Package: bdc 1.1.6

Bruno Ribeiro

bdc: Biodiversity Data Cleaning

It brings together several aspects of biodiversity data-cleaning in one place. 'bdc' is organized in thematic modules related to different biodiversity dimensions, including 1) Merge datasets: standardization and integration of different datasets; 2) pre-filter: flagging and removal of invalid or non-interpretable information, followed by data amendments; 3) taxonomy: cleaning, parsing, and harmonization of scientific names from several taxonomic groups against taxonomic databases locally stored through the application of exact and partial matching algorithms; 4) space: flagging of erroneous, suspect, and low-precision geographic coordinates; and 5) time: flagging and, whenever possible, correction of inconsistent collection date. In addition, it contains features to visualize, document, and report data quality – which is essential for making data quality assessment transparent and reproducible. The reference for the methodology is Ribeiro and colleagues (2022) <doi:10.1111/2041-210X.13868>.

Authors:Bruno Ribeiro [aut, cre], Santiago Velazco [aut], Karlo Guidoni-Martins [aut], Geiziane Tessarolo [aut], Lucas Jardim [aut], Steven Bachman [ctb], Rafael Loyola [ctb]

bdc_1.1.6.tar.gz
bdc_1.1.6.zip(r-4.7-any)bdc_1.1.6.zip(r-4.6-any)bdc_1.1.6.zip(r-4.5-any)
bdc_1.1.6.tgz(r-4.6-any)bdc_1.1.6.tgz(r-4.5-any)
bdc_1.1.6.tar.gz(r-4.7-any)bdc_1.1.6.tar.gz(r-4.6-any)
bdc_1.1.6.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
bdc/json (API)

# Install 'bdc' in R:
install.packages('bdc', repos = c('https://bdc-proj.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/brunobrr/bdc/issues

Pkgdown/docs site:https://brunobrr.github.io

On CRAN:

Conda:

bdcbiodiversity-dataworkflow

6.54 score 25 stars 77 scripts 560 downloads 23 exports 112 dependencies

Last updated from:77672a7826 (on master). Checks:7 WARNING, 2 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-develWARNING250
source / vignettesOK236
linux-releaseWARNING198
macos-releaseWARNING236
macos-oldrelWARNING238
windows-develWARNING201
windows-releaseWARNING197
windows-oldrelWARNING198
wasm-releaseOK150

Exports:%>%bdc_basisOfRecords_notStandardbdc_clean_namesbdc_coordinates_country_inconsistentbdc_coordinates_emptybdc_coordinates_from_localitybdc_coordinates_outOfRangebdc_coordinates_precisionbdc_coordinates_transposedbdc_country_from_coordinatesbdc_country_standardizedbdc_create_figuresbdc_create_reportbdc_eventDate_emptybdc_filter_out_flagsbdc_filter_out_namesbdc_query_names_taxadbbdc_quickmapbdc_scientificName_emptybdc_standardize_datasetsbdc_summary_colbdc_year_from_eventDatebdc_year_outOfRange

Dependencies:askpassbase64encbitbit64blobbslibcachemclassclassIntclicliprcodetoolsCoordinateCleanercpp11crayoncrosstalkcrulcurldata.tableDBIdbplyrdigestdoParalleldplyrDTduckdbe1071evaluatefarverfastmapfontawesomeforeachfsgenericsgeosphereggplot2gluegtableherehighrhmshtmltoolshtmlwidgetshttpcodehttrisobanditeratorsjquerylibjsonliteKernSmoothknitrlabelinglaterlazyevallifecyclemagrittrmemoisemimeoaiopensslotelpillarpkgconfigplyrprettyunitsprogresspromisesproxypurrrqs2R6rappdirsRColorBrewerRcppRcppParallelreadrrgbifrgnparserrlangrmarkdownrnaturalearthrprojroots2S7sassscalessfstringdiststringfishstringistringrsystaxadbterratibbletidyrtidyselecttinytextriebeardtzdbunitsurltoolsutf8vctrsviridisLitevroomwhiskerwithrwkxfunxml2yaml

Readme and manuals

Help Manual

Help pageTopics
Identify records from doubtful source (e.g., 'fossil', MachineObservation')bdc_basisOfRecords_notStandard
Clean and parse scientific namesbdc_clean_names
Identify records within a reference countrybdc_coordinates_country_inconsistent
Identify records with empty geographic coordinatesbdc_coordinates_empty
Identify records lacking or with invalid coordinates but containing locality informationbdc_coordinates_from_locality
Identify records with out-of-range geographic coordinatesbdc_coordinates_outOfRange
Flag low-precise geographic coordinatesbdc_coordinates_precision
Identify transposed geographic coordinatesbdc_coordinates_transposed
Get country names from coordinatesbdc_country_from_coordinates
Standardizes country names and gets country codebdc_country_standardized
Create figures reporting the results of the bdc packagebdc_create_figures
Create a report summarizing the results of data quality testsbdc_create_report
Identify records with empty event datebdc_eventDate_empty
Remove columns with the results of data quality testsbdc_filter_out_flags
Filter out records according to their taxonomic statusbdc_filter_out_names
Harmonizing taxon names against local stored taxonomic databasesbdc_query_names_taxadb
Create a map of points using ggplot2bdc_quickmap
Identify records with empty scientific namesbdc_scientificName_empty
Standardize datasets columns based on metadatabdc_standardize_datasets
Create or update the column summarizing the results of data quality testsbdc_summary_col
Extract year from eventDatebdc_year_from_eventDate
Identify records with year out-of-rangebdc_year_outOfRange