get_environmental_data: Environmental data extraction functions from surveys

In pbs-assess/gfdata: Data Extraction for DFO PBS Groundfish

Environmental data extraction functions from surveys

Description

Environmental data extraction functions from surveys. See Details section.

Usage

get_sensor_data_trawl(
  ssid = NULL,
  attribute = c("temperature", "depth", "dissolved oxygen", "salinity"),
  spread_attributes = FALSE
)

get_sensor_data_trawl_fe(
  fishing_event_id = NULL,
  attribute = c("temperature", "depth", "dissolved oxygen", "salinity"),
  sensor_name = NULL
)

get_sensor_data_ll_td(
  ssid = NULL,
  attribute = c("temperature", "depth"),
  spread_attributes = FALSE
)

get_sensor_data_ll_td_fe(
  fishing_event_id = NULL,
  attribute = c("temperature", "depth")
)

get_sensor_data_ll_ctd(
  ssid = NULL,
  attribute = c("temperature", "depth", "dissolved oxygen", "salinity"),
  spread_attributes = FALSE
)

get_sensor_data_ll_ctd_fe(
  fishing_event_id = NULL,
  attribute = c("temperature", "depth", "dissolved oxygen", "salinity")
)

Arguments

ssid	A numeric vector of survey series IDs. Run get_ssids() for a look-up table of available survey series IDs with surveys series descriptions.
attribute	A character vector of sensor attributes to filter for. Run get_sensor_attributes() for a look-up table of available attributes.
spread_attributes	Logical for whether the attributes should be returned in a wider format. Allows for user to choose whether data are output in wide format (⁠TRUE``) with min and max values for each attribute for each fishing event, or in long format (⁠FALSE“) with only mean values for each attribute and fishing event.
fishing_event_id	A vector of fishing events to filter for
sensor_name	A character vector of sensor names to filter for.

Details

get_sensor_data_trawl(): Environmental data extraction for sensors deployed on trawl survey gear

get_sensor_data_trawl_fe(): Environmental data extraction for trawl surveys, for individual fishing events.

get_sensor_data_ll_td(): Environmental data extraction for sensors deployed on longline survey gear.

get_sensor_data_ll_td_fe(): Environmental data extraction for sensors deployed on longline survey gear for individual fishing events.

get_sensor_data_ll_ctd(): Environmental data extraction for ctd's deployed on longline surveys. Ctd deployments are not tied directly to longline survey fishing event id's. The unique fishing event id's from the deployments can be linked to longline survey data by joining on the block designation (site number).

get_sensor_data_ll_ctd_fe(): Envirnmental data extraction (ctd data) near longline survey sites for individual fishing events.

Examples

## Not run: 
d <- get_sensor_data_trawl(ssid = 1, "temperature")
head(d)
head(get_sensor_data_trawl_fe(d$fishing_event_id[[1]], "temperature"))

d <- get_sensor_data_ll_td(ssid = 40)
head(d)
head(get_sensor_data_ll_td_fe(d$fishing_event_id[[1]],"temperature"))

d <- get_sensor_data_ll_ctd(40)
head(d)

## End(Not run)

pbs-assess/gfdata documentation built on June 15, 2025, midnight