NEWS
DAISIEprep 1.0.0 (2024-12-17)
NEW FEATURES
- Package data (
/data) added to make it easier to load data in tutorial. Some data has been moved from inst/extdata into /data (#42).
- A new
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).
- A new vignette explaining the feature of forcing non-endemic species to be extracted as singletons has been added (collaboration with @luislvalente, #45).
- The DAISIEprep tutorial vignette has been improved. The explanations are more clear, with simpler data loading (@luislvalente, #42).
MINOR IMPROVEMENTS
- Input checking added to
add_island_colonist() (collaboration with @luislvalente, #48).
- Warn in
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).- The package website now has a structured vignette dropdown menu (#49).
BUG FIXES
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).
DEPRECATED AND DEFUNCT
DAISIEprep 0.4.2
NEW FEATURES
MINOR IMPROVEMENTS
BUG FIXES
- Fix for a bug when the ancestral state reconstruction (see
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.
DEPRECATED AND DEFUNCT
DAISIEprep 0.4.1
NEW FEATURES
MINOR IMPROVEMENTS
... (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()).- Tests have been added to check arguments can be passed through
... in
add_asr_node_states().
BUG FIXES
DEPRECATED AND DEFUNCT
DAISIEprep 0.4.0 (2024-04-02)
NEW FEATURES
- The rate model (
rate_model) can now be selected in add_asr_node_states()
and passed to castor::asr_mk_model(). Feature suggested by @rsetienne.
MINOR IMPROVEMENTS
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.- Function documentation for
add_island_colonist() arguments has been improved.
Suggested by @rsetienne.
- Unit tests have been added for
add_asr_node_states().
- Unit test for
add_missing_species() has been updated.
- Markdown formatting has been enabled for Roxygen documentation.
BUG FIXES
DEPRECATED AND DEFUNCT
DAISIEprep 0.3.3
NEW FEATURES
MINOR IMPROVEMENTS
- Addition of corHMM section to Extending ASR article, contributed by @TheoPannetier.
BUG FIXES
- Bug fix in
sse_states_to_endemicity() (#17).
DEPRECATED AND DEFUNCT
DAISIEprep 0.3.2 (2023-04-25)
NEW FEATURES
MINOR IMPROVEMENTS
- Converted Extending_asr vignette to article
- Removed remote dependencies due to CRAN rules
BUG FIXES
DEPRECATED AND DEFUNCT
DAISIEprep 0.3.1
NEW FEATURES
MINOR IMPROVEMENTS
- Updates to Sensitivity vignette
BUG FIXES
DEPRECATED AND DEFUNCT
DAISIEprep 0.3.0
NEW FEATURES
- New vignette on performance of
extract_island_species()
MINOR IMPROVEMENTS
- Updates to Extending ASR vignette and Sensitivity vignette
BUG FIXES
- Bug fix for
benchmark() function
DEPRECATED AND DEFUNCT
DAISIEprep 0.2.1
NEW FEATURES
MINOR IMPROVEMENTS
- Higher test coverage
plot_phylod() tip labels are now white space separated
BUG FIXES
- Bug fixes for
benchmark() function
DEPRECATED AND DEFUNCT
DAISIEprep 0.2.0
NEW FEATURES
- Stable version of DAISIEprep
- New functions
- New documentation and vignettes
MINOR IMPROVEMENTS
- Addition of several functions
BUG FIXES
- Bug fixes for various functions
DEPRECATED AND DEFUNCT
DAISIEprep 0.1.0
NEW FEATURES
- Beta version of DAISIEprep
- Ready for users
MINOR IMPROVEMENTS
BUG FIXES
DEPRECATED AND DEFUNCT