phylocomr 0.3.4
CRAN release: 2023-04-21
- Maintenance release to:
- fix CRAN issues related to compiler warnings
[-Warray-parameter=],[-Wstringop-overflow=], and[-Wstringop-truncation]
- fix CRAN issues related to compiler warnings
phylocomr 0.3.3
CRAN release: 2022-12-05
- Maintenance release to:
- fix CRAN issues related to compiler warnings
- add new maintainer info (#33)
phylocomr 0.3.0
CRAN release: 2019-11-25
NEW FEATURES
- via (#26) (see below) - we now no longer use file paths passed in directly to functions, but instead write to temporary files to run with Phylocom so that we do not alter at all the users files. We note this in the README and package level manual file
?phylocomr - package gains new manual file
?phylocomr-inputsthat 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)
BUG FIXES
- for all data.frame traits inputs to fxns, check that the first column is called
name(Phylocom doesn’t accept anything else) (#27) - fix was originally for
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-R
phylocomr 0.2.0
CRAN release: 2019-11-13
BUG FIXES
- two fixes for
ph_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)
phylocomr 0.1.2
CRAN release: 2018-11-29
BUG FIXES
- fix to internals of all functions that handle a phylogeny.
ph_phylomaticwas 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.