icesTAF (version 3.1-1)

icesTAF-package: Functions to Support the ICES Transparent Assessment Framework

Description

Functions to support the ICES Transparent Assessment Framework, to organize data, methods, and results used in ICES assessments.

Details

Initial TAF steps:

draft.data	draft DATA.bib file
draft.software	draft SOFTWARE.bib file
period	paste period string for DATA.bib
taf.bootstrap	set up data files and software

Running scripts:

clean	clean TAF directories
make	run R script if needed
makeAll	run all TAF scripts as needed
makeTAF	run TAF script if needed
msg	show message
sourceAll	run all TAF scripts

File management:

convert.spaces	convert spaces
cp	copy files
mkdir	create directory
os.linux	operating system
os.macos	operating system
os.windows	operating system
read.taf	read TAF table from file
sourceDir	read all *.R files
taf.library	load package from TAF library
taf.unzip	unzip file

Tables:

div	divide column values
flr2taf	convert FLR to TAF
long2taf	convert long format to TAF
plus	rename plus group column
rnd	round column values
sam2taf	convert SAM to TAF
taf2long	convert TAF to long format
taf2xtab	convert TAF to crosstab
tt	transpose TAF table

Plots:

lim	compute axis limits
taf.colors	predefined colors
taf.png	open PNG graphics device

Example tables:

catage.long	long format
catage.taf	TAF format
catage.xtab	crosstab format

Administrative tools, rarely used in scripts:

deps	list dependencies
dos2unix	convert line endings
download	download file
file.encoding	examine file encoding
latin1.to.utf8	convert file encoding
line.endings	examine line endings
process.bib	read and process metadata
rmdir	remove empty directory
unix2dos	convert line endings

References

ICES Transparent Assessment Framework: http://taf.ices.dk.

To explore example TAF stock assessments, see the introductory video and tutorial.