Package index • BioticExplorerServer

Package documentation

Quick access to the package documentation.

BioticExplorerServer BioticExplorerServer-package: R Package for Downloading Server-Side Data for BioticExplorer

Main workflow

Functions to download and compile IMR Biotic survey data into a DuckDB database. compileDatabase() creates a database and updateDatabase() refreshes changed years. The other functions are called internally but can also be used independently. All functions require IMR intranet access (VPN or HI-adm WiFi).

compileDatabase(): Download IMR Biotic database and to place it into a duckdb database
updateDatabase(): Incrementally update a BioticExplorer database
downloadDatabase(): Download and parse NMD data for the BioticExplorer database
downloadDatabaseToFiles(): Download and parse NMD Biotic data to files
indexDatabase(): Index BioticExplorer database
repairDatabaseEncoding(): Check and repair byte-escaped text in a BioticExplorer database

Database path helpers

Resolve default database locations and locate an existing local database. These helpers only inspect local paths; they do not contact the IMR APIs.

defaultDbPath(): Default location of the IMR Biotic database
dbPathCandidates(): Plausible locations of the IMR Biotic database
findDatabase(): Locate an existing IMR Biotic database

Biotic data processing

Functions to parse a single NMD Biotic XML file into R data tables. Called internally by the download functions but can be used independently to inspect or process individual XML files.

bioticToDatabase(): Read and process a NMD Biotic xml file for further use in the BioticExplorer database
print(<bioticProcData>): Print processed NMD Biotic data (bioticProcData) objects

Reference data preparation

Functions to download and refresh the bundled reference datasets from the IMR API. Run these to update cruise series, gear codes, or taxa lists, then save the result with usethis::use_data(..., overwrite = TRUE).

prepareCruiseSeriesList(): Prepare cruise series list
prepareGearList(): Prepare gear list
prepareReferenceCodes(): Prepare coded-field reference list
prepareTaxaList(): Prepare taxa list

Bundled datasets

Reference datasets bundled with the package. Updated by running the corresponding prepare*() functions.

cruiseSeries: Cruise series list
gearList: Gear code list
icesAreas: ICES fishing areas