get_rfmos_datasets_level0: Extract primary gridded tuna RFMOs datasets from the Tuna...

In ptaconet/rtunaatlas: IRD Sardara Tuna Atlas R facilities

Description

This function extracts the primary gridded time series coming from the tuna Regional fisheries management organizations and stored in the Tuna atlas database. Data include geo-spatial gridded catch and efforts.

Usage

get_rfmos_datasets_level0(rfmo,variable,year_tunaatlas,iattc_ps_raise_flags_to_schooltype,iattc_ps_dimension_to_use_if_no_raising_flags_to_schooltype,iattc_ps_catch_billfish_shark_raise_to_effort,iattc_ps_effort_to_extract,iccat_ps_include_type_of_school)

Arguments

rfmo	string. Acronym of the RFMO. Accepted values: "IOTC", "ICCAT", "IATTC", "WCPFC", "CCSBT". See additional parameters to set if rfmo is set to "IATTC" or "ICCAT"
variable	string. Variable to extract. Values accepted: "catch", "effort"
year_tunaatlas	numeric. The year of the datasets to extract (i.e. year the datasets were released). Starts in 2017
iattc_ps_raise_flags_to_schooltype	boolean. Use only if rfmo=="IATTC". Raise dataset with flag stratification to dataset with schooltype stratification? See section Details for more information.
iattc_ps_dimension_to_use_if_no_raising_flags_to_schooltype	NULL or string. Use only if rfmo=="IATTC". Not nullable if raise_flags_to_schooltype is set to FALSE. if not NULL, either set to "flag" or "schooltype"
iattc_ps_catch_billfish_shark_raise_to_effort	boolean. Use only if rfmo=="IATTC" and variable=="catch". IATTC Purse Seine datasets are available in separate files for tuna, billfish and sharks. TRUE: raise billfish (resp. shark) catch to ratio effort tuna / effort billfish (resp. shark). FALSE: keep billfish (resp. shark) catch as they are provided in the billfish (resp. shark) catch datasets.
iattc_ps_effort_to_extract	NULL or string. Use only if rfmo=="IATTC" and variable=="effort". IATTC Purse Seine datasets are available in separate files for tunas, billfishes and sharks. Which effort data should be kept between these 3 files? "tuna","billfish","shark". See section Details for more information.
iccat_ps_include_type_of_school	boolean. Use only if rfmo=="ICCAT". Set TRUE if you want the output dataset with school type stratification. FALSE will provide the stratification without the type of school. See section Details for more information.

Details

The output dataset lists catch or effort of tuna, tuna-like and shark species in the area of competence of the RFMO specified. Catches or efforts are usually stratified by year, month, species (for catches only), fishing gear, vessel flag reporting country, fishing mode (i.e. type of school used), area (1° or 5° square) and unit. Some of these dimensions can be missing depending on the confidentialy policies of each RFMO. The output dataset is computed using public domain datasets released by the RFMOs.

Details on the use of the parameter iattc_ps_raise_flags_to_schooltype: For confidentiality policies, information on flag and school type for the geo-referenced catches is available in separate files for IATTC Purse seine datasets.

• If the parameter iattc_ps_raise_flags_to_schooltype is set to TRUE, for each stratum, the catch/effort from the flag-detailed dataset will be raised to the catch/effort from the school type-detailed dataset to get an estimation of the catches by flag and school type in each stratum.

• If the parameter iattc_ps_raise_flags_to_schooltype is set to FALSE, one single dataset will be used and in this case, the parameter dimension_to_use_if_no_raising_flags_to_schooltype must be set:

  • If the parameter iattc_ps_dimension_to_use_if_no_raising_flags_to_schooltype is set to flag, only the data with flag information will be used.

  • If the parameter iattc_ps_dimension_to_use_if_no_raising_flags_to_schooltype is set to schooltype, only the data with schooltype information will be used.

Details on the use of the parameter iattc_ps_catch_billfish_shark_raise_to_effort: In addition to the separation flag / schooltype (see above), IATTC Purse seine catch-and-effort are available in 3 separate files according to the group of species: tuna, billfishes, sharks. This is due to the fact that PS data is collected from 2 sources, observer and fishing vessel logbooks. Observer records are used when available, and for unobserved trips logbooks are used. Both sources collect tuna data, but only observers collect shark and billfish data. So as an example a strata may have observer effort and the number of sets from the observed trips would be counted for tuna, shark and billfish. But there may have also been logbook data for unobserved sets in the same strata, so the tuna catch and number of sets for a cell would be added. This would make a higher total number of sets for tuna catch than shark or billfish. So efforts in the billfish and shark datasets might represent only a proportion of the total effort allocated in some strata since it is the observed effort, i.e. for which there was an observer onboard. As a result, catch in the billfish and shark datasets might represent only a proportion of the total catch allocated in a some strata.

• TRUE: Raise billfish (resp. shark) catch to the ratio effort tuna / effort billfish (resp. shark).

• FALSE: Keep billfish (resp. shark) catch as they are provided in the billfish (resp. shark) catch datasets.

Details on the use of the parameter iattc_ps_effort_to_extract: For the same reason as above, this parameter enables to select the effort dataset that the user wants to use:

• tuna: Keep the effort from the tuna dataset. Likely to be the best approximation of effort.

• billfish: Keep the effort from the billfish dataset.

• shark: Keep the effort from the shark dataset.

Details on the use of the parameter iccat_ps_include_type_of_school: ICCAT delivers two catch-and-efforts datasets for purse seiners: one that gives the detail of the type of school (Fad|Free school) for purse seine fisheries and that starts in 1994 (called Task II catch|effort by operation mode Fad|Free school) and one that does not give the information of the type of school and that covers all the time period (from 1950) (called Task II catch|effort). These data are redundant (i.e. the data from the dataset Task II catch|effort by operation mode are also available in the dataset Task II catch|effort) but in the latter, the information on the type of school is not available.

• If the parameter iccat_ps_include_type_of_school is set to TRUE, both datasets will be combined to produce a dataset that covers the whole time period, with fishing mode information (Fad | free school).

• If the parameter iccat_ps_include_type_of_school is set to FALSE, only the dataset without the type of school information will be used. The output dataset will hence not have the stratification by type of school.

The output dataset is expressed with the RFMO coding system.

Author(s)

Paul Taconet, [e-mail]

See Also

Other process data: convert_units, create_calendar, create_grid, map_codelist, raise_datasets_by_dimension, raise_get_rf, raise_incomplete_dataset_to_total_dataset, rasterize_geo_timeseries, spatial_curation_downgrade_resolution, spatial_curation_intersect_areas, spatial_curation_reallocate_data, spatial_curation_upgrade_resolution

Examples

# Retrieve IATTC georeferenced catch data from 2017, with dataset with flag dimension raised to dataset with schoolytpe dimension
iattc_catch<-get_rfmos_datasets_level0("iattc","catch",2017,iattc_ps_raise_flags_to_schooltype=TRUE)
head(iattc_catch)

ptaconet/rtunaatlas documentation built on Sept. 21, 2021, 10:43 p.m.