readTHECCC: Read the model output CCC raw file ("THE" CCC file)

In MichaelFolkes/ctctools: Analytical tools For The Pacific Salmon Commission's Chinook Technical Committee.

Usage

readTHECCC(filename, stocks = NULL, fisheries = NULL,
  newmodel = c(NA, TRUE, FALSE), agegroups.n = 4, fisheries.n = NA)

Arguments

stocks	A data frame that could have the columns named "stockname" & "stocknum", other columns can be included (origin, region, etc). If NA, then this data frame is defined inside the function based on the newmodel argument below. If NULL (the defualt) then no stock definition is used and only stock number is exported in the results.
fisheries	A data frame with columns named "fisheryname" & "fishnum" other columns can be included (origin, region, etc). If NA then this data frame is defined inside the function based on the newmodel. If NULL (the defualt) then no fishery definition is used and only fishery number is exported in the results.
newmodel	A Boolean. If TRUE, this relies on the new definition of 40 stocks and 48 fisheries. If FALSE, this uses the definition of 30 stocks and 25 fisheries. If NA (the default) no stock or fishery definition columns are linked to the data.
agegroups.n	An integer of length one. The number of ages found in row 1 of each data set. Default is 4.
fisheries.n	An integer of length one. The number of fisheries. The default is NA. If the fisheries argument above (a data frame of the fisheries) is NA or user defined then fisheries.n can remain NA as the function will estimate this value from the fisheries definition data frame. If the fisheries argument is NULL (no fishery definitions needed) then fisheries.n must be included (likely 25 or 40 fisheries).

Value

A list of six lists. First element is the CCC filename. Second element is the stock definition data frame. The third element is the fishery definition data frame. The forth element is a list comprising as many elements as data sets in the CCC file. A single data set is a stock-year combination. If there are 40 years and 30 stocks, the list will have a length of 40*30=1200. Each CCC element is a list of 7 elements. The fifth element is a data frame ("data.pop"), which has data for all years and stocks combined. The sixth element is a data frame ("data.fishery"), which has data for all stocks, years, and fisheries combined.

Examples

## Not run: 
#new stock and fishery:
data.ccc <- readTHECCC("2017p.ccc", stocks=NA, fisheries=NA, newmodel = TRUE)

#or current/old stock and fishery:
data.ccc <- readTHECCC("1702p.ccc", stocks=NA, fisheries=NA, newmodel = FALSE)
length(data.ccc)
names(data.ccc)
length(data.ccc$data.ccc)
str(data.ccc$data.pop)

## End(Not run)

MichaelFolkes/ctctools documentation built on May 7, 2019, 4:56 p.m.