CHANGELOG.md

In dosreislab/mcmc3r: Tools to work with MCMCtree

Changelog

Important changes to this project will be documented in this file.

We try to follow Keep a Changelog, and we use Semantic Versioning.

[0.5.5] - 2024-03-27

Removed

• Update DESCRIPTION file:
• Remove Morpho and Rdpack from Import.

Fixed

• Update Morpho.R script:
• Check whether users have Morpho installed when running function proc2MCMCtree, stop if not -> error and warning solved.
• Update .checkData and .checkArr functions so that checks with class() do not raise warnings -> warning solved.
• Update calibrations.R file:
• Remove additional parenthesis in line 45 (i.e. from pv <- pL(qv, tL=1)) to pv <- pL(qv, tL=1))) -> error solved.
• Update dBD.R script:
• Define parameter x as @param -> warning solved.
• Update mcmc2densitree:
• Change cex.labels to cex.lab (line 18, @param section) as the latter is used in the function -> warning solved.

Changed

• Update DESCRIPTION file:
• Upgrade RoxygenNote to 7.3.1.
• Upgrade minimum R version to (>= 3.5.0).
• Update Morpho.R script:
• Add \dontrun{} for examples in proc2MCMCtree that require package Morpho in case users do not have this package installed.
• Update mcmc2anc.R script:
• Add \dontrun{} for examples section to avoid warnings when using rgl.
• Change lines 45-46 so that lines are not wider than 100 characters as before they were truncated in the PDF manual.
• Update vignette Reproduce_Carnivora_analysis.Rmd:
• Add eval=FALSE in all code snippets. Package Morpho is not imported and running these examples raises errors.
• Define code snippets from section 4 onward using {r}.
• Add mcm3r:: before calling a function within this package in the code snippets.
• Replace some = with <- as it is encouraged in R.
• Fix some typos.
• Update carnivores.R script:
• Fix typo in surname.

[0.5.4] - 2024-02-09

Added

• Function mcmc.sum to calculate summary statistics on MCMCtree's output.

[0.5.3] - 2023-12-07

Added

• Functions pL and qL to calculate the probability and quantile functions for the minim bound (truncated-Cauchy) calibrations.

[0.5.2] - 2023-04-24

Added

• Function mcmc2anc for ancestral character reconstruction from an MCMC sample.
• Directory misc/ape4s, and moved all ape4s files into it.

Changed

• The analysis of carnivores vignette, Reproduce_Carnivora_analysis.Rmd, to streamline the text and add an example of ancestral reconstruction.

[0.5.1] - 2023-03-30

Added

• Function mcmc2densitree to plot densitrees using the MCMC output from either MCMCtree or BPP.
• microcebus and hominid BPP A00 MCMC datasets.
• Carnivora data to misc/carnivora, suitable for reproducing MCMC sampling of divergence times using molecular and morphometric data with MCMCtree.

Changed

• The analysis of carnivores vignette, Reproduce_Carnivora_analysis.Rmd, to simplify the text and to add MCMC sampling using MCMCtree. Added files figtree.jpg and densitree.jpg to illustrate the vignette.

[0.4.7] - 2023-02-02

Fixed

• An error was returned in several instances of testing input where class(x) was used to check matrices due to a new behaviour of classes in matrices from R > v4.x. Now inherits is used to test matrix classes instead of class.

[0.4.6] - 2021-12-02

Fixed

• A bug in the dBD example (missing comment character).

[0.4.5] - 2021-07-15

Changed

• Function gauss.quad so it now accepts a se argument (as for stepping.stones). This solves a bug when running gauss.quad.boot.

[0.4.4] - 2021-07-14

Added

• Function gauss.quad.boot to calculate marginal likelihood on bootstrap replicates using the Gaussian quadrature method. Documentation for gauss.quad.boot and stepping.stones.boot are merged.

[0.4.3] - 2020-03-24

Added

• Function dBL to calculate the kernel density for the birth-death process with species sampling.

[0.4.2] - 2020-03-13

Added

• Functions dL, dB and dU to calcute the fossil calibration densites used in MCMCtree (useful for plotting the densities).

[0.4.1] - 2020-02-24

Fixed

• An error in block.boot that caused generation of empty likelihood block samples.

[0.4.0] - 2020-12-31

Added

• Functions block.boot and stepping.stones.boot to perform block (stationary) bootstrap resampling to estimate the standard error for the log-marginal likelihood under the stepping stones method. Suitable for short MCMC runs for which the delta approximation to estimate the standard error may not work well.

[0.3.2] - 2020-12-30

Fixed

• Functions stepping.stones and gauss.quad so that they work correctly with incomplete mcmctree MCMC output files.

[0.3.1] - 2020-02-24

Changed

• Function bayes.factors so that bootstrap CI's are printed with models as rows and 95% CI as columns.

[0.3.0] - 2018-10-14

Added

A collection of functions for working with continuous morphological data. These are the functions used in Álvarez-Carretero et al. (2018, bioRxiv, 441105).

[0.2.0] - 2018-10-08

Changed

• Function bayes.factors so that it now calculates bootstrap CIs for posterior probabilities. Prior probabilities can now be used.

Tags: Added, Changed, Deprecated, Removed, Fixed, Security

dosreislab/mcmc3r documentation built on March 29, 2024, 6:45 p.m.