03 0.0008021439 8.326114 2.623177e-07 +#> f_T245_to_phenol 6.227599e-01 0.3985340558 1.562627 6.949413e-02 +#> f_phenol_to_anisole 1.000000e+00 0.6718439825 1.488441 7.867789e-02 +#> sigma 2.514628e+00 0.4907558883 5.123989 6.233157e-05 #> Lower Upper -#> T245_0 99.246061370 1.084640e+02 +#> T245_0 99.246061385 1.084640e+02 #> k_T245 0.039631621 4.746194e-02 -#> k_phenol 0.218013878 7.525762e-01 +#> k_phenol 0.218013879 7.525762e-01 #> k_anisole 0.005370739 8.305299e-03 -#> f_T245_to_phenol 0.547559083 6.924813e-01 +#> f_T245_to_phenol 0.547559081 6.924813e-01 #> f_phenol_to_anisole 0.000000000 1.000000e+00 #> sigma 1.706607296 3.322649e+00
endpoints(fit.1)
#> $ff #> T245_phenol T245_sink phenol_anisole phenol_sink -#> 6.227599e-01 3.772401e-01 1.000000e+00 6.894640e-11 +#> 6.227599e-01 3.772401e-01 1.000000e+00 3.773626e-10 #> #> $distimes #> DT50 DT90 #> T245 15.982025 53.09114 #> phenol 1.711229 5.68458 -#> anisole 103.784092 344.76329 +#> anisole 103.784093 344.76329 #>
# formation fraction from phenol to anisol is practically 1. As we cannot # fix formation fractions when using the ilr transformation, we can turn of # the sink in the model generation @@ -215,28 +215,28 @@ quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
summary(fit.2)$bpar
#> Estimate se_notrans t value Pr(>t) Lower -#> T245_0 1.038550e+02 2.1623653027 48.028439 4.993108e-19 99.271020526 -#> k_T245 4.337042e-02 0.0018343666 23.643268 3.573555e-14 0.039650977 -#> k_phenol 4.050582e-01 0.1177237248 3.440752 1.679252e-03 0.218746585 -#> k_anisole 6.678741e-03 0.0006829745 9.778903 1.872894e-08 0.005377083 -#> f_T245_to_phenol 6.227599e-01 0.0342197865 18.198825 2.039410e-12 0.547975628 +#> T245_0 1.038550e+02 2.1623653066 48.028439 4.993108e-19 99.271020284 +#> k_T245 4.337042e-02 0.0018343666 23.643268 3.573556e-14 0.039650976 +#> k_phenol 4.050582e-01 0.1177237473 3.440752 1.679254e-03 0.218746587 +#> k_anisole 6.678742e-03 0.0006829745 9.778903 1.872894e-08 0.005377083 +#> f_T245_to_phenol 6.227599e-01 0.0342197875 18.198824 2.039411e-12 0.547975637 #> sigma 2.514628e+00 0.3790944250 6.633250 2.875782e-06 1.710983655 #> Upper -#> T245_0 108.43904097 +#> T245_0 108.43904074 #> k_T245 0.04743877 -#> k_phenol 0.75005577 +#> k_phenol 0.75005585 #> k_anisole 0.00829550 -#> f_T245_to_phenol 0.69212306 +#> f_T245_to_phenol 0.69212308 #> sigma 3.31827222
endpoints(fit.1)
#> $ff #> T245_phenol T245_sink phenol_anisole phenol_sink -#> 6.227599e-01 3.772401e-01 1.000000e+00 6.894640e-11 +#> 6.227599e-01 3.772401e-01 1.000000e+00 3.773626e-10 #> #> $distimes #> DT50 DT90 #> T245 15.982025 53.09114 #> phenol 1.711229 5.68458 -#> anisole 103.784092 344.76329 +#> anisole 103.784093 344.76329 #>
plot_sep(fit.2)
# }
diff --git a/docs/dev/reference/mixed-1.png b/docs/dev/reference/mixed-1.png index 3400c4aa..28a376f4 100644 Binary files a/docs/dev/reference/mixed-1.png and b/docs/dev/reference/mixed-1.png differ diff --git a/docs/dev/reference/mixed.html b/docs/dev/reference/mixed.html index 18a67af8..7bf8dd56 100644 --- a/docs/dev/reference/mixed.html +++ b/docs/dev/reference/mixed.html @@ -72,7 +72,7 @@ mkin - 0.9.50.4 + 1.0.3.9000 @@ -121,7 +121,7 @@