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Commits on Sep 25, 2024

• temporary version 0.6 as tar.gz

  cdormann

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• added relaxation in test of named vector in predict_tapnet; also added the DEoptim-version of fit_tapnet (not sure I have tested this thoroughly, though)

  cdormann

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Commits on Dec 1, 2023

• new version (0.5), with quite a few small bug fixes, particular in make_tapnet; see tapnet-package description for change-log

  cdormann

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Commits on Nov 3, 2023

• fixed tapnet2df bug for networks without trait information

  cdormann

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Commits on Feb 21, 2023

• Fixed a missing ")". Thanks to Amanda for reporting.

  cdormann

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Commits on Jan 27, 2023

• experimental changes to the tmatch function, adding a penalty to prevent "width" from going to infinity for the unstandardised tmatch; also new wishes in the wishlist

  cdormann

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Commits on Nov 10, 2022

• added "fix this" to "tapnet_packaging.R", as a type of wishlist; tapnet version 0.4 compiled, with some changes to tapnet2df, ensuring that all networks use same PEMs

  cdormann

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Commits on Sep 29, 2022

• fixed little error in make_tapnet (misunderstanding of my own code decisison that NULL is opposite of 0)

  cdormann

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• (1) added option to hand over a n x m matrix of handcrafted interaction probabilities (e.g. forbidden link mask) to fit_tapnet; (2) gof_tapnet now also outputs the fitted I_mat; (3) moved to versio…

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  cdormann

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Commits on Sep 28, 2022

• added option in include externally computed "forbidden links" as matrix into the fitting; see "tapnet_packaging" for test cases.

  cdormann

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Commits on Sep 26, 2022

• updated package, setting "fit.delta" to a default of false (function: fit_tapnet)

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Commits on Sep 25, 2022

• added a function "fit_abund" to make the prediction matrix only from abundances, without traits (as a reference); uses tapnet-object as input

  cdormann

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Commits on Sep 17, 2022

• added bjornloglik as function and to loglik_tapnet; can be called through fit_tapnet; expanded test code a bit (in tapnet_packaging); updated version 0.4 tar.gz

  cdormann

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Commits on Sep 15, 2022

• here's the tar.gz of version 0.4

  cdormann

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• Updated the package description; made a new tar.gz in version 0.4

  cdormann

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• I tried to augment the code so that fitting without PEMs is also possible. This started with a new option "no" to tmatch_type_pems in the fit_tapnet function. But it led to all sorts of nested if-s…

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Commits on Apr 6, 2021

• added a data link to the wishlist

  cdormann

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Commits on Feb 1, 2021

• should have been included in last commit ...

  cdormann

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• replaced "dontrun"s by "donttests", as this is better style, apparently

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Commits on Jan 20, 2021

• added static built vignettes (forced add at command line, because some gitignore excludes directories)

  cdormann

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• no message

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Commits on Jan 19, 2021

• CRAN release build; static PDF replaces dynamic but VERY slow vignette; after about 40 winbuilder checks I have sorted out all issues introduced by roxygen (?)

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Commits on Jan 18, 2021

• included a vignette (the supplement of the Am Nat paper); small changes to include the vignette in description

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Commits on Jun 10, 2020

• cleaned up all code according to devtools::check (largely cosmetic changes)

  cdormann

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• updated .gitignore to exclude .tar.gz (previous commit incorrect on this point)

  cdormann

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• altered structure of tapnet repository: created a new subdirectory "tapnet" with the code, and moved all package-relevant files there, keeping everything else at the higher level; this was done in …

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• used devtools::check to test integrity of package: lots of warnings, none essential

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Commits on Oct 31, 2019

• * corrected "alias" in Tinoco.R

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Commits on Oct 4, 2019

• * typo in function arguments of fit_tapnet

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• * corrected code for tapnet example in predict_tapnet

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Commits on Oct 2, 2019

• *added the tapnet option to predict_tapnet, and accordingly updated tapnet description

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Commits on Sep 22, 2019

• added Jochen as author to the overall package and some functions

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Commits on Sep 20, 2019

• * rewrote the shiftlorm (Jochen) function (took out the exp, as this was already part of the par_vec2list)

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Commits on Sep 19, 2019

• * added abundance data to the Tinoco data set and updated description

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Commits on Sep 10, 2019

• initial commit with all functions, documentation and a packaging/testing file

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