gfcmSTAR-package: Tools to Work with GFCM Stock Assessment Results (STAR)
In gfcm/gfcmSTAR: Tools to Work with GFCM Stock Assessment Results (STAR)

Description Details Script Note Author(s) References See Also

Tools that support the Stock Assessment Results (STAR) framework of the General Fisheries Commission for the Mediterranean.

Import:

`import.many.templates`	import many templates
`import.many.csv`	import many CSV files
`read.star.csv`	read a pair of CSV files
`read.template`	read STAR template
`read.template.v10`	read STAR template version 1.0
`read.template.v21`	read STAR template version 2.1
`read.properties`	read SharePoint properties
`set.classes`	convert data types
`template.version`	detect STAR template version

Export:

`export.many.csv`	export many STAR objects to CSV files
`write.star.csv`	write STAR object to CSV files

Manipulate strings:

`append.id`	modify existing `Assessment_ID`
`combo`	combine reference year, species, and GSA
`gsa.names`	convert GSA codes to full GSA names

Lookup tables:

`lookup.gsa`	geographical subareas (GSA)
`lookup.species`	species

Quality control:

`diff.stars`	show differences between STAR objects
`identical.stars`	check if STAR objects are identical
`peek`	examine a metadata field
`qc`	run all quality checks
`qc.exists`	file exists
`qc.xlsx`	file extension is ‘xlsx’
`qc.star`	file is a STAR template
`qc.vpa`	`VPA_Model` is `Yes` or `No`
`qc.ts.names`	time series column names are intact
`qc.ts.numbers`	time series are numbers and not strings
`report`	report files successfully imported
`write.report`	write a report object to a text file

A fully annotated script to import and export a large collection of STARs is found here:

import.R

It demonstrates administrative procedures to quality check and handle STAR templates that may contain errors. This script can also be found on the local hard drive:

1	system.file("scripts/import.R", package="gfcmSTAR")

STAR objects store Metadata as class c("simple.list", "list") in order to have it display in a compact and readable format in the console. It is easy to convert to a normal list or data frame:

1
2
3

star$Metadata                 # simple.list (default)
unclass(star$Metadata)        # list
as.data.frame(star$Metadata)  # data.frame

The main drawback of the simple.list format is that date-time objects are shown as integers in the console. This is only a minor display issue - the date-time objects are stored as POSIXct objects and are easy to access: