From 7f35f5d98968f059176f4c339e1db8f17d5c4bf1 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 15 Feb 2021 19:15:50 +0100 Subject: Don't let pkgdown add release dates It didn't pick up the release of 1.0.3, and most of the other release dates were duplicated. --- NEWS.md | 8 +-- _pkgdown.yml | 3 ++ docs/news/index.html | 143 ++++++++++++++++++--------------------------------- docs/pkgdown.yml | 2 +- 4 files changed, 57 insertions(+), 99 deletions(-) diff --git a/NEWS.md b/NEWS.md index 6152555c..440286ea 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,12 +1,12 @@ -# mkin 1.0.3 +# mkin 1.0.3 (2021-02-15) - Review and update README, the 'Introduction to mkin' vignette and some of the help pages -# mkin 1.0.2 +# mkin 1.0.2 (Unreleased) - 'mkinfit': Keep model names stored in 'mkinmod' objects, avoiding their loss in 'gmkin' -# mkin 1.0.1 +# mkin 1.0.1 (2021-02-10) - 'confint.mmkin', 'nlme.mmkin', 'transform_odeparms': Fix example code in dontrun sections that failed with current defaults @@ -18,7 +18,7 @@ - Increase test tolerance for some parameter comparisons that also proved to be platform dependent -# mkin 1.0.0 +# mkin 1.0.0 (2021-02-03) ## General diff --git a/_pkgdown.yml b/_pkgdown.yml index f632ddb0..aaade416 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -7,6 +7,9 @@ development: template: bootswatch: spacelab +news: + cran_dates: false + reference: - title: Main functions desc: Essential functionality diff --git a/docs/news/index.html b/docs/news/index.html index 82fb92bd..1428dc78 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -141,26 +141,23 @@ Source: NEWS.md -
+

-mkin 1.0.3 Unreleased -

+mkin 1.0.3 (2021-02-15)
  • Review and update README, the ‘Introduction to mkin’ vignette and some of the help pages
-
+

-mkin 1.0.2 Unreleased -

+mkin 1.0.2 (Unreleased)
  • ‘mkinfit’: Keep model names stored in ‘mkinmod’ objects, avoiding their loss in ‘gmkin’
-
+

-mkin 1.0.1 2021-02-10 -

+mkin 1.0.1 (2021-02-10)

  • ‘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

    • @@ -169,10 +166,9 @@

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

-
+

-mkin 1.0.0 2021-02-03 -

+mkin 1.0.0 (2021-02-03)

General

@@ -200,8 +196,7 @@

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

+mkin 0.9.50.3 (2020-10-08)

  • ‘parms’: Add a method for mmkin objects

  • ‘mmkin’ and ‘confint(method = ’profile’): Use all cores detected by parallel::detectCores() per default

    • @@ -216,8 +211,7 @@

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

+mkin 0.9.50.2 (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

    • @@ -225,8 +219,7 @@

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

+mkin 0.9.50.1 (2020-05-11)

  • Support SFORB with formation fractions

  • ‘mkinmod’: Make ‘use_of_ff’ = “max” the default

    • @@ -235,16 +228,14 @@

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

+mkin 0.9.49.11 (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)

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

  • ‘mean_degparms, nlme_data, nlme_function’: Three new functions to facilitate building nlme models from mmkin row objects

    • @@ -256,8 +247,7 @@

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

+mkin 0.9.49.9 (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

    • @@ -265,8 +255,7 @@

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

+mkin 0.9.49.8 (2020-01-09)

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

  • ‘loftest’: Add a lack-of-fit test

    • @@ -277,8 +266,7 @@

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

+mkin 0.9.49.7 (2019-11-01)

  • 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.

    • @@ -286,8 +274,7 @@

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

+mkin 0.9.49.6 (2019-10-31)

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

  • Add an ‘update’ method for mkinfit objects which remembers fitted parameters if appropriate

    • @@ -306,8 +293,7 @@

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

+mkin 0.9.49.5 (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.

