See CHANGELOG.md for changes, v0.5.5

[sabifo4]

Changes made to the mcmc3r R package after addressing issue "Simplification of dependencies":

Date: 2024-03-27 Version: 0.5.5

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.