Nothing
taxize
package was updated in taxize v0.9.97
- changes made to comply with the changes in the APG dataset structure (#41)conditionz
in the phylomatic_names()
function for handling messages from the taxize
package about the user not having an API key set (#36) (#40)phylocomr
version that has fixes for various mis-behavior (#38) (#39)phylomatic_local()
function now using phylocomr::ph_phylomatic
instead of shelling out to Phylocom via system
. A number of parameters are gone due to the change internally (#30) (#35)rbladj()
function now using phylocomr::ph_bladj
instead of shelling out to Phylocom via system
(#30) (#35)phylomatic_local()
, see ?phylomatic_trees
phylomatic_names()
and the README on using NCBI Entrez API keysbladj
(#18)httr
with crul
for http requests (#25)verbose
param in phylomatic()
function changed to mssgs
phylomatic_local()
to use Phylomatic locally.
Phylomatic is a set of Awk scripts, which have to be downloaded
by the user. After downloading, this function uses the local version
of Phylomatic (Same as that that runs as a web service). This is
advantageous especially when dealing with large queries. (#13)clean
parameter in phylomatic()
and phylomatic_local()
to expect a logical (TRUE
or FALSE
) instead of a "true" or "false". (#15)phytools::read.newick()
instead of ape::read.tree()
, which handles
the result of clean=FALSE
in phylomatic()
and phylomatic_local()
(#16)storedtree
parameter of phylomatic()
and
phylomatic_local()
the tree from Zanne et al. is also available by using
storedtree="zanne2014"
(#19)Any scripts or data that you put into this service are public.
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