Match bcfishobs records to the FDIS site visits they came from

About half of the province's fish observation records carry FDIS Database: fshclctn_id <n> in source: the collection id the FDIS export keys on (issue #23). A record is matched to a visit when the visit's collection (the first field of site_visit), species and date agree. One collection holds several sites and dates, so a record can match several visits of one collection on the same date: those are kept, one row per pair, and flagged many. A record whose collection is in the export but whose species and date match no visit is collection_only; one whose collection is not in the export is unmatched; a record with no FDIS key is not_fdis.

Usage

knw_bcfishobs_match(conn, visits, species, species_codes = knw_species())

Arguments

conn

a DBI connection to a database holding bcfishobs.observations.

visits

data.frame with site_visit and date (Date), one row per visit, and the per-visit species table species below.

species

data.frame with site_visit and species_code, one row per visit and species caught (any code), as 0230's catch.rds has them.

species_codes

character the bcfishobs species to read.

Value

A list: matched, a tibble with one row per bcfishobs record and matched visit (observation_key, fish_observation_point_id, species_code, observation_date, fshclctn_id, site_visit, match); summary, counts per species and match class.

Details

Codes that the export records differently from bcfishobs (DV pooled into BT, hybrid codes) are matched as written: a bcfishobs DV matches a visit's DV.

Examples

if (FALSE) { # \dontrun{
conn <- DBI::dbConnect(RPostgres::Postgres())
sites <- readRDS("data/fdis/build/sites.rds")
catch <- readRDS("data/fdis/build/catch.rds")
knw_bcfishobs_match(conn, sites, catch, c("BT", "CH"))$summary
} # }