Changelog

Source: NEWS.md

DAISIEprep 0.4.2

NEW FEATURES

• None

MINOR IMPROVEMENTS

• None

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

• None

DAISIEprep 0.4.1

NEW FEATURES

• None

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

• None

DEPRECATED AND DEFUNCT

• None

DAISIEprep 0.4.0

CRAN release: 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

• None

DEPRECATED AND DEFUNCT

• None

DAISIEprep 0.3.3

NEW FEATURES

• None

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

• None

DAISIEprep 0.3.2

CRAN release: 2023-04-25

NEW FEATURES

• None

MINOR IMPROVEMENTS

• Converted Extending_asr vignette to article
• Removed remote dependencies due to CRAN rules

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

DAISIEprep 0.3.1

NEW FEATURES

• None

MINOR IMPROVEMENTS

• Updates to Sensitivity vignette

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

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

• None

DAISIEprep 0.2.1

NEW FEATURES

• None

MINOR IMPROVEMENTS

• Higher test coverage
• plot_phylod() tip labels are now white space separated

BUG FIXES

• Bug fixes for benchmark() function

DEPRECATED AND DEFUNCT

• None

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

• None

DAISIEprep 0.1.0

NEW FEATURES

• Beta version of DAISIEprep
• Ready for users

MINOR IMPROVEMENTS

• None

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None