README.md

In TobieSurette/gulf.data: Southern Gulf of St Lawrence Data Access

gulf.data Package

The gulf.data package contains functions for accessing and manipulating southern Gulf of Saint Lawrence data sets, which include data from: - Snow Crab Annual Science Survey - Northumberland Strait Annual Science Survey - ALSI Lobster and rock crab collector (Atlantic Lobster Settlement Index) data. - Lobster SCUBA transect survey data.

Installation:

The gulf.data package can be installed directly from GitHub by running the following code from R:

library(devtools)
install.packages("sp", dependencies = TRUE)
install.packages("rgdal", dependencies = TRUE)
install.packages("akima", dependencies = TRUE)
install_github("TobieSurette/gulf.utils")
install_github("TobieSurette/gulf.metadata")
install_github("TobieSurette/gulf.data")

Data Access:

Reading Functions:

Function | Description ------------------ | -------------------------------------------------- read.scsset | Read snow crab survey set/tow data. read.scscat | Read snow crab survey by-catch data. read.scsbio | Read snow crab survey crab biological measurement data. read.scslen | Read snow crab survey fish length data. read.gulf.set | Read set/tow data from groundfish surveys. read.gulf.cat | Read catch summary data from groundfish surveys. read.gulf.bio | Read biological sampling data from groundfish surveys. read.gulf.len | Read length-frequency data from groundfish surveys. read.oracle | Read data from Oracle database. read.scobs | Read snow crab observer data. read.logbook | Read fishery logbook data. read.ziff | Read groundfish and pelagic fishery logbook data (Zonal Interchange File Format data files). read.vms | Read fishery Vessel Monitoring System data. read.minilog | Read Minilog probe data. read.star.oddi | Read Star Oddi probe data. read.scanmar | Read Scanmar acoustic trawl monitoring data. read.netmind | Read Netmind acoustic trawl monitoring data. read.esonar | Read eSonar acoustic trawl monitoring data. read.notus | Read Notus acoustic trawl monitoring data. read.gps | Read GPS track data. read.colorimeter | Read colorimeter measurement data. read.alsi | Read Atlantic Lobster Settlement Index data. read.azmp | Read oceanographic data from the Atlantic Zonal Monitoring Program.

Data Field Functions:

Function | Description ------------------ | -------------------------------------------------- category | Determine or extract animal category data. chela.height | Determine or extract crab chela height data. egg.condition | Extract egg condition data. gear | Extract sampling gear data. grow | Predict growth. key | Extract index key for a data set. maturity | Determine or extract animal maturity data. missing.legs | Extract or format crustacean missing leg data. sampler | Extract or format field sampler data. sex | Extract or format biological sex data. species | Extract or convert species identification data. tow.id | Extract survey tow identification data. tow.number | Extract survey trawl tow number data. trip | Extract field trip data. vessel | Extract sampling or fishing vessel data. weight | Extract or calculate catch or sample weight data. wingspread | Extract trawl wing spread data.

Environmental Data Functions:

Function | Description ------------------ | -------------------------------------------------- depth | Extract elevation and bathymetry data. temperature | Extract water temperature data.

Data Summary Functions:

Function | Description ------------------ | -------------------------------------------------- catch | Generate catch data summary. freq | Generate size-frequency data summary. summary | Generate data summary.

Taxonomic, Maturity and Moult Stage Functions:

Function | Description ------------------ | ------------------------------------------------------------------------------------ species | Extract or convert species identification data. taxon | Extract taxonomic identification data. is.category | Detemine if snow crab belongs to a specified biological category. is.pubescent | Determine if animal is pubescent (i.e. immature with developping gonads). is.mature | Determine if animal is sexually mature. is.primiparous | Determine if female is primiparous, i.e. is carrying first clutch of eggs. is.multiparous | Determine if female is multiparous, i.e. is carrying second or more clutch of eggs. is.senile | Determine if crustacean is sexually senile. is.new.shell | Determine if crustacean has new shell (i.e. new moult). is.soft.shell | Determine if crustacean has a soft shell. is.hard.shell | Determine if crustacean has a hard shell (i.e. not soft moult). is.skip.moulter | Determine if crustacean has skipped a moult. is.fish | Determine if female is multiparous, i.e. is carrying second or more clutch of eggs. is.invertebrate | Determine if animal is invertbrate. is.shrimp | Determine if animal species is a type of shrimp.

Metadata tables:

Function | Description ------------------ | -------------------------------------------------- glossary | Science and data terms glossary data table. probe | Data probe list and descriptions table. project | Data project definitions and descriptions table. region | Administrative regions definitions and descriptions table. species | Species codes data table. species.foreign | Foreign species codes data table. survey | Science surveys data table.

Examples:

# Read snow crab survey data:
x <- read.scsset(year = 2020, valid = 1, survey = "regular") # Read valid regular survey tows for 2020.
x <- read.scsbio(year = 2020, category = "COM")              # Read commercial snow crab biological data for 2020.
x <- read.scscat(year = 2020, species = c("cod", "plaice"))  # Read Atlantic cod and American plaice catch data for 2020.
x <- read.scslen(year = 2020, species = c("cod", "plaice"))  # Read Atlantic cod and American plaice size data for 2020.

# Prepare commercial snow crab data:
b <- read.scsbio(year = 2020)                                # Read commercial snow crab biological data for 2020.
s <- read.scsset(year = 2020, valid = 1, survey = "regular") # Read valid regular survey tows for 2020.
import(s, fill = 0) <- catch(b, category = "COM")            # Merge commercial crab catch data to tow data table.

# Import male size-frequency data: 
b <- read.scsbio(2020, category = "M")                       # Read commercial snow crab biological data for 2020.
s <- read.scsset(year = 2020, valid = 1, survey = "regular") # Read valid regular survey tows for 2020.
import(s, fill = 0) <- freq(b, by = c("date", "tow.id"))     # Merge male crab size-frequency data to tow data table.

TobieSurette/gulf.data documentation built on Jan. 19, 2025, 7:50 p.m.