ape is distributed in three different ways:
If you need to install R, all required information can be found on the CRAN website.
There are many different ways to install R packages, so your way is certainly the best one; only the essential information are given here.
ape requires R 3.2.0 or higher. In addition, the package Rcpp (0.12.0 or higher) must be installed on your machine.
There are no other requirement and ape runs under all operating systems where R can be installed, and under any running environment (Emacs/ESS, RStudio, ...)
Three other packages are suggested
: expm, gee, and igraph. This means that ape can be installed and used even if these packages are not installed, but you won't be able to use a few of ape's functions (e.g., compar.gee). Anyway, most package installation procedures also install the suggested packages (and Rcpp at the same time).
The version of ape on CRAN is considered stable. There is no fixed schedule for a new release though they usually happen once or twice in a year.
The testing version includes new features that will be included in the future version on CRAN. It is mainly directed to maintainers of packages depending on ape, though it can be used by those who are curious about new features.
If you want to know more about ape's development, see the Development section.
Like for installation from CRAN, installing a package from GitHub can be done in different ways, so your way is certainly the best one.