Package: EcoCleanR 1.0.3

EcoCleanR: Enhancing Data Quality of Biogeographic Ranges with Application for Marine Invertebrates

Provides step-by-step automation for integrating biodiversity data from multiple online aggregators, merging and cleaning datasets while addressing challenges such as taxonomic inconsistencies, georeferencing issues, and spatial or environmental outliers. Includes functions to extract environmental data and to define the biogeographic ranges in which species are most likely to occur. For methodological details see the associated publication.<doi:10.1002/ecog.08203>.

Authors:Priyanka Soni [aut, cre], Austin Hendy [ctb], David Bottjer [ctb], Vijay Barve [ctb]

EcoCleanR_1.0.3.tar.gz
EcoCleanR_1.0.3.zip(r-4.7-any)EcoCleanR_1.0.3.zip(r-4.6-any)EcoCleanR_1.0.3.zip(r-4.5-any)
EcoCleanR_1.0.3.tgz(r-4.6-any)EcoCleanR_1.0.3.tgz(r-4.5-any)
EcoCleanR_1.0.3.tar.gz(r-4.7-any)EcoCleanR_1.0.3.tar.gz(r-4.6-any)
EcoCleanR_1.0.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
EcoCleanR/json (API)

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

Bug tracker:https://github.com/sonipri/ecocleanr/issues

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

Datasets:
  • ecodata - Dataset1: Documentation of data file - ecodata.rda
  • ecodata_cleaned - Dataset4: Documentation of data file - ecodata_cleaned.rda
  • ecodata_corrected - Dataset2: Documentation of data file - ecodata_corrected.rda
  • ecodata_with_outliers - Dataset3: Documentation of data file - ecodata_with_outliers.rda
  • ecodata_x - Dataset5: Documentation of data file - ecodata_x.rda
  • example_sp_invertebase - Dataset6: Documentation of data file - example_sp_invertebase.rda

On CRAN:

Conda:

4.95 score 7 scripts 246 downloads 25 exports 105 dependencies

Last updated from:2f74bbfaa4. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK287
source / vignettesOK269
linux-release-x86_64OK311
macos-release-arm64OK225
macos-oldrel-arm64OK270
windows-develOK248
windows-releaseOK236
windows-oldrelOK234
wasm-releaseOK187

Exports:decimal_placesdistance_calcec_db_mergeec_extract_env_layersec_filter_by_uncertaintyec_flag_non_east_atlanticec_flag_non_east_pacificec_flag_non_regionec_flag_non_west_atlanticec_flag_non_west_pacificec_flag_outlierec_flag_precisionec_flag_with_localityec_geographic_mapec_geographic_map_w_flagec_impute_env_valuesec_merge_corrected_coordinatesec_plot_distanceec_plot_var_rangeec_rm_duplicateec_rm_duplicate_occuridec_trail_zeroec_var_summaryec_worms_synonymhaversine_kmeans

Dependencies:askpassbackportsbitbit64brewcachemcallrcheckmateclassclassIntclicliprcommonmarkcpp11crayoncrulcurldata.tableDBIdescdigestdplyre1071evaluatefarverfastmapfsgenericsgeodatageosphereggplot2gluegtablehighrhmshttpcodehttr2isobandISOcodesjsonliteKernSmoothknitrlabelinglatticelifecyclemagrittrMASSmemoisemimemregions2opensslotelpatchworkpillarpkgbuildpkgconfigpkgloadprettyunitsprocessxprogressproxypspurrrR.methodsS3R.ooR.utilsR6rappdirsrasterRColorBrewerRcpprdflibreadrredlandrlangroxygen2rprojroots2S7scalessdmpredictorssfspstringistringrsysterratibbletidyrtidyselecttriebeardtzdbunitsurltoolsutf8vctrsviridisLitevroomwithrwkworrmswraprxfunxml2yaml

EcoCleanR: Overview on Steps for Data cleaning and defining Biogeographic ranges
Introduction: | Step1: Remove duplicates | Step2: Remove bad taxa | Step3: Georeferencing using external tool | Step4: Extreme high uncertainty | Step5: Coordinate precision and rounding | Step6: Records tagged to wrong ocean/sea | Step7: Extract the environmental data | Step8: Identify outliers | Step9: Display final accepted biogeographic range
Rendered fromdata_cleaning.Rmdusingknitr::rmarkdown

Last update: 2026-02-13
Started: 2025-04-12

EcoCleanR: Overview on Steps for Data merging from online bioiversity resources
Introduction | Load packages | Input species name | Create a attribute list with TDWG standardize names | GBIF - data extraction and standardization | OBIS- data extraction and standardization | IDIGBIO - data extraction and standardization | Local file (InvertEbase) - data read and standardization | Merging the databases
Rendered fromdata_merging.Rmdusingknitr::rmarkdown

Last update: 2026-02-13
Started: 2025-04-12

Readme and manuals

Help Manual

Help pageTopics
Get Decimal Places of Coordinate Valuesdecimal_places
Calculate geographic distance and mahalanobis distance to estimate outlier probability of a data pointdistance_calc
Merge the Data sets Extracted from Various datasources.ec_db_merge
Extract the Environmental dataec_extract_env_layers
Flag the Occurrences those has Extreme Uncertainty Error Radiusec_filter_by_uncertainty
Flag the occurrences those are not in east Atlantic and are inlandec_flag_non_east_atlantic
Flag occurrences those are not in east Pacific and are inlandec_flag_non_east_pacific
Flag Occurrences those are in wrong ocean basins and are inlandec_flag_non_region
Flag Occurrences those are not in west Atlantic and are inlandec_flag_non_west_atlantic
Flag occurrences those are not in east Pacific and are inlandec_flag_non_west_pacific
Flag Outlier Occurrences - using Spatial and Non-spatial Attributesec_flag_outlier
Flag occurrences those has bad precisionec_flag_precision
Filter records to georeference using GEOLocateec_flag_with_locality
Map view of occurrence data pointsec_geographic_map
Map view to visualize data points with outlier probability 0 to 1 on a map viewec_geographic_map_w_flag
Impute Environmental Variables using Mean Values of occurrences within a certain radiusec_impute_env_values
Merge the Update Georeferenced Occurrence Points back to the Main Data File.ec_merge_corrected_coordinates
Scatter Plot between geo_distance vs maha_distance with geo- and maha- Quantile Threshold to Demonstrate the Outliers outside those threshold.ec_plot_distance
Plot cleaned data overlay overall occurrence data to demonstrate accepted ranges of spatial and non-spatial attributesec_plot_var_range
Remove Duplicate Records from the Merged Dataec_rm_duplicate
Remove Duplicate Records from the Merged Data based on occurrenceIDec_rm_duplicate_occurid
Trail Zeros from the Coordinate Valuesec_trail_zero
A Summary Table of Final Cleaned Spatial and Environmental Variablesec_var_summary
Check Accepted Synonyms from WoRMs Taxonomyec_worms_synonym
dataset1: Documentation of data file - ecodata.rdaecodata
dataset4: Documentation of data file - ecodata_cleaned.rdaecodata_cleaned
dataset2: Documentation of data file - ecodata_corrected.rdaecodata_corrected
dataset3: Documentation of data file - ecodata_with_outliers.rdaecodata_with_outliers
dataset5: Documentation of data file - ecodata_x.rdaecodata_x
dataset6: Documentation of data file - example_sp_invertebase.rdaexample_sp_invertebase
Calculate Harversine distancehaversine_kmeans