Morpho

[sabifo4]

General updates:

• Changed the name of "write.morpho" to "write_morpho". Apparently, according to this site, if a function is called "write.morpho", it is like calling generic "write" for class "morpho". As we do not have class "morpho", then I decided to use an underscore as suggested in some forums. The statement in the link is the following:
  First, a caveat: a function named gen.cl will be invoked by the generic gen for class cl

• Added "simulate_morpho" function in "morpho.R". All the details about the parameters are given in the details section. Maybe, it is very detailed, but we can always cut information from there. Just have a look and let me know if it is ok like this or we should cut information. It is also very detailed when it comes to the examples, as there is one example for every scenario I have thought of.

• I talked to Andy, who is also working with landmark data, and he told me if there was an easy way to actually get many files with landmark points at once and, afterwards, put them in a 3D array so they can be read in "geomorph" in a straightforward manner. I have created the function "lmk_imp" inside "morpho.R", which does this task. The two possible formats of the input files are described in the details section of the function.

Description of new/updated files:

• Simulated tree, class "phylo", used in the examples given in "simulate_morpho". Files associated: "R/tree.R", "data/tree.rda", "data-raw/tree.R", "man/tree.Rd".
• Updated "write_morpho.Rd", hence "man/write_morpho.Rd" was created. and "R/morpho.R" updated. It can take extra arguments to write an output file when this function is called within "simulate_morpho".
• New function "simulate_morpho()". Files associated: "man/simulate_morpho.Rd" created and "R/morpho.R" updated.
• New function "lmk_inp()". Files associated: "man/lmk_imp.Rd" created and "R/morpho.R" updated.

NOTES:

• The NAMESPACE file in my local repo has now the following:

  exportPattern("^[[:alpha:]]+")
  importFrom("utils", "write.table", "read.csv")
  importFrom("stats", "var", "cov", "rnorm")

  As before, this file has not been updated here as it says that the NAMESPACE in this repo has been created by roxygen2 and should not be manually updated.

• The DESCRIPTION file has imported the following packages:

  Imports:
  geomorph, ape, corpcor, mvtnorm

  As the NAMESPACE, this file has not been updated in this repo.

[mariodosreis]

I don't like the renaming of the functions. Revert function names as before. I.e., write.morpho(), etc.