Changes in version 0.7.0                        

  - updated cache from Open Tree of Life: now with 318 chronograms

                        Changes in version 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.

                 Changes in version 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

                 Changes in version 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

                 Changes in version 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)

                 Changes in version 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

                 Changes in version 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

                 Changes in version 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

                        Changes in version 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

                        Changes in version 0.3.1                        

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

                       Changes in version 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