datelife 0.6.5
- data:
- updated
opentree_chronograms object. It now has 253
chronograms from Open Tree of Life and uses “xz” compression.
- examples:
- functions:
- added functions
matrix_to_table and
matrices_to_table that go from a matrix of patristic
distances to a table of taxon name pairs and respective node ages.
- bug fix on
use_calibrations_bladj that used element
$present_calibrations instead of $matched_calibrations
get_otol_chronogram is another name to call
get_opentree_chronograms- added taxonomic source options argument to
make_datelife_query. You can choose from OTT, NCBI, IRMNG
and GBIF.
- function
congruify_and_mrca: output has congruified
topology with nodelables as attribute.
use_calibrations_bladj takes an output of
congruify_and_mrca functions.
- added function method
congruify_and_mrca
datelife 0.6.1
- Functions:
get_otol_chronograms was updated and renamed to
get_opentree_chronograms- Update
match_all_calibrations
- Added a
summary method for datelifeResult
objects
- Documentation:
- Added a “More” section describing return value attributes (will
rename to “Attributes”)
- Eliminated unnecessary examples
- Vignettes: added case study vignette
- Description: added
BiocManager package to imports
datelife 0.6.0
- Dependencies: Bioconductor packages are used conditionally
- Package website with
pkgdown
- documentation: expanded for all functions
- examples and function files are written to tempdir()
- function rename:
get_biggest_phylo to
get_biggest_multiphylo
datelife 0.5.0
- functions:
datelife_query_check is deprecateduse_each_calibration renamed to
use_calibrations_each- plotting functions have been moved to
datelifeplot
package
datelife 0.3.1
- Now muscle or mafft can be used for alignment of BOLD sequences
datelife 0.2.19
- MrBayes and TreePL as dating methods
- Fully ultrametric summary chronograms and datelife() outputs
- Overlay and lineage through time plots of source chronograms
- Groves to summarize trees