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Spawner evidence per visit for the char species, from maturity codes

Source: R/spawner_evidence.R
knw_spawner_evidence.Rd

scripts/0293's response, as 0240 fixed it: a visit carries spawner evidence for bull trout when a BT fish (DV pooled where link pools it) was coded SP or ST at any date, or M in August to October. Only visits that caught the species and maturity-coded at least one of its fish can carry the response; on a visit nobody coded, evidence was impossible, so those visits get NA. Electrofishing catches no adult Pacific salmon, so this is the only spawning response the export can give.

Usage

knw_spawner_evidence(
  fish,
  visits,
  codes,
  species = "BT",
  coded = c("IM", "M", "MT", "SP", "ST"),
  large_mm = 350
)

Arguments

fish

data.frame with site_visit, species_code, maturity_code, length_mm (0230's fish.rds).

visits

data.frame with site_visit, month and pooling ("BT+DV" where DV counts as BT, from knw_fdis_species()).

codes

data.frame with code and species_group.

species

character(1) the species; "BT" is the only one the codes support today.

coded

character the maturity codes that count as a coded fish.

large_mm

numeric(1) the length at and above which a spawner is large (a migratory-adult size); the split comes back as S_large, S_small.

Value

A tibble, one row per visit: site_visit, species_code, n_coded, S (0/1, NA where no fish was coded), S_large, S_small, kind (the strongest evidence kind: SP/ST, M Sep-Oct, M Aug, M other months, adult size only, none).

Examples

fish <- data.frame(site_visit = c("v1", "v1", "v2", "v3"), species_code = c("BT", "BT", "DV", "BT"),
                   maturity_code = c("IM", "M", "SP", NA), length_mm = c(90, 410, 300, 500))
visits <- data.frame(site_visit = c("v1", "v2", "v3"), month = c(9, 6, 9),
                     pooling = c("BT", "BT+DV", "BT"))
codes <- data.frame(code = c("BT", "DV"), species_group = "char")
knw_spawner_evidence(fish, visits, codes)
#> # A tibble: 3 × 7
#>   site_visit species_code n_coded     S S_large S_small kind           
#>   <chr>      <chr>          <int> <int>   <int>   <int> <chr>          
#> 1 v1         BT                 2     1       1       0 M Sep-Oct      
#> 2 v2         BT                 1     1       0       1 SP/ST          
#> 3 v3         BT                 0    NA      NA      NA adult size only