2.2 Input and Output files
PAReTT uses two primary forms of input that are specified when the user
is prompted to provide the name of the input file. The first is a basic
text file, indicated as “.txt”, while the second is a standard comma
separated value file, indicated as “.csv”. While it is preferred to
specify the full name of the file (e.g., “Species.txt”), PAReTT was
scripted with checkpoints to ensure the proper format of input files
even when only a name is given and should read the input file as long as
they are in the current working directory. If the files are not stored
in the current working directory the full file path is preferred.
Output files differ based on the specific data being retrieved. For
example, timelines are retrieved as pictures in the JPEG format while
time trees for both taxa as well as specific lists of species are
retrieved in the Newick format, which is readable by most phylogenetic
software programs including FigTree (Rambaut, 2017) and MEGA (Kumar et al. , 2018); these trees can also be viewed directly in PAReTT.
Any species in the provided list for which the divergence time could not
be resolved in the tree or were substituted by a similar species are
stored as a table for review. Divergence time data for pairs are printed
on screen and divergence times, based on the mean adjusted time, for
species lists are stored in ‘dataframe’ objects and provide the option
to store the output as a vectorized three column matrix in a comma
separated value file. Output files are stored in the active working
directory.