NEWS

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datelife 0.6.9

• 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.

datelife 0.6.8 (2023-06-19)

• 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 0.6.7 (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 0.6.6 (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 0.6.5 (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 0.6.1 (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 0.6.0 (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 0.5.0

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

datelife 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