From c73b2f30ec836c949885784ab576e814eb8070a9 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 9 Mar 2021 17:35:47 +0100 Subject: Some improvements for borderline cases - fit_with_errors for saem() - test_log_parms for mean_degparms() and saem() --- docs/dev/news/index.html | 161 ++++++++++++++++++----------------------------- 1 file changed, 62 insertions(+), 99 deletions(-) (limited to 'docs/dev/news/index.html') diff --git a/docs/dev/news/index.html b/docs/dev/news/index.html index 31c392f7..10585403 100644 --- a/docs/dev/news/index.html +++ b/docs/dev/news/index.html @@ -71,7 +71,7 @@ mkin - 1.0.3.9000 + 1.0.4.9000 @@ -141,10 +141,9 @@ Source: NEWS.md -
-

-mkin 1.0.3.9000 Unreleased -

+
+

+mkin 1.0.4.9000

General

@@ -159,29 +158,35 @@

  • 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

    • +

  • ‘mean_degparms’: New argument ‘test_log_parms’ that makes the function only consider log-transformed parameters where the untransformed parameters pass the t-test for a certain confidence level. This can be used to check more plausible parameters for ‘saem’

    • -
    +
    +

    +mkin 1.0.4 (Unreleased)

    +
      +

    • ‘plot.mixed.mmkin’: Reset graphical parameters on exit

      • +

    • All plotting functions setting graphical parameters: Use on.exit() for resetting graphical parameters

      • +
    +
    +

    -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

      • @@ -190,10 +195,9 @@

    • 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

    @@ -221,8 +225,7 @@

    -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

      • @@ -237,8 +240,7 @@

    -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

      • @@ -246,8 +248,7 @@

    -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

      • @@ -256,16 +257,14 @@

    -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

      • @@ -277,8 +276,7 @@

    -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

      • @@ -286,8 +284,7 @@

    -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

      • @@ -298,8 +295,7 @@

    -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.

      • @@ -307,8 +303,7 @@

    -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

      • @@ -327,8 +322,7 @@

    -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

      • @@ -346,8 +340,7 @@

    -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

      • @@ -363,8 +356,7 @@

    -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)

      • @@ -373,8 +365,7 @@

    -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’

      • @@ -382,8 +373,7 @@

    -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’.

      • @@ -391,8 +381,7 @@

    -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

      • @@ -404,8 +393,7 @@

    -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

      • @@ -413,8 +401,7 @@

    -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

      • @@ -422,8 +409,7 @@

    -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

      • @@ -432,16 +418,14 @@

    -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

      • @@ -451,8 +435,7 @@

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

    +mkin 0.9.45.1 (2016-12-20)

    New features

    @@ -463,8 +446,7 @@

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

    +mkin 0.9.45 (2016-12-08)

    Minor changes

    @@ -477,8 +459,7 @@

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

    +mkin 0.9.44 (2016-06-29)

    Bug fixes

    @@ -489,8 +470,7 @@

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

    +mkin 0.9.43 (2016-06-28)

    Major changes

    @@ -528,8 +508,7 @@

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

    +mkin 0.9.42 (2016-03-25)

    Major changes

    @@ -549,8 +528,7 @@

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

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

    Minor changes

    @@ -572,8 +550,7 @@

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

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

    Bug fixes

    @@ -593,8 +570,7 @@

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

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

    Major changes

    @@ -614,8 +590,7 @@

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

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

    Minor changes

    @@ -635,8 +610,7 @@

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

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

    Major changes

    @@ -657,8 +631,7 @@

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

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

    Major changes

    @@ -689,8 +662,7 @@

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

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

    New features

    @@ -711,8 +683,7 @@

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

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

    New features

    @@ -744,8 +715,7 @@

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

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

    New features

    @@ -781,8 +751,7 @@

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

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

    Bug fixes

    @@ -793,8 +762,7 @@

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

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

    New features

    @@ -825,8 +793,7 @@

    -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

      • @@ -835,8 +802,7 @@

    -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

      • @@ -845,8 +811,7 @@

    -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

      • @@ -869,8 +834,7 @@

    -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

      • @@ -879,8 +843,7 @@

    -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

      • -- cgit v1.2.1