Package: ohvbd 1.0.1.9000

ohvbd: One Health VBD Hub

Interface with the One Health VBD (vector-borne disease) Hub <https://vbdhub.org/> and related repositories (VectorByte <https://www.vectorbyte.org>, GBIF <https://www.gbif.org> and AREAdata <https://pearselab.github.io/areadata/>) directly to find, download, and subset vector-borne disease data.

Authors:Francis Windram [aut, cre, cph]

ohvbd_1.0.1.9000.tar.gz
ohvbd_1.0.1.9000.zip(r-4.7-any)ohvbd_1.0.1.9000.zip(r-4.6-any)ohvbd_1.0.1.9000.zip(r-4.5-any)
ohvbd_1.0.1.9000.tgz(r-4.6-any)ohvbd_1.0.1.9000.tgz(r-4.5-any)
ohvbd_1.0.1.9000.tar.gz(r-4.7-any)ohvbd_1.0.1.9000.tar.gz(r-4.6-any)
ohvbd_1.0.1.9000.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ohvbd/json (API)

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

Bug tracker:https://github.com/fwimp/ohvbd/issues

Pkgdown/docs site:https://ohvbd.vbdhub.org

On CRAN:

Conda:

6.15 score 2 stars 13 scripts 326 downloads 51 exports 30 dependencies

Last updated from:057bfaae60. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK181
source / vignettesOK317
linux-releaseOK178
macos-releaseOK192
macos-oldrelOK189
windows-develOK140
windows-releaseOK129
windows-oldrelOK115
wasm-releaseOK150

Exports:ad_basereqassoc_adassoc_gadmcheck_db_statuscheck_ohvbd_configclean_ad_cacheclean_ohvbd_cacheextractfetchfetch_adfetch_citationsfetch_citations_vdfetch_citations_vtfetch_gadm_sfsfetch_gbiffetch_glean_vd_chunkedfetch_glean_vt_chunkedfetch_vdfetch_vd_countsfetch_vtfilter_dbfind_vd_columnsfind_vd_idsfind_vt_idsforce_dbformat_time_overlap_bargenerate_vt_templateget_default_ohvbd_cachegleanglean_adglean_gbifglean_vdglean_vthas_dbis_cachedis_fromlist_ohvbd_cachematch_countriesmatch_speciesohvbd_dbohvbd_db<-ohvbd.idssearch_hubsearch_vdsearch_vd_smartsearch_vtsearch_vt_smartset_default_ohvbd_cacheset_ohvbd_compatteevb_basereq

Dependencies:askpassclicpp11curldata.tabledplyrgenericsgluehttr2lifecyclelubridatemagrittropensslpillarpkgconfigpurrrR6Rcpprlangstringistringrsysterratibbletidyrtidyselecttimechangeutf8vctrswithr

Citing data retrieved using ohvbd
Citations | ohvbd citation tools | A basic example | Missing columns | Orphaned data | Forcing the db | Missing Dataset IDs | Retrieving GBIF citations
Rendered fromcitations.Rmdusingknitr::rmarkdown

Last update: 2026-03-04
Started: 2026-01-20

Retrieving data from VectorByte
Introduction | A note before we begin | Setting up the cache | Finding IDs | Filtering dbs | Getting data | Specific fetch functions | Extracting data | Specific glean functions | Putting it all together | Smart searching of VectorByte databases | Futher steps
Rendered fromretrieving-data.Rmdusingknitr::rmarkdown

Last update: 2026-03-04
Started: 2024-06-30

Sourcing climatic data from AREAdata
Introduction | AREAdata | Setting up the cache | Data | Deconstructing fetch_ad() | metric | gid | use_cache and cache_location | Example | Extracting specific data | Dates and date ranges | Places | Resiliance | Associating AREAdata climatic variables with other data | Managing the AREAdata cache | refresh_cache for fetch_ad() | Cache management tools
Rendered fromuse-areadata.Rmdusingknitr::rmarkdown

Last update: 2026-03-04
Started: 2024-08-08

Readme and manuals

Help Manual

Help pageTopics
Generate a base request string for the AREAdata databasead_basereq
Associate other data sources with AREAdata dataassoc_ad
Associate other data sources with gadm IDsassoc_gadm
Check whether databases are currently onlinecheck_db_status
Print current ohvbd configuration variablescheck_ohvbd_config
Delete all rda files from ohvbd AREAdata cache (Deprecated)clean_ad_cache
Delete files from ohvbd cache directoriesclean_ohvbd_cache
Extract specified data from a set of responses (Deprecated)extract
Fetch specified data from a set of idsfetch
Fetch AREAdata datasetfetch_ad
Try to find the relevant citations for a datasetfetch_citations
Retrieve citations for vecdyn datafetch_citations_vd
Retrieve citations for vectraits datafetch_citations_vt
Fetch gadm mapping shapefilesfetch_gadm_sfs
Fetch GBIF dataset/s by IDfetch_gbif
Fetch and parse multiple VecDyn datasets by ID in chunksfetch_glean_vd_chunked
Get and parse multiple VecTraits datasets by ID in chunksfetch_glean_vt_chunked
Fetch VecDyn dataset/s by IDfetch_vd
Fetch VecDyn dataset length by IDfetch_vd_counts
Fetch VecDyn metadata tablefetch_vd_meta
Fetch VecTraits dataset/s by IDfetch_vt
Filter hub search results by databasefilter_db
Get current columns in VecDyn datasetsfind_vd_columns
Get current IDs in VecDynfind_vd_ids
Get current IDs in VecTraitsfind_vt_ids
Force an object to appear to come from a specific databaseforce_db
Format and print date overlapsformat_time_overlap_bar
Generate a vectraits template from a short set of survey responsesgenerate_vt_template
Get ohvbd cache locationsget_default_ohvbd_cache
Extract specified data from a set of responsesglean
Extract data from AREAdata datasetsglean_ad
Parse data from requests to GBIFglean_gbif
Parse data from requests to VecDynglean_vd
Parse data from requests to VecTraitsglean_vt
Test whether an object has provenance informationhas_db
Check whether an object has been loaded from cache by ohvbdis_cached
Test whether an object is considered to be from a particular databaseis_from
List all ohvbd cached fileslist_ohvbd_cache
Match country names to their equivalent naturalearth WKT polygonsmatch_countries
Match species names to their GBIF backbone idsmatch_species
Internal attributesohvbd_attrs
Database provenanceohvbd_db ohvbd_db<-
Option: dry runs of ohvbd searchesohvbd_dryrun
Create a new ohvbd ID vectorohvbd.ids
Search vbdhub.orgsearch_hub
Search VecDyn by keywordsearch_vd
Search VecDyn using the explorer's filterssearch_vd_smart
Search VecTraits by keywordsearch_vt
Search VecTraits using the explorer's filterssearch_vt_smart
Set the default ohvbd cache locationset_default_ohvbd_cache
Set ohvbd compatability mode to TRUEset_ohvbd_compat
Tee a pipeline to extract the data at a given pointtee
Generate a base request object for the vectorbyte databasesvb_basereq