v 1.5.1

galah 1.5.1

Mask function names from other packages

An experimental feature of version 1.5.1 is the ability to call functions from other packages (#161), as synonyms for galah_ functions. These are:

• identify() ({graphics}) as a synonym for galah_identify()
• select() ({dplyr}) as a synonym for galah_select()
• group_by() ({dplyr}) as a synonym for galah_group_by()
• slice_head() ({dplyr}) as a synonym for the limit argument in atlas_counts()
• st_crop() ({sf}) as a synonym for galah_polygon()
• count() ({dplyr}) as a synonym for atlas_counts()

These are implemented as S3 methods for objects of class data_request, which are created by galah_call(). Hence new function names only work when piped after galah_call().

Experimental support for GBIF queries

The Global Biodiversity Information Facility (GBIF) is the umbrella organisation to which all other atlases supply data. Hence it is logical to be able to query GBIF and it's "nodes" (i.e. the living atlases) via a common API (#172). Supported functions are:

• search_taxa and galah_identify for name matching
• show_all(fields) and show_all(assertions)
• show_all() calls that give 'collections' information are limited to 20 records by default, as GBIF datasets are often huge. search_all() is generally more reliable
• show_values() for any GBIF field
• galah_filter and galah_group_by (and therefore filter and group_by(), see above), but NOT galah_select.
• atlas_counts() (and therefore count(), see above)
• atlas_occurrences() & atlas_species(); both are implemented via the 'downloads' system, meaning that queries can be larger, but may be slow

The current implementation is experimental and back-end changes are expected in future. Users who require a more stable implementation should use the {rgbif} package.

Minor improvements

• galah_config() gains a print function, and now uses fuzzy matching for the atlas field to match to region, organisation or acronym (as defined by show_all(atlases)). An example use case is to match to organisations via acronyms, e.g. galah_config(atlas = "ALA").
• Improved support for data from Spain via gbif.es (name-matching, lists, spatial)
• Swapped provider for data from France; formerly gbif.fr, now OpenObs, as per advice from maintainers (#156, #165)
• Reading data from disk now uses readr::read_csv in place of utils::read.csv for improved speed
• show_all (and associated sub-functions) gain a limit argument, set to NULL (i.e. no limit) by default
• galah no longer imports {data.table}, since the only function previously used from that package (rbindlist) is duplicated by dplyr::bind_rows
• Help files are now built without markdown for improved speed (mainly while building)

Bug fixes:

• New function url_paginate() to handle cases where pagination is needed, but total data length is unknown (e.g. show_all_lists(), #170).
• galah_select(group = "assertions") is always enacted properly by atlas_occurrences, and won't lead to overly long urls (#137). When called without any other field names, recordID is added to avoid triggering the 'default' set of columns.
• atlas_species works again after some minor changes to the API; but requires a registered email to function