PacFIN.Utilities.RdThe PacFIN.Utilities package provides functions for filtering, summarizing, expanding, and compiling composition data, and writing out the final products:
length-
age- and
age-at-length compositions.
Many of the functions described below write summary output to the console, and several create plots for visualizing data at various steps in processing. The information written to the console can be captured using the sink function to encapsulate your workflow:
sink("myfilename.txt", split=TRUE)
... do work ...
The second call closes the file.
cleanPacFIN Filters raw PacFIN data
plotRawData Plots commonly viewed raw PacFIN data
plotCleaned Plots the product of cleanPacFIN
In addition, the getExpansion_1 function has a "plot" argument to create plots documenting the expansions it creates. It also writes summary output to the console.
getSeason For treating data from seasonal fisheries, such as Petrale.
getExpansion_1 creates the values for the sample to tow expansion.
getExpansion_2 computes the expansion values from the tow upwards to a user-specified stratification
There is one manual step in the workflow. After running the expansion functions, data columns Expansion_Factor_1 and Expansion_Factor_2 are available to use in manually setting the Final_Expansion_Factor.
Age data are expanded separately from lengths
WA fish are generally only expanded using Expansion_Factor_2.
Other expansions are the product of Expansion_Factor_1 * Expansion_Factor_2
For age-at-length comps, set Final_Expansion_Factor to 1. Each fish represents only itself.
getComps uses the column specified in weightid and the user-specified
stratification to create comps.
doSexRatio separates the unsexed fish into males and females
writeComps formats the composition data for SS3 and writes it to a file.
You can run these manually to reset the initial values.
getState Run by cleanPacFIN to initialized the state column.
getGearGroup Run by cleanPacFIN to initialize geargroups.
capValues Used to limit the maximum value in a vector.