  • The argument ‘reweight.method’ to mkinfit and mmkin is now obsolete, use ‘error_model’ and ‘error_model_algorithm’ instead

    • @@ -325,8 +311,7 @@

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

+mkin 0.9.48.1 (2019-03-04)

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

  • Add the function ‘AIC.mmkin’ to make it easy to compare columns of mmkin objects

    • @@ -342,8 +327,7 @@

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

+mkin 0.9.47.5 (2018-09-14)

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

  • Move two vignettes to a location where they will not be built on CRAN (to avoid more NOTES from long execution times)

    • @@ -352,8 +336,7 @@

-mkin 0.9.47.3 Unreleased -

+mkin 0.9.47.3

  • ‘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’

    • @@ -361,8 +344,7 @@

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

+mkin 0.9.47.2 (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’.

    • @@ -370,8 +352,7 @@

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

+mkin 0.9.47.1 (2018-02-06)

  • Skip some tests on CRAN and winbuilder to avoid timeouts

  • ‘test_data_from_UBA_2014’: Added this list of datasets containing experimental data used in the expertise from 2014

    • @@ -383,8 +364,7 @@

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

+mkin 0.9.46.3 (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

    • @@ -392,8 +372,7 @@

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

+mkin 0.9.46.2 (2017-10-10)

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

  • DESCRIPTION: Add ORCID

    • @@ -401,8 +380,7 @@

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

+mkin 0.9.46.1 (2017-09-14)

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

  • plot.mkinfit: Use all data points of the fitted curve for y axis scaling for the case of separate plots for each observed variable

    • @@ -411,16 +389,14 @@

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

+mkin 0.9.46 (2017-07-24)
  • 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)

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

  • Update URLs in documentation

    • @@ -430,8 +406,7 @@

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

+mkin 0.9.45.1 (2016-12-20)

New features

@@ -442,8 +417,7 @@

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

+mkin 0.9.45 (2016-12-08)

Minor changes

@@ -456,8 +430,7 @@

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

+mkin 0.9.44 (2016-06-29)

Bug fixes

@@ -468,8 +441,7 @@

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

+mkin 0.9.43 (2016-06-28)

Major changes

@@ -507,8 +479,7 @@

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

+mkin 0.9.42 (2016-03-25)

Major changes

@@ -528,8 +499,7 @@

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

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

Minor changes

@@ -551,8 +521,7 @@

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

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

Bug fixes

@@ -572,8 +541,7 @@

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

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

Major changes

@@ -593,8 +561,7 @@

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

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

Minor changes

@@ -614,8 +581,7 @@

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

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

Major changes

@@ -636,8 +602,7 @@

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

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

Major changes

@@ -668,8 +633,7 @@

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

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

New features

@@ -690,8 +654,7 @@

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

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

New features

@@ -723,8 +686,7 @@

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

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

New features

@@ -760,8 +722,7 @@

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

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

Bug fixes

@@ -772,8 +733,7 @@

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

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

New features

@@ -804,8 +764,7 @@

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

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

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

  • R/geometric_mean.R, man/geometric_mean.Rd: Add geometric mean function

    • @@ -814,8 +773,7 @@

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

+mkin 0.9-28 (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

  • Add historical remarks and some background to the main package vignette

    • @@ -824,8 +782,7 @@

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

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

  • Fork the GUI into a separate package gmkin

  • DESCRIPTION, NAMESPACE, TODO: Adapt and add copyright information

    • @@ -848,8 +805,7 @@

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

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

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

  • Default values for kinetic rate constants are not all 0.1 any more but are “salted” with a small increment to avoid numeric artefacts with the eigenvalue based solutions

    • @@ -858,8 +814,7 @@

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

+mkin 0.9-22 (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

  • Fix plot.mkinfit as it passed graphical arguments like main to the solver

    • diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 5e10d15f..71325fcc 100644 --- a/docs/pkgdown.yml +++ b/docs/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: 2021-02-15T16:49Z +last_built: 2021-02-15T18:11Z urls: reference: https://pkgdown.jrwb.de/mkin/reference article: https://pkgdown.jrwb.de/mkin/articles -- cgit v1.2.1