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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
packageThese binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.