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Load and join IPHC FISS set and catch data

Source: R/load-iphc-dat.R
load_iphc_dat.Rd

These data start with year 1996.

Usage

load_iphc_dat(species = NULL)

Arguments

species

Optional vector specifying the species_common_name to subset the IPHC data.

Value

A tibble with 273,714 rows and 22 columns, containing the processed IPHC catch and set data. The main columns include:

  • year. Year the set was hauled.

  • station. Permanent station ID named by IPHC.

  • station_key. Unique key for the set; can be used to join set table to non-Pacific halibut catch data from FISS Survey download page. Occasionally there are multiple sets at the same station but this column is always unique. It's also unique across years.

  • species_common_name. Species name used in GFBio.

  • species_science_name. Scientific name used in GFBio.

  • number_observed. Number of hooks with the species of interest. Some species such as skates and shortspine thornyheads were not enumerated to the species level in early years and so these values are NA.

  • longitude. Longitude in decimal degrees of the midpoint of the set.

  • latitude. Latitude in decimal degrees of the midpoint of the set.

  • usable. IPHC indication of whether station was deemed effective ("Y") or ineffective ("N") for assessment.

  • hooks_retrieved. Number of hooks retrieved.

  • hooks_observed. Number of hooks observed for non-Pacific halibut species catch. For Pacific halibut this is the value of hooks_retrieved.

  • pbs_standard_grid. Stations defined as 'standard' in gfiphc.

  • inside_wcvi. Logical: inside Vancouver Island waters (2018 only) vs. anywhere else; you may want to exclude these from spatiotemporal modelling.

  • sample_type. Type of observations.

    • "20 hooks" - Observation of the first 20 (non-halibut) hooks of each skate.

    • "all hooks" - All hooks observed.

  • depth_m. Average of beginning and end depth of set in metres.

  • temp_c. Temperature at profiler max pressure (degrees Celsius).

  • soak_time_min. Time interval gear was in water (minutes).

  • avg_no_hook_per_skate. Average number of hooks per skate at setting.

  • no_skates_hauled. Number of skates hauled (no metadata on IPHC website).

  • no_skates_set. Number of skates set, not adjusted for baits or average number of hooks per skate.

  • effective_skates. When all hooks are observed, this is the effective skate number found in the raw IPHC FISS set data. For 1995-1997 this value comes from gfiphc. For cases where only a subset of hooks are observed, the effective skate based on all observed hooks is scaled as: effective_skates * (hooks_observed / hooks_retrieved). See eqn G.4 in Anderson et al. (2019).

  • baits_returned. The number of baited hooks remaining. These are unavailable (NA) for some Pacific halibut records where the sample_type = '20 hooks'.

The tibble also contains the following attributes:

  • iphc_download_date. Date when the data was downloaded, e.g., "2024-05-23".

  • data_preparation_date. Date the data was prepared, e.g., "2024-06-11".

Details

This function joins the IPHC catch data with the set metadata. This is needed because Pacific halibut are enumerated for all hooks_retrieved in a year but non-halibut species are only enumerated for hooks_observed in a year. The catch and set dataframes are saved separately for space efficiency. Note that in 2012 a bait experiment was run where the typically used chum bait was only used on only 4 skates (see Appendix G.3 Anderson et al. 2019 and Henry et al. 2013). Therefore we have estimated the hooks_observed for Pacific halibut in 2012 as avg_no_hook_per_skate * .data$no_skates_hauled and because the IPHC has effective_skates = 0, this is returned here as NA. This total estimate of hooks observed for Pacific halibut is therefore for all baits, not chum-only.

References

Anderson, S.C., E.A. Keppel, A.M. Edwards. 2019. A reproducible data synopsis for over 100 species of British Columbia groundfish. DFO Can. Sci. Advis. Sec. Res. Doc. 2019/041. vii + 321 p.

Henry, E., Soderlund, E., Dykstra, C.L., Geernaert, T.O., and Ranta, A.M. 2013. 2012 standardized stock assessment survey. In Int. Pac. Halibut Comm. Report of Assessment and Research Activities 2012. pp. 503–538.

Examples

if (FALSE) { # \dontrun{
# Retrieve and process the IPHC data
iphc_data <- load_iphc_dat()
} # }