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/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() functionThese 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.
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