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:

Author(s)

Colin Millar and Arni Magnusson.

References

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

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

The TAF Wiki provides additional help resources.

Import a boot data script from ICES datasets repo

Description

Download an ‘R’ file from the ICES datasets repo to fetch data including adding metadata via roxygen2 fields to the top of the file.

Usage

add.data.script(name, install.deps = TRUE, commit = FALSE)

Arguments

Examples

## Not run: 

# Create boot folder
mkdir(taf.boot.path())

# Create boot script, boot/mydata.R
add.data.script(name = "vms")

# Create metadata, boot/DATA.bib
taf.roxygenise(files = "vms.R")

# Run boot script, creating boot/data/vms/...
taf.boot()

## End(Not run)

Print a directory tree

Description

Print the directory tree and file contents in a pretty way

Usage

dir.tree(path = ".")

Arguments

See Also

list.files

Examples

## Not run: 

library(icesTAF)

# Download a TAF analysis
dir.tree()

## End(Not run)

Download a TAF analysis

Description

Download the code for a TAF analysis from GitHub.

Usage

download.analysis(repo, dir = tempdir())

Arguments

See Also

run.analysis

Examples

## Not run: 

library(icesTAF)

# Download a TAF analysis
run_dir <- download.analysis("ices-taf/2019_san.sa.6", dir = ".")

# run the analysis
run.analysis(run_dir)

## End(Not run)

Draft or create a boot data script

Description

Create an ‘R’ file to fetch data including adding metadata via roxygen2 fields to the top of the file.

Usage

draft.data.script(name, title, description, format, originator, year, period,
  access, content)

Arguments

Examples

## Not run: 

# Create boot folder
mkdir("boot")

# Create boot script, boot/mydata.R
draft.data.script(name="mydata", title="Title", description="Description",
                  format="txt", originator="Me", year="2022",
                  period=c(2000,2020), access="Public",
                  content='write(pi, file="pi.txt")')

# Create metadata, boot/DATA.bib
taf.roxygenise(files="mydata.R")

# Run boot script, creating boot/data/mydata/pi.txt
taf.boot()

## End(Not run)

Various TAF Helper Functions

Description

These functions are called by user-level functions. The functionality is documented in the user-level functions.

Usage

## S3 method for class 'roxy_tag_tafKey'
roxy_tag_parse(x)

## S3 method for class 'roxy_tag_tafOriginator'
roxy_tag_parse(x)

## S3 method for class 'roxy_tag_tafYear'
roxy_tag_parse(x)

## S3 method for class 'roxy_tag_tafPeriod'
roxy_tag_parse(x)

## S3 method for class 'roxy_tag_tafAccess'
roxy_tag_parse(x)

## S3 method for class 'roxy_tag_tafSource'
roxy_tag_parse(x)

See Also

icesTAF-package gives an overview of the package.

Install packages dependencies of a TAF analysis

Description

Search R scripts for packages that are required and install them.

Usage

install.deps(path = ".", ...)

Arguments

See Also

deps

Examples

## Not run: 

library(icesTAF)

# Download a TAF analysis
download("https://github.com/ices-taf/2019_san.sa.6/archive/refs/heads/master.zip")
unzip("master.zip")

# move into analysis folder
setwd("2019_san.sa.6-master")

# list dependencies
deps()

# install dependencies
install.deps()

## End(Not run)

Run a TAF analysis

Description

Run the code for a TAF analysis locally.

Usage

run.analysis(dir)

Arguments

See Also

download.analysis

Examples

## Not run: 

library(icesTAF)

# Download a TAF analysis
run_dir <- download.analysis("ices-taf/2019_san.sa.6", dir = ".")

# run the analysis
run.analysis(run_dir)

## End(Not run)

Functions re-exported from the TAF package

Description

These functions are re-exported from the TAF package.

