Changelog • datelife

datelife v0.6.9

fix bug in check_ott_input()
fix bug in make_datelife_query() when getting ott ids
use spaces instead of “_” to run tnrs, avoids bug from rotl::tnrs_match_names() v3.0.14
faster and more accurate way to get study ids and tree ids from opentree API on get_opentree_chronograms() that have branch lengths in Myrs, no relative time.
update to chronogram database, now with 292 chronograms.
get_taxon_summary() now manages case when datelife_result is empty; throws warning instead of criptic error.
better testthat suite for datelife_search() inner functions.

CRAN release: 2023-06-19

CRAN release: 2023-05-09

added vignette for bold data workflow
use_calibrations_bladj.matchedCalibrations():
- can use a root age provided by the user
- if there is no root age, provides a heavy warning and uses the age of the maximum calibration available plus one unit of standard deviation – if multiple calibrations available, or plus 0.1*calibration age if only one calibration is available.
update links in pkgdown/badges.Rmd and pkgdown/presentation.Rmd

CRAN release: 2022-12-15

when congruification fails, return NA and produce a warning on functions that use geiger::congruify.phylo():
changes to congruify_and_mrca_multiPhylo():
- filters out results of congruify_and_mrca_phylo() that do not inherit data.frame; usually this happens when congruification fails
- correctly assigns congruified phy as attribute
use_calibrations_bladj.matchedCalibrations() correctly uses calibrations argument
get_ott_children() has error handling for when OpenTree APIs might be down, or there is no internet connection
various fixes to make_datelife_query() et al. functions
added a new vignette for making datelife query functions (allows testing various functionalities)

CRAN release: 2022-06-21

data:
- updated opentree_chronograms object. It now has 253 chronograms from Open Tree of Life and uses “xz” compression.
examples:
- set to not test 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

CRAN release: 2022-01-31

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

CRAN release: 2022-01-17

functions:
- datelife_query_check is deprecated
- use_each_calibration renamed to use_calibrations_each
- plotting functions have been moved to datelifeplot package