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Catch, presence and absence per FDIS site visit and species

Source: R/fdis_species.R
knw_fdis_species.Rd

One row per visit and species in species: how many were caught (summed over the codes that count as that species), how many of them were measured into each size class of breaks, whether the species is present, and whether an absence claim is blocked by a code that could hide it.

Usage

knw_fdis_species(
  sites,
  catch,
  fish,
  codes,
  breaks,
  species = knw_species(),
  pooled = NULL
)

Arguments

sites

data.frame with site_visit, watershed_group_code, year and catch_status.

catch

data.frame with site_visit, species_code, n_caught and n_measured (0230's catch.rds).

fish

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

codes

data.frame with code, catch_class, species_group and blocks_absence_of (data/fdis_species_codes.csv, read as character).

breaks

size-class breaks, as knw_size_class() takes them.

species

character species codes to keep rows for.

pooled

NULL, or a data.frame with watershed_group_code and obs_year_max naming the groups where DV records are pooled into BT, up to that year (NA for no limit), as link::lnk_species_pooling() reports them.

Value

A tibble with site_visit, species_code, n_caught, n_measured, one n_<size_class> column per class in breaks, n_unmeasured, pooling ("BT+DV" or "BT" for BT, NA otherwise), present, absence_blocked and status (present, absent, blocked, unknown).

Details

Presence follows scripts/0290's pooling rule for bull trout and the code table for everything else:

  • a species is present when a code that counts as it was caught. For BT the codes are BT alone, or every char code except SLV (BT, DV, BT/DV, DV/BT, DVxBT) where link pools Dolly Varden records into bull trout for that watershed group and year (pooled);

  • an absence is blocked when the visit caught a code whose blocks_absence_of names the species or its species group (char for BT), or, for BT, any other char code (DV counts as a BT absence where DV is not pooled, as link counts it);

  • a visit whose catch_status is unknown carries no absence.

n_caught is NA where every counting code's count was a sentinel (caught, abundance unknown). Size-class counts exist only for the species groups breaks tiles (a measured fish of another species has a length and no class); n_unmeasured is the counted fish with no usable length.

Examples

sites <- data.frame(site_visit = c("v1", "v2"), watershed_group_code = "BULK",
                    year = 2010L, catch_status = c("fish", "zero"))
catch <- data.frame(site_visit = c("v1", "v1"), species_code = c("DV", "CH"),
                    n_caught = c(3, 2), n_measured = c(2, 0))
fish <- data.frame(site_visit = "v1", species_code = c("DV", "DV"), length_mm = c(55, 120))
codes <- data.frame(code = c("DV", "CH", "BT"), catch_class = "fish",
                    species_group = c("char", "CH", "char"), blocks_absence_of = "")
breaks <- data.frame(species_group = c("char", "char"), size_class = c("fry", "juvenile"),
                     length_min_mm = c(0, 80), length_max_mm = c(80, Inf))
# DV is a BT absence unless pooled; pooling makes v1 a BT visit with 3 fish
knw_fdis_species(sites, catch, fish, codes, breaks, species = c("BT", "CH"))
#> # A tibble: 4 × 11
#>   site_visit species_code n_caught n_measured n_fry n_juvenile n_unmeasured
#>   <chr>      <chr>           <dbl>      <dbl> <int>      <int>        <dbl>
#> 1 v1         BT                  0          0     0          0            0
#> 2 v1         CH                  2          0     0          0            2
#> 3 v2         BT                  0          0     0          0            0
#> 4 v2         CH                  0          0     0          0            0
#> # ℹ 4 more variables: pooling <chr>, present <lgl>, absence_blocked <lgl>,
#> #   status <chr>
knw_fdis_species(sites, catch, fish, codes, breaks, species = "BT",
                 pooled = data.frame(watershed_group_code = "BULK", obs_year_max = NA))
#> # A tibble: 2 × 11
#>   site_visit species_code n_caught n_measured n_fry n_juvenile n_unmeasured
#>   <chr>      <chr>           <dbl>      <dbl> <int>      <int>        <dbl>
#> 1 v1         BT                  3          2     1          1            1
#> 2 v2         BT                  0          0     0          0            0
#> # ℹ 4 more variables: pooling <chr>, present <lgl>, absence_blocked <lgl>,
#> #   status <chr>