Usage

makeAll(...)

taf.install(targz = NULL, lib = "boot/library", quiet = FALSE)

parse.repo(repo)

taf2long(x, names = c("Year", "Age", "Value"))

write.taf(x, file = NULL, dir = NULL, quote = FALSE, row.names = FALSE,
  fileEncoding = "UTF-8", underscore = TRUE, ...)

utf8.to.latin1(file, force = FALSE)

download(url, dir = ".", mode = "wb", chmod = file_ext(url) == "",
  destfile = file.path(dir, basename(url)), quiet = TRUE, ...)

clean.boot(force = FALSE)

flr2taf(x, colname = "Value")

get.remote.sha(owner, repo, ref, seven = TRUE)

taf.bootstrap(...)

xtab2taf(x, colname = "Year")

long2taf(x)

source.taf(script, rm = FALSE, clean = TRUE, detach = FALSE,
  taf = NULL, quiet = FALSE)

ds.file(package, author, year, title, version, source)

div(x, cols, by = 1000, grep = FALSE, ...)

detach.packages(quiet = FALSE)

rnd(x, cols, digits = 0, grep = FALSE, ...)

taf2xtab(x)

ds.package(package, author, year, title, version, source)

long2xtab(x)

os.linux()

taf.png(filename, width = 1600, height = 1200, res = 200, ...)

os.macos()

os()

period(x, y = NULL)

tt(x, column = FALSE)

clean.data(folder = "boot/data", quiet = FALSE, force = FALSE)

## S3 method for class 'trellis'
zoom(x, size = 1, main = 1.2 * size, lab = size,
  axis = size, strip = size, sub = 0.9 * size, legend = 0.9 * size,
  splom = 0.9 * size, ...)

zoom(x, ...)

unix2dos(file)

dos2unix(file)

mkdir(path)

convert.spaces(file, sep = "_")

lim(x, mult = 1.1)

is.r.package(targz, spec = NULL, warn = TRUE)

clean.software(folder = "boot/software", quiet = FALSE, force = FALSE)

taf.boot.path(..., fsep = .Platform$file.sep)

sourceAll(...)

plus(x)

taf.sources(type)

msg(...)

process.entry(bib, quiet = FALSE, force = FALSE, clean = FALSE)

taf.data.path(..., fsep = .Platform$file.sep)

download.github(repo, dir = ".", quiet = FALSE)

deps(path = ".", base = FALSE, installed = TRUE, available = TRUE,
  list = FALSE)

taf.session(sort = FALSE, imports = TRUE, details = FALSE)

os.unix()

xtab2long(x, names = c("Year", "Age", "Value"))

os.windows()

draft.data(originator = NULL, year = format(Sys.time(), "%Y"),
  title = NULL, period = NULL, access = "Public", source = NULL,
  file = "", append = FALSE,
  data.files = dir(taf.boot.path("initial/data")),
  data.scripts = dir(boot.dir(), pattern = "\\.R$"))

read.taf(file, check.names = FALSE, stringsAsFactors = FALSE,
  fileEncoding = "UTF-8", ...)

clean(dirs = c("data", model.dir(), "output", "report"), force = FALSE)

model.script()

taf.libPaths(remove = FALSE)

draft.software(package, author = NULL, year = NULL, title = NULL,
  version = NULL, source = NULL, file = "", append = FALSE)

sourceDir(...)

taf.boot(software = TRUE, data = TRUE, clean = TRUE, force = FALSE,
  taf = NULL, quiet = FALSE)

file.encoding(file)

latin1.to.utf8(file, force = FALSE)

clean.library(folder = "boot/library", quiet = FALSE, force = FALSE)

tafpng(...)

sourceTAF(...)

taf2html(x, file = "", align = "", header = align,
  digits = getOption("digits"), center = "style=\"text-align:center\"",
  left = "style=\"text-align:left\"",
  right = "style=\"text-align:right\"", append = FALSE)

source.all(...)

extract.subdir(targz, subtargz, subdir)

taf.library(package, messages = FALSE, warnings = FALSE)

read.bib(file)

boot.exists()

boot.dir()

stamp.description(targz, spec, sha.full)

make.all(...)

make.taf(script, ...)

