Package index • timefishr

Download raw data

Functions to refresh and download the raw fish community datasets.

timefish_refresh_snapshot(): Refresh the local TimeFish snapshot without reinstalling the package
timefish_update(): Update the installed TimeFish data in one step
timefish_download(): Download a filtered TimeFish table
timefish_download_census() timefish_download_uvc() timefish_download_uvcs(): Download filtered TimeFish UVC data
timefish_download_location(): Download filtered TimeFish location data
timefish_download_taxonomic(): Download filtered TimeFish taxonomic data

Functions to inspect, query, and summarise the bundled TimeFish data.

timefish_tables(): List available TimeFish tables
timefish_columns(): Columns in a TimeFish table
timefish_available_cores(): Report available CPU cores for parallel execution
timefish_between(): Create a TimeFish range filter
timefish_query(): Query a TimeFish table by any column
timefish_query_local_join(): Query by year/location and return one joined data frame
timefish_query_bundle(): Query multiple TimeFish tables at once
timefish_path(): Path to a TimeFish table
timefish_read_table(): Read a TimeFish table
timefish_census(): Read the census table
timefish_location(): Read the location table
timefish_taxonomic(): Read the taxonomic table
timefish_data(): Read all TimeFish tables
timefish_join(): Join the TimeFish data tables
timefish_summary_by_year(): Summarise TimeFish data by year
timefish_summary_by_geo(): Summarise TimeFish data by geography

Functions to estimate comparable effort and standardize unequal sampling.

timefish_minimum_sampling_area(): Estimate the minimum comparable sampled area across localities
timefish_select_transects_by_area(): Randomly select transects by locality until a target sampled area is reached
timefish_minimum_individuals(): Estimate the minimum number of individuals for rarefaction
timefish_rarefy_abundance(): Rarefy abundance-like focal counts
timefish_rarefy_richness(): Rarefy richness-like focal counts
timefish_rarefy_focal(): Rarefy focal-individual counts to a common number of individuals
timefish_sample_individuals(): Sample a fixed number of individuals and keep species identity by group