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_group_by()
, which groups and summarises record counts based on categorical field values, similar to dplyr::group_by()
(#90, #95)galah_down_to
galah_down_to()
+ atlas_taxonomy()
, which uses tidy evaluation like other galah_
functions (#101, #120)galah_call
|>
, %>%
) by first using galah_call()
, narrowing queries with galah_
functions and finishing queries with an atlas_
function (#60, #120).galah_filter
(#91, #92)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)search_taxonomy()
renamed to ala_taxonomy()
ala_taxonomy
no longer fails for nodes ranked as informal
or unranked
(#86)data.tree
packagegalah
galah_config()
ala_config()
has been renamed to galah_config()
to improve internal consistency (#68)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)find_cached_files()
lists all user cached files and stored metadata (#57)clear_cached_files()
removes previously cached files and stored metadata (#71)ala_counts()
, ala_occurrences()
, ala_media()
and ala_species()
now have refresh_cache
argument to remove previously cached files and replace with the current query (#71)ala_media()
caches media metadata if galah_config(caching = TRUE)
search_fields()
allows the user to pass a qid
as an argument (#59)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)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)ala_config()
allows users to specify an international Atlas to download data from (#21)ala_media()
includes the file path to the downloaded media in the returned metadata (#22)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)select_taxa()
has an optional all_ranks
argument to return intermediate rank information (#35)select_taxa()
behaves as expected when character strings of 32 or 36 characters are provided (#23)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)ala_media()
now takes the same select_
arguments as other ala_
functions (#18)search_fields
now has media
as a type
argument optionverbose == TRUE
(#8)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)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)First version of galah
, built on earlier functionality from the ALA4R
package.