Changelog

Source: NEWS.md

datelife v0.6.8

• fix bug in function extract_calibrations_phylo()
• update messages in calibrations_match()
• add faster function to retrieve descendants
• updates for new rotl version
• fix uri in DESCRIPTION

datelife v0.6.7

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

datelife v0.6.6

CRAN release: 2022-12-15

• when congruification fails, return NA and produce a warning on functions that use geiger::congruify.phylo():
  • congruify_and_mrca_phylo()
  • extract_calibrations_phylo()
  • congruify_and_check()
• 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)

datelife v0.6.5

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

datelife v0.6.1

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

datelife v0.6.0

CRAN release: 2022-01-17

• 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 v0.5.0

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

datelife v0.3.1

• Now muscle or mafft can be used for alignment of BOLD sequences

datelife v0.2.19

• 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