[-Warray-parameter=], [-Wstringop-overflow=],
and [-Wstringop-truncation]-fno-common (#29) (#31)?phylocomr?phylocomr-inputs that
details the four types of inputs to functions and what format they are
expected in, including how they differ for passing in data.frame’s
vs. file paths (#28)name (Phylocom doesn’t accept anything
else) (#27)ph_aot(), but realized this
touches almost all functions: Phylocom is case sensitive. We were
already making sure all taxon names in phylogenies (tips and nodes) were
lowercased, and were lowercasing names in tables passed in, but were not
fixing case in file paths passed in by the user. Now across all
functions we make sure case is all lowercase for taxon names in any user
inputs, so case problems should no longer be an issue. (#26) via @Jez-Rph_bladj(): 1) now we lowercase the taxon
name column in the ages data.frame before writing the data.frame to disk
to avoid any mismatch due to case (we write the phylogeny to disk with
lowercased names); 2) bladj expects the root node name from the
phyologeny to be in the ages file; we now check that (#25)inherits
for class (#23)ph_phylomatic was working fine with very simple trees in
all lowercase. we now internally lowercase all node and tip labels, on
any phylogeny inputs (phylo object, newick string, file path (read, then
re-write back to disk)). phylomatic wasn’t working with any uppercase
labels.
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