Overview | Loading TaxResolveR | Scientific-name preparation | Cleaning names | Parsing names | Classifying names | Validating species-name structure | Standardising names | Preparing taxonomic queries | Taxonomic resolution | Complete workflow with taxresolve() | Reproducible offline example | Assessing taxonomic matches | Flagging records for manual review | Summarising results | Detailed reporting | Exporting results | Handling problematic input | Recommended reproducible workflow | Further documentation
Package: TaxResolveR 0.1.0
TaxResolveR: Taxonomic Name Resolution and Validation Tools
Provides reproducible tools for cleaning, parsing, classifying, standardising, validating and resolving scientific names in ecological and biodiversity datasets. Taxonomic matches can be assessed for match quality and taxonomic status, records requiring manual review can be identified, and resolution results can be summarised, reported and exported. Taxonomic name resolution can use the 'GBIF' species matching service and the GBIF Backbone Taxonomy described by GBIF Secretariat (2023) <doi:10.15468/39omei>.
Authors:
TaxResolveR_0.1.0.tar.gz
TaxResolveR_0.1.0.zip(r-4.7-any)TaxResolveR_0.1.0.zip(r-4.6-any)TaxResolveR_0.1.0.zip(r-4.5-any)
TaxResolveR_0.1.0.tgz(r-4.6-any)TaxResolveR_0.1.0.tgz(r-4.5-any)
TaxResolveR_0.1.0.tar.gz(r-4.7-any)TaxResolveR_0.1.0.tar.gz(r-4.6-any)
TaxResolveR_0.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
TaxResolveR/json (API)
| # Install 'TaxResolveR' in R: |
| install.packages('TaxResolveR', repos = c('https://prdelosriosescalante.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/prdelosriosescalante/taxresolver/issues
Last updated from:9a0073a956. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | OK | 134 | ||
| source / vignettes | OK | 221 | ||
| linux-release | OK | 137 | ||
| macos-release | OK | 155 | ||
| macos-oldrel | OK | 196 | ||
| windows-devel | OK | 73 | ||
| windows-release | OK | 67 | ||
| windows-oldrel | OK | 72 | ||
| wasm-release | OK | 112 |
Exports:assess_taxonomic_matchclassify_scientific_namesclean_scientific_namesexport_taxonomic_resultsflag_taxonomic_reviewparse_scientific_namesprepare_taxonomic_queriesresolve_taxonomystandardize_scientific_namessummarize_taxonomic_resolutiontaxonomic_resolution_reporttaxresolvevalidate_species_names
Dependencies:askpassclicurlgluehttr2lifecyclemagrittropensslR6rlangsysvctrswithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Assess taxonomic match quality | assess_taxonomic_match |
| Classify scientific names | classify_scientific_names |
| Clean scientific names | clean_scientific_names |
| Export Taxonomic Resolution Results | export_taxonomic_results |
| Flag taxonomic records for manual review | flag_taxonomic_review |
| Parse scientific names | parse_scientific_names |
| Prepare taxonomic queries | prepare_taxonomic_queries |
| Resolve scientific names against a taxonomic source | resolve_taxonomy |
| Standardize scientific names | standardize_scientific_names |
| Summarize Taxonomic Resolution Results | summarize_taxonomic_resolution |
| Create a Taxonomic Resolution Report | taxonomic_resolution_report |
| Resolve and assess scientific names | taxresolve |
| Validate Species Names | validate_species_names |