Changelog

Source: NEWS.md

DAISIEprep (development version)

BUG FIXES

• Fix for a bug in 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).

DAISIEprep 1.0.1

CRAN release: 2025-10-30

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.

NEW FEATURES

• New DAISIE FAQ vignette (@Neves-P & @luislvalente, #55 & #56).

MINOR IMPROVEMENTS

• Updated test-coverage.yaml GitHub actions workflow.

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

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