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Pull catch data from the NWFSC data warehouse

PullCatch.fn.Rd

Pull catch data from the NWFSC data warehouse for a single species or all observed species, where the latter is specified by leaving both Name = NULL and SciName = NULL.

Usage

PullCatch.fn(
  Name = NULL,
  SciName = NULL,
  YearRange = c(1980, 5000),
  SurveyName = NULL,
  SaveFile = lifecycle::deprecated(),
  Dir = NULL,
  verbose = TRUE
)

Arguments

Name

A character entry with the desired common name of the species you want to pull data for from the data warehouse. Use a vector of names if you want information for more than one species or if the desired species is included in the database using more than one name, e.g., vermilion rockfish (see the example below). Use the SciName argument if you know the latin name.

SciName

A character entry with the desired scientific name of the species you want to pull data for from the data warehouse. Use a vector of names if you want information for more than one species or if the desired species is included in the database using more than one name, e.g., vermilion rockfish (see the example below). Use the Name argument if you know the common name.

YearRange

An integer vector of length two with the range of years to pull data for.

SurveyName

A character entry from one of the following options that specifies which survey to pull the data for:

  • Triennial,

  • AFSC.Slope,

  • NWFSC.Combo,

  • NWFSC.Slope,

  • NWFSC.Shelf,

  • NWFSC.Hypoxia,

  • NWFSC.Santa.Barb.Basin,

  • NWFSC.Shelf.Rockfish (not yet working),

  • NWFSC.Hook.Line (not yet working),

  • NWFSC.Video,

  • Triennial.Canada

Currently, you must pull data one survey at a time, though we are working on allowing for a vector of survey names and NWFSC.Shelf.Rockfish and NWFSC.Hook.Line are not supported. The default of NULL is a placeholder that must be replaced with an entry.

SaveFile

Deprecated with nwfscSurvey 2.3. Output will be save automatically if the Dir input is specified.

Dir

The directory where you want the output file to be saved. The name of the file within Dir will start with Catch_ and end with .rdata. Default NULL which will not save an output file.

verbose

A logical that specifies if you want to print messages and warnings to the console. The default is TRUE.

Details

The data available in the warehouse are cleaned pior to being downloaded with the intent that they provide the best available information for use in an index-standardization procedure. The removed samples may be of use to others with a less-restrictive goal than producing an index of abundance. For example, life-stage samples are excluded because they are not collected using the same protocols as standard samples. To download all data, we currently recommend going to the NWFSC data warehouse and using the csv link to extract data for a single species at a time. In the future, we hope to add functionality to this package such that downloading all data can be done easily within this function. See Issue #43 for more information.

Author

Chantel Wetzel (maintainer) based on code by John Wallace

Examples

if (FALSE) { # \dontrun{
# SurveyName is only arg that has to be specified
dat <- PullCatch.fn(SurveyName = "NWFSC.Combo")

# Example with specified common name
catch_dat <- PullCatch.fn(
  Name = "vermilion rockfish",
  SurveyName = "NWFSC.Combo"
)

# Example with specified scientific name
catch_dat <- PullCatch.fn(
  SciName = "Eopsetta jordani",
  SurveyName = "NWFSC.Combo"
)

# Example with multiple names
catch_dat <- PullBio.fn(Name = c(
  "vermilion rockfish",
  "vermilion and sunset rockfish"
), SurveyName = "NWFSC.Combo")

} # }