From 798195d367111e592e5247309b90fac29ed7ddfd Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 3 Jul 2019 16:45:09 +0200 Subject: Update DESCRIPTION, improve NEWS Static documentation rebuilt by pkgdown --- docs/news/index.html | 20 ++++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) (limited to 'docs/news/index.html') diff --git a/docs/news/index.html b/docs/news/index.html index df6d53db..f8504768 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -122,22 +122,22 @@ -
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-mkin 0.9.49.5 (2019-06-04) Unreleased +mkin 0.9.49.5 (2019-07-03) Unreleased

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  • 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 tries direct minimization and a three step procedure, and returns the model with the highest likelihood.

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  • 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

  • Add a test that checks if we get the best known AIC for parent only fits to 12 test datasets. Add these test datasets for this purpose.

  • New function ‘mkinerrplot’. This function is also used for residual plots in ‘plot.mmkin’ if the argument ‘resplot = “errmod”’ is given, and in ‘plot.mkinfit’ if ‘show_errplot’ is set to TRUE.

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  • Remove dependency on FME, only use nlminb for optimisation

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  • Use the numDeriv package to calculate hessians

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  • Add a benchmark vignette to document the impact on performance. For very simple fits, the new code is a bit slower, presumably because of the time it takes to calculate the hessian matrices with and without parameter transformation

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  • The code for manual weighting was removed

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  • The fitting time reported in the summary now includes the calculation of the hessians

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  • Remove dependency on FME, only use nlminb for optimisation (‘Port’ algorithm). I cannot remember cases where one of the other optimisation algorithms was preferable, except that I sometime used Levenberg-Marquardt for speed in cases where I did not expect to get trapped in a local minimum.

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  • Use the numDeriv package to calculate hessians. This results in slightly different confidence intervals, takes a bit longer, but is apparently more robust

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  • Add a simple benchmark vignette to document the impact on performance.

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  • The code for manual weighting was removed. This functionality might get added again at a later time.

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  • The fitting time reported in the summary now includes the time used for calculation of the hessians

  • Adapt tests

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  • Fix an error in the FOCUS chi2 error level calculations that occurred if parameters were specified in parms.ini that were not in the model. A warning was already issued, but when fitting via mmkin this could easily go unnoticed.

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  • Fix an error in the FOCUS chi2 error level calculations that occurred if parameters were specified in parms.ini that were not in the model. A warning was already issued, but when fitting in parallel via mmkin this could go unnoticed.

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