A patch release to due to testing errors occurring since {ggplot2}
v4.0.0 was released. Tests using plot_phylod() which
depends on {ggtree} and thus {ggplot2} are temporarily skipped due to
errors on R devel to prevent the package becoming archived, and will be
fixed shortly in another patch release.
This release also updates the package maintainer email.
test-coverage.yaml GitHub actions
workflow./data) added to make it easier to load
data in tutorial. Some data has been moved from
inst/extdata into /data (#42).force_nonendemic_singleton argument has been
added to extract_island_species(). This allows enforcing
non-endemic island species to be extracted as singleton lineages on the
island (under most scenarios) using the "asr" extraction
method. A new extract_nonendemic_forced() function is added
(collaboration with @luislvalente, #45).add_island_colonist()
(collaboration with @luislvalente, #48).create_endemicity_status() when species
provided by user not found in phylogeny (collaboration with @luislvalente,
#46).extract_multi_tip_species() now returns an
Island_colonist objects with col_max_age set
to TRUE. This enables DAISIE to make full use of max and
min age information (#51).plot_phylod() now plots the x-axis with the time
counting from right to left to correctly label years before present
(collaboration with @luislvalente, #50).is_multi_tip_speices() now checks that multi-tip
monophyletic species have the same endemicity status to be considered
multi-tip. This fixes a bug where species in the phylogeny with multiple
tips but labelled according to where they are sampled with only a single
island sample extracted using the "min" algorithm would
error (#51).add_asr_node_states()) produces nested island
colonists which was causing some island species to become
duplicated in the island_tbl previous versions. The fix
adds a new internal function to the package
rm_duplicate_island_species() which is called in
extract_island_species() when
extraction_method = asr. This function uses the
nested_asr_species argument (added to
extract_island_species()) to determine whether duplicated
island species should be kept as smaller, more recent colonist and
removed from the larger, older clade
(nested_asr_species = "split"), or whether the smaller,
more recent colonist should be removed and the larger, older clade
should retain the species (nested_asr_species = "group").
Both choices result in duplicates being removed.... (dots) have been added as an argument
to add_asr_node_states() in order to pass other arguments
to the castor R package functions called for ancestral
state reconstruction (castor::ask_mk_model() and
castor::asr_max_parsimony()).... in add_asr_node_states().rate_model) can now be selected in
add_asr_node_states() and passed to
castor::asr_mk_model(). Feature suggested by @rsetienne.add_missing_species() now errors when the species name
supplied to species_to_add_to is not found in the
island_tbl. Suggested by @luislvalente.add_island_colonist()
arguments has been improved. Suggested by @rsetienne.add_asr_node_states().add_missing_species() has been
updated.sse_states_to_endemicity() (#17).extract_island_species()benchmark() functionplot_phylod() tip labels are now white space
separatedbenchmark() function
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