DAISIEprep v1.0.0

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