From 5c2b184748abd5002e79d7e86c2764613f96d97e Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Sat, 6 Feb 2021 09:31:11 +0100 Subject: Update static docs --- docs/news/index.html | 177 ++++++++++++++++++++++++++------------------------- docs/pkgdown.yml | 4 +- 2 files changed, 91 insertions(+), 90 deletions(-) diff --git a/docs/news/index.html b/docs/news/index.html index 7a307709..c568202b 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -141,19 +141,20 @@ Source: NEWS.md -
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-mkin 1.0.1 Unreleased +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!)

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+

-mkin 1.0.0 2021-02-03 +mkin 1.0.0 2021-02-03

@@ -180,9 +181,9 @@

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-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

    • @@ -196,18 +197,18 @@

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

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+

-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

    • @@ -215,17 +216,17 @@

  • 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

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+

-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
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+

-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

    • @@ -236,18 +237,18 @@

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

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+

-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

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+

-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

    • @@ -257,18 +258,18 @@

  • ‘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

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+

-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.

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+

-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

    • @@ -286,9 +287,9 @@

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

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+

-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.

    • @@ -305,9 +306,9 @@

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

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+

-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

    • @@ -322,9 +323,9 @@

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

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+

-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

    • @@ -332,27 +333,27 @@

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

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+

-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’

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+

-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’.

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+

-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

    • @@ -363,27 +364,27 @@

  • ‘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

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+

-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

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+

-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

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+

-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

    • @@ -391,17 +392,17 @@

  • Documentation updates

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-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
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+

-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

    • @@ -410,9 +411,9 @@

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

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

@@ -422,9 +423,9 @@

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

@@ -436,9 +437,9 @@

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

@@ -448,9 +449,9 @@

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

@@ -487,9 +488,9 @@

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

@@ -508,9 +509,9 @@

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

@@ -531,9 +532,9 @@

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

@@ -552,9 +553,9 @@

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

@@ -573,9 +574,9 @@

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

@@ -594,9 +595,9 @@

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

@@ -616,9 +617,9 @@

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

@@ -648,9 +649,9 @@

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

@@ -670,9 +671,9 @@

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

@@ -703,9 +704,9 @@

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

@@ -713,7 +714,7 @@

  • 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.

    • @@ -740,9 +741,9 @@

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

@@ -752,9 +753,9 @@

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

@@ -767,7 +768,7 @@

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.

@@ -784,9 +785,9 @@
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-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

    • @@ -794,9 +795,9 @@

  • 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

    • @@ -804,9 +805,9 @@

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

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+

-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

    • @@ -828,9 +829,9 @@

  • Add gmkin workspace datasets FOCUS_2006_gmkin and FOCUS_2006_Z_gmkin

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+

-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

    • @@ -838,9 +839,9 @@

  • Backtransform fixed ODE parameters for the summary

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+

-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

    • diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index d05f3168..463d6e59 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -1,4 +1,4 @@ -pandoc: 2.2.1 +pandoc: 2.9.2.1 pkgdown: 1.6.1 pkgdown_sha: ~ articles: @@ -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: 2021-02-04T10:34Z +last_built: 2021-02-06T08:30Z urls: reference: https://pkgdown.jrwb.de/mkin/reference article: https://pkgdown.jrwb.de/mkin/articles -- cgit v1.2.1