as_daisie_datatable() when one or more branching times of an island colonist are older than the island age. The clade is now split so that each branching time older than the island age becomes its own _MaxAge singleton row, while the colonisation time and any in-island branching times remain together as the main _MaxAge clade row. Previously the splitting loop could fail to terminate correctly or error with missing value where TRUE/FALSE needed when all branching times exceeded the island age (#60).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