make(recipe, prereq, target, include = TRUE, engine = source,
  debug = FALSE, force = FALSE, recon = FALSE, ...)

boot.dir.inside(inside = ".")

model.dir()

line.endings(file)

already.in.taf.library(targz, lib)

taf.unzip(zipfile, files = NULL, exdir = ".", unzip = NULL, ...)

process.bibfile(type, clean = TRUE, quiet = FALSE)

cp(from, to, move = FALSE, ignore = FALSE, overwrite = TRUE,
  quiet = TRUE)

makeTAF(...)

rmdir(path, recursive = FALSE)

source.dir(dir, pattern = "\\.[r|R]$", all.files = FALSE,
  recursive = FALSE, quiet = TRUE, ...)

sam2taf(x, colname = NULL, year = TRUE)

taf.skeleton(path = ".", force = FALSE, pkgs = "icesTAF")

Details

Follow the links below to see the documentation. makeAll, taf.install, parse.repo, taf2long, write.taf, utf8.to.latin1, download, clean.boot, flr2taf, get.remote.sha, taf.bootstrap, xtab2taf, long2taf, source.taf, ds.file, div, detach.packages, rnd, taf2xtab, ds.package, long2xtab, os.linux, taf.png, os.macos, os, period, tt, clean.data, zoom.trellis, zoom, unix2dos, dos2unix, mkdir, convert.spaces, lim, is.r.package, clean.software, taf.boot.path, sourceAll, plus, taf.sources, msg, process.entry, taf.data.path, download.github, deps, taf.session, os.unix, xtab2long, os.windows, draft.data, read.taf, clean, model.script, taf.libPaths, draft.software, sourceDir, taf.boot, file.encoding, latin1.to.utf8, clean.library, tafpng, sourceTAF, taf2html, source.all, extract.subdir, taf.library, read.bib, boot.exists, boot.dir, stamp.description, make.all, make.taf, make, boot.dir.inside, model.dir, line.endings, already.in.taf.library, taf.unzip, process.bibfile, cp, makeTAF, rmdir, source.dir, sam2taf

TAF Colors

Description

Predefined colors that can be useful in TAF plots.

Usage

taf.green
taf.orange
taf.blue
taf.dark
taf.light

See Also

TAF-package gives an overview of the package.

Examples

taf.green

opar <- par(mfrow=c(3,1))
barplot(5:1, main="Five",
        col=c(taf.green, taf.orange, taf.blue, taf.dark, taf.light))

barplot(6:1, main="Six", col=c(taf.green, taf.orange, taf.blue,
                               taf.dark, taf.light, "white"))

barplot(7:1, main="Seven", col=c("black", taf.dark, taf.light,
                                 taf.green, taf.orange, taf.blue, "white"))
par(opar)

Process a TAF repo with the taf roclet

Description

This function builds documentation for a TAF repository using roxygen syntax headers. It depends on the roxygen2 package adding some extra functionality to produce citation entries for data sources

Usage

taf.roxygenise(path = ".", files)

Arguments

Examples

## Not run: 

# Create boot folder
mkdir("boot")

# Create boot script, boot/mydata.R
draft.data.script(name="mydata", title="Title", description="Description",
                  format="txt", originator="Me", year="2022",
                  period=c(2000,2020), access="Public",
                  content='write(pi, file="pi.txt")')

# Create metadata, boot/DATA.bib
taf.roxygenise(files="mydata.R")

# Run boot script, creating boot/data/mydata/pi.txt
taf.boot()

## End(Not run)

TAF Skeleton

Description

Create initial directories and R scripts for a new TAF analysis using a stock assessment created on stockassessment.org.

Usage

taf.skeleton.sa.org(path = ".", stockname, force = FALSE)

Arguments

Value

Full path to analysis directory.

See Also

package.skeleton creates an empty template for a new R package.

TAF-package gives an overview of the package.

Examples

## Not run: 
taf.skeleton.sa.org(stockname = "WBCod_2021_cand01")

## End(Not run)