check_ott_input()
make_datelife_query()
when getting ott idsrotl::tnrs_match_names()
v3.0.14get_opentree_chronograms()
that have branch lengths in Myrs, no relative time.get_taxon_summary()
now manages case when datelife_result
is empty; throws warning instead of criptic error.testthat
suite for datelife_search()
inner functions.extract_calibrations_phylo()
calibrations_match()
use_calibrations_bladj.matchedCalibrations()
:pkgdown/badges.Rmd
and pkgdown/presentation.Rmd
NA
and produce a warning on functions that use geiger::congruify.phylo()
:congruify_and_mrca_phylo()
extract_calibrations_phylo()
congruify_and_check()
congruify_and_mrca_multiPhylo()
:congruify_and_mrca_phylo()
that do not inherit data.frame
; usually this happens when congruification failsphy
as attributeuse_calibrations_bladj.matchedCalibrations()
correctly uses calibrations
argumentget_ott_children()
has error handling for when OpenTree APIs might be down, or there is no internet connectionmake_datelife_query()
et al. functionsopentree_chronograms
object. It now has 253 chronograms from Open Tree of Life and uses "xz" compression.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.use_calibrations_bladj
that used element $present_calibrations instead of $matched_calibrationsget_otol_chronogram
is another name to call get_opentree_chronograms
make_datelife_query
. You can choose from OTT, NCBI, IRMNG and GBIF.congruify_and_mrca
: output has congruified topology with nodelables as attribute.use_calibrations_bladj
takes an output of congruify_and_mrca
functions.congruify_and_mrca
get_otol_chronograms
was updated and renamed to get_opentree_chronograms
match_all_calibrations
summary
method for datelifeResult
objectsBiocManager
package to importspkgdown
get_biggest_phylo
to get_biggest_multiphylo
datelife_query_check
is deprecateduse_each_calibration
renamed to use_calibrations_each
datelifeplot
packageAdd the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.