bridgeTreeData-class: bridgeTree Data Class

In hannahlowens/BridgeTree: Tools for Building and Managing Data for Comparative Phylogenetics of Ecological Niches

Description

A class for managing metadata associated with bridgeTree queries and data manipulation.

Slots

userQueryType

A vector of type character specifying whether the user made their original taxonomic query based on a vector of taxon names or a phylogeny.

userSpecTaxonomicSources

A vector of type character that presents a list of taxonomic sources for cleaning taxonomy of queries. This can be user-specified or default.

cleanedTaxonomy

A dataframe with containing input taxon names, the closeset match according to gnr_resolve, and a list of taxonomic datasources that contain the matching name, generated by studyTaxonList.

occSources

A vector of class "character" containing a list of occurrence data sources, generated when passing a bridgeTreeData object through taxaQuery.

occNLimit

The limit of occurrence records to return for each species when executing occ through taxaQuery.

occurrenceSearchDate

The date on which the occurrence search query was conducted.

occResults

The results of an taxQuery search, stored as a named list, each of the items named after a searched taxon and containing a dataframe with occurrence information.

hannahlowens/BridgeTree documentation built on May 3, 2019, 4:33 p.m.