ape is a package in evolution: the first version of ape was released on 27 August 2002. The current version on CRAN is 5.8 and has been released on 11 April 2024. There have been, up to now, 103 releases of ape, with a very substantial increase in the quantity of code.

You can find a detailed log file HERE listing all changes (new features, bug fixes, ...) since the first release of ape. The CRAN keeps an archive of previous releases of the package.

The following sections give some details on how a new release of ape is prepared, a list of documents useful for developers, and some miscellaneous code not included in ape.

New Release

ape is used in many applications (for instance, see the CRAN package covid19.analytics), so everything that is changed, included or removed from the package must be considered carefully. With the release of ape 5.5, the core of ape has reached a state where major changes are unlikely—at least in the near future. The main data classes (detailed in the next section) are now stable, efficient, versatile, portable, and scalable. A relatively large number of functions are provided to read, manipulate, analyse, simulate, and write these data.

As the maintainer of ape, I am in charge of what's included into or removed from the package. This is not trivial since more than 300 packages on CRAN depend on ape, and (according to CRAN's rules) any new version of the latter should not break these reverse dependencies. Besides, in my experience, contributions must usually be checked more or less carefully and additional files might have to be updated (NAMESPACE, cross-links among .Rd files, ...)

Contributions to ape usually fall into two categories:

• new functions, in which case I ask the contributor(s) to also write the .Rd file(s);
• fixes or other improvements of existing code in which case the form of the contribution may vary:
  • this could be simply an e-mail saying change 'x' for 'y' on line XX in ape/R/xxx.R;
  • a diff file from the sources;
  • the complete code of a function if a re-write is necessary (e.g., for more efficiency);
  • a pull-request (PR) on GitHub if you use this platform.

NEW! It has appeared recently that a small change in ape can create issues in other packages on CRAN. Because of the CRAN policy, any new version of ape should not create such difficulties. Generally, these are not detectable until those packages are checked as sketched above.
Therefore, any change in ape must be assessed and pondered carefully. It might be that I reject a PR on GitHub which does not mean that the suggested change is not interesting, but maybe it had to be edited to avoid issues in other packages. The whole process is still in evolution and could change in the future.

The function is.binary.tree is obsolete before being deprecated: see the details HERE.

Documents

• The manual is the reference to use the 300+ functions in ape. It is available in several forms:
  • as a PDF document (ca. 300 pages) HERE;
  • from R as simple text accessible in the usual way (e.g., ?read.tree);
  • as HTML pages with hyperlinks among pages accessible from with the command help.start().
• Several vignettes are distributed with the package to go deeper in some issues:
  • Drawing Phylogenies in R: Basic and Advanced Features With ape.—Explains the rationale behind ape´s graphical functions, and how to make complex figures with phylogenies, their annotations, and other data.
  • Enumeration and Simulation of Random Tree Topologies.—Describes how phylogenetic trees are simulated in ape and discusses some issues related to solving multichotomies.
  • Moran´s Autocorrelation Coefficient in Comparative Methods.—Clarifies the use of Moran´s autocorrelation coefficient to quantify whether the distribution of a trait among a set of species is affected or not by their phylogenetic relationships.
• The following document explains how trees are coded in R (classes "phylo" and "multiPhylo"), and how these data structures can be passed to C.
  
  Definition of Formats for Coding Phylogenetic Trees in R
  
  Previous versions of this document (these are outdated and given here for the record):
  • October 2012
  • July 2008
  • December 2006
  • June 2006
    
    
• The coding scheme used in ape to code DNA sequences (class "DNAbin") is explained in the next document. Its aim is to provide fast algorithms and efficient programs for comparing sequences:
  
  A Bit-Level Coding Scheme for Nucleotides [HTML] [PDF]
  
  
• The following document describes the class "bitsplits" for coding splits of taxa:
  
  Definition of the Class "bitsplits"
  
  
• The class "AAbin" has been introduced in ape a few years ago to code amino acid sequences. It is still under development: see the help page ?AAbin for current information, or write directly to me for more information.

Misc. Code