Changelog

Source: NEWS.md

DAISIEprep (development version)

DAISIEprep 1.0.0

CRAN release: 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

• None

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