One Health VBD Hub
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Documentation for package ‘ohvbd’ version 1.0.0
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| ad_basereq | Generate a base request string for the AREAdata database |
| assoc_ad | Associate other data sources with AREAdata data |
| assoc_gadm | Associate other data sources with gadm IDs |
| check_db_status | Check whether databases are currently online |
| check_ohvbd_config | Print current ohvbd configuration variables |
| clean_ad_cache | Delete all rda files from ohvbd AREAdata cache (Deprecated) |
| clean_ohvbd_cache | Delete files from ohvbd cache directories |
| extract | Extract specified data from a set of responses (Deprecated) |
| fetch | Fetch specified data from a set of ids |
| fetch_ad | Fetch AREAdata dataset |
| fetch_citations | Try to find the relevant citations for a dataset |
| fetch_citations_vd | Retrieve citations for vecdyn data |
| fetch_citations_vt | Retrieve citations for vectraits data |
| fetch_gadm_sfs | Fetch gadm mapping shapefiles |
| fetch_gbif | Fetch GBIF dataset/s by ID |
| fetch_glean_vd_chunked | Fetch and parse multiple VecDyn datasets by ID in chunks |
| fetch_glean_vt_chunked | Get and parse multiple VecTraits datasets by ID in chunks |
| fetch_vd | Fetch VecDyn dataset/s by ID |
| fetch_vd_counts | Fetch VecDyn dataset length by ID |
| fetch_vd_meta | Fetch VecDyn metadata table |
| fetch_vt | Fetch VecTraits dataset/s by ID |
| filter_db | Filter hub search results by database |
| find_vd_columns | Get current columns in VecDyn datasets |
| find_vd_ids | Get current IDs in VecDyn |
| find_vt_ids | Get current IDs in VecTraits |
| force_db | Force an object to appear to come from a specific database |
| format_time_overlap_bar | Format and print date overlaps |
| generate_vt_template | Generate a vectraits template from a short set of survey responses |
| get_default_ohvbd_cache | Get ohvbd cache locations |
| glean | Extract specified data from a set of responses |
| glean_ad | Extract data from AREAdata datasets |
| glean_gbif | Parse data from requests to GBIF |
| glean_vd | Parse data from requests to VecDyn |
| glean_vt | Parse data from requests to VecTraits |
| has_db | Test whether an object has provenance information |
| is_cached | Check whether an object has been loaded from cache by ohvbd |
| is_from | Test whether an object is considered to be from a particular database |
| list_ohvbd_cache | List all ohvbd cached files |
| match_countries | Match country names to their equivalent naturalearth WKT polygons |
| match_species | Match species names to their GBIF backbone ids |
| ohvbd.ids | Create a new ohvbd ID vector |
| ohvbd_attrs | Internal attributes |
| ohvbd_db | Database provenance |
| ohvbd_db<- | Database provenance |
| ohvbd_dryrun | Option: dry runs of ohvbd searches |
| search_hub | Search vbdhub.org |
| search_vd | Search VecDyn by keyword |
| search_vd_smart | Search VecDyn using the explorer's filters |
| search_vt | Search VecTraits by keyword |
| search_vt_smart | Search VecTraits using the explorer's filters |
| set_default_ohvbd_cache | Set the default ohvbd cache location |
| set_ohvbd_compat | Set ohvbd compatability mode to TRUE |
| tee | Tee a pipeline to extract the data at a given point |
| vb_basereq | Generate a base request object for the vectorbyte databases |