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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:

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().

Minor improvements

  • Reading data from disk now uses readr::read_csv in place of utils::read.csv for improved speed
  • 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 atlas_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

galah 1.5.0

CRAN release: 2022-10-27

Expanded support for querying other International Living Atlases

  • Support for complex queries to 10 Living Atlases, including France, Guatemala and Sweden. Complex queries can be constructed using galah_call(), filtered with galah_ functions, and downloaded with atlas_ functions. Previously, this functionality was only possible with queries to the ALA (#126)

collect_media()

Updates to galah_geolocate()

show_all(), search_all() & show_values(), search_values()

Minor improvements

  • Apply data quality profiles in a pipe with the galah_apply_profile() function (#130)
  • Improved internal consistency of galah_ functions (#133)
  • galah_geolocate() no longer depends on archived {wellknown} package (#141)
  • Added support for queries to exclude/include missing values (e.g. galah_filter(species != "") or galah_filter(species == "") (#143)
  • Re-download a previously-minted DOI with collect_doi() (#140)
  • More checks to ensure galah fails gracefully when an API fails (#157)

Bug fixes

galah 1.4.0

CRAN release: 2022-01-24

Revamped syntax

  • ala_ functions are renamed to use the prefix atlas_. This change reflects their functionality with international atlases (i.e., atlas_occurrences, atlas_counts, atlas_species, atlas_media, atlas_taxonomy, atlas_citation) (#103)
  • select_taxa is replaced by 3 functions: galah_identify, search_taxa and search_identifiers. galah_identify is used when building data queries, whereas search_taxa and search_identifiers are now exclusively used to search for taxonomic information. Syntax changes are intended to reflect their usage and expected output (#112, #122)
  • select_ functions are renamed to use the prefix galah_. Specifically, galah_filter, galah_select and galah_geolocate replace select_filters, select_columns and select_locations. These syntax changes reflect a move towards consistency with dplyr naming and functionality (#101, #108)
  • find_ functions that provide a listing of all possible values renamed to show_all_ (i.e., show_all_profiles, show_all_ranks, show_all_atlases, show_all_cached_files, show_all_fields, show_all_reasons). find_ functions that require and input and return specific results renamed to search_ (i.e., search_field_values, search_profile_attributes) (#112, #113)

galah_group_by

galah_down_to

Pipe queries using galah_call

  • Build data queries using piping syntax (i.e., |>, %>%) by first using galah_call(), narrowing queries with galah_ functions and finishing queries with an atlas_ function (#60, #120).
  • S3 methods are now implemented to functions to allow for piping (#40)

Minor improvements

  • Improved error messages using {glue} and {rlang} (#117)
  • Revamped syntax functions return output as tibbles (#110, #118)
  • Pass vectors to galah_filter (#91, #92)
  • Cache valid fields for faster field look up (#73, #116)
  • New vignettes for updated syntax (#104, #105), plus improvements to previous vignettes.
  • Updated R Markdown-style documentation and added warnings for deprecated functions (#113, #121)

Bug fixes

  • galah no longer returns error when ALA system is down and/or API fails (#102, #119)
  • search_taxa returns correct IDs for search terms with parentheses (#96)
  • search_taxa returns best-fit taxonomic result when ranks are specified in data.frame or tibble (#115)

galah 1.3.1

CRAN release: 2021-08-21

search_taxonomy() renamed to ala_taxonomy()

  • bug fix: ala_taxonomy no longer fails for nodes ranked as informal or unranked (#86)
  • this function now returns a tree built using the data.tree package
  • change in function name required for greater consistency with other data-providing functions in galah

Vignettes

  • vignettes are now pre-compiled to avoid failing on CRAN (#85)
  • expanded vignette on navigating taxonomic information (#42)

galah 1.3.0

CRAN release: 2021-08-06

galah_config()

search_taxonomy()

  • search_taxonomy() provides a means to search for taxonomic names and check the results are ‘correct’ before proceeding to download data via ala_occurrences(), ala_species() or ala_counts() (e.g., not ambiguous or homonymous) (#64 #75)
  • search_taxonomy() returns information of author and authority of taxonomic names (#79)
  • search_taxonomy() consistently orders column names, including in correct taxonomic order by rank (#81)

Caching helper functions

Minor improvements

  • Cache files are saved in RDS format, making query attributes easier to find, including data DOI, search url (#55, #32, #28)
  • ala_media() caches media metadata if galah_config(caching = TRUE)
  • search_fields() allows the user to pass a qid as an argument (#59)
  • Users can now optionally skip filter and count validation checks to spatial and biocache web services by setting galah_config(run_checks = FALSE). This helps users avoid slowing down data request download speeds when many requests are made in quick succession via galah_filter() or ala_occurrences() (#61, #80)
  • ala_counts(), select_columns() and search_fields() now use match.arg to approximate strings through fuzzy matching (#66)
  • Better handling of cache errors and improved error messages (#70)

Bug fixes

  • select_columns(group = 'assertions') now sends qa = includeall to ALA web service API to return all assertion columns (#48)
  • ala_occurrences() returns data DOI when ala_occurrences(mint_doi = TRUE) and re-downloads data when called multiple times (#56)
  • ala_occurrences() no longer converts field names with all-CAPS to camelCase (#62)

galah 1.2.0

CRAN release: 2021-07-02

Living Atlases

  • ala_config() allows users to specify an international Atlas to download data from (#21)

Minor improvements

  • ala_media() includes the file path to the downloaded media in the returned metadata (#22)
  • Data returned from ala_occurrences() contains the search_url used to download records; this takes the user to the website search page (#32)
  • ala_species() provides a more helpful error if no species are found (#39)
  • Data quality filters are created using the specific web service argument, rather than constructing filters from the attributes (#37)
  • select_taxa() has an optional all_ranks argument to return intermediate rank information (#35)

Bug fixes

  • R > 4.0.0 is now required (#43, #45)
  • select_taxa() behaves as expected when character strings of 32 or 36 characters are provided (#23)
  • Caching functionality for ala_occurrences() uses the columns as expected (#30)
  • galah_filter() negates assertion filters when required, fixing the issue of assertion values being ignored (#27)
  • select_taxa() no longer throws an error when queries of more than one term have a differing number of columns in the return value (#41)
  • ala_counts() returns data.frame with consistent column classes when a group_by parameter is called multiple times and ala_config(caching = TRUE) (#47)
  • ala_ functions fail gracefully if a non-id character string is passed (#49)

galah 1.1.0

CRAN release: 2021-05-05

Downloading media

  • ala_media() now takes the same select_ arguments as other ala_ functions (#18)
  • Filtering by media metadata e.g. licence type is possible (#19)
  • search_fields now has media as a type argument option
  • Performance improvement in download times (#13)
  • Progress bar displayed for downloads when verbose == TRUE (#8)
  • All media download types are supported

select_ functions

  • galah_location auto-detects the type of argument provided and so takes a single argument, query, in place of sf and wkt (#17)
  • select_taxa auto-detects the type of argument provided and so takes a single argument, query, in place of term and term_type (#16)

Minor improvements

  • Provide more useful error message for empty occurrence download (#7)
  • ala_counts uses the group_by field name as the returned data.frame column name (#6)
  • ala_occurrences sends sourceId parameter to ALA (#5)
  • search_fields provides a more helpful error for invalid types (#11)

galah 1.0.0

CRAN release: 2021-04-06

First version of galah, built on earlier functionality from the ALA4R package.