Functions to Support the ICES Transparent Assessment Framework

Functions to support the ICES Transparent Assessment Framework <> to organize data, methods, and results used in ICES assessments. ICES is an organization facilitating international collaboration in marine science.


icesTAF 3.0-0 (2019-04-25)

o Added function period() to paste period string for DATA.bib entries.

o Removed argument 'name' from taf.skeleton(). The default behavior is now to create initial directories and scripts in the current working directory.

o Changed taf.library() so it loads a package instead of changing the library path.

o Changed default size of taf.png(). Changed text size in zoom() accordingly and renamed arguments. The zoom() function is now generic.

o Changed write.taf() so it gives a warning if column names are duplicated.

icesTAF 2.3-0 (2019-04-08)

o Added function sourceDir() to read all *.R files from a directory.

o Added function zoom() to change text size in a lattice plot.

o Added arguments 'config', 'data', and 'software' to taf.bootstrap().

o Added argument 'append' to and Code contributed by Alexandros Kokkalis.

o Added argument 'colname' to xtab2taf().

o Improved so the default value of 'year' is the current year and user can pass period=FALSE.

o Improved file.encoding() so it handles spaces in filenames.

o Improved os.unix() so it recognizes both Linux and macOS operating systems.

o Improved process.bib() so it supports 'bundle' field and multiple filenames in 'source' field, separated by newlines.

o Improved write.taf() so file="" prints to screen, regardless of dir.

icesTAF 2.2-0 (2019-02-22)

o Added function file.encoding() to examine file encoding. Added functions and to convert file encoding.

o Added function line.endings() to examine line endings.

o Added arguments 'author', 'year', and 'title' to, and improved it so it also handles software other than R packages.

o Added argument 'clean' to taf.bootstrap().

o Added argument 'create' to taf.library().

o Improved process.bib() so it does not require taf.bootstrap() to create 'data' and 'software' directories.

o Improved taf.skeleton() so every script starts with library(icesTAF) and mkdir() to create a working directory.

icesTAF 2.1-0 (2019-01-08)

o Added functions taf.bootstrap() and process.bib() to set up data files and software.

o Added functions and to create initial draft versions of metadata files.

o Added functions os(), os.linux() and os.macos() to detect more operating systems than before.

o Updated colors (,,, taf.dark, taf.light) to make them equally intense and easy to distinguish.

o This release introduces package dependencies to parse BibTeX files (bibtex) and install packages from GitHub (remotes), with further underlying package dependencies.

icesTAF 2.0-0 (2018-12-07)

o Added function taf.library() to work with packages in a local TAF library.

o Added function rmdir() to remove an empty directory.

o Added functions os.unix() and to determine OS family.

o Added function taf.unzip() to extract files from zip archives.

o Moved functions read.dls() and write.dls() to the 'icesAdvice' package.

o Changed clean(), makeAll(), makeTAF(), sourceAll(), and taf.skeleton() to align with new data-model workflow.

o Renamed function tafpng() to taf.png().

o Added argument 'destfile' to download().

icesTAF 1.6-2 (2018-08-03)

o Added argument 'underscore' to write.taf().

o Added argument 'stringsAsFactors' to read.taf().

o Improved multitable support for read.taf() and write.taf().

icesTAF 1.6-1 (2018-06-28)

o Changed sourceTAF(), sourceAll(), makeTAF(), and makeAll() so they never delete the 'begin' folder.

o Changed sourceAll(), makeTAF(), makeAll() so they don't set the working directory.

o Changed clean() so user can specify directories to remove.

o Changed write.taf() to search in the global workspace if 'x' is a string.

o Changed cp() to enforce safeguards when moving files.

icesTAF 1.6-0 (2018-05-15)

o Removed function upload(). Initial data and model files are now in the 'begin' folder of each assessment.

o Added function plus() to rename plus group column.

o Added argument 'dir' to write.taf().

o Changed read.taf() and write.taf() so they can read/write many tables in one call.

o Changed write.taf() so the name of the data frame is the default filename.

o Changed cp() to preserve the timestamp when copying a file.

icesTAF 1.5-3 (2018-04-27)

o Changed default file encoding in read.taf() to UTF-8.

icesTAF 1.5-1 (2018-03-20)

o Replaced argument 'local' with 'rm' in sourceTAF().

o Added argument 'colname' to flr2taf().

icesTAF 1.5-0 (2018-01-25)

o Added functions makeTAF() and makeAll() to run TAF scripts as needed.

o Added arguments 'include' and 'engine' to make().

o Added argument 'local' to sourceTAF(), replacing the 'rm' argument.

o Changed sourceAll() to only run TAF scripts: data.R, input.R, model.R, output.R, and report.R.

icesTAF 1.4-1 (2017-12-05)

o Added argument 'grep' to div() and rnd().

icesTAF 1.4-0 (2017-10-30)

o Added function upload() to upload file to TAF database. Added function download() to download file in binary mode.

o Added function msg() to show a message, as well as the current time.

o Added function tafpng() to open a graphics device. Added function lim() to compute axis limits.

o Added function div() to divide column values with a common number. Added function rnd() to round column values.

o Added function taf.skeleton() to create an empty template for a TAF analysis.

o Added function deps() to list dependencies.

o Renamed function sourceAtoZ() to sourceAll().

o Added argument 'move' to cp(). Added argument 'clean' to sourceTAF(). Added argument 'column' to tt().

o Added color objects:,,, taf.dark, and taf.light.

o Added example data frame summary.taf to demonstrate div() and rnd().

icesTAF 1.3-2 (2017-06-03)

o Improved package description.

icesTAF 1.3-0 (2017-05-27)

o Added function make() to run script if needed, and sourceAtoZ() to run all scripts in alphabetical order. Added clean() to remove TAF directories.

icesTAF 1.2-0 (2017-05-19)

o Added function sourceTAF() to run scripts. Added cp() to copy files and mkdir() to create a directory. Added read.taf() and write.taf() to read and write TAF tables. Added long2taf(), taf2xtab(), tt(), and xtab2taf to convert between table formats.

o Renamed functions readDLS() and writeDLS() to read.dls() and write.dls().

o Removed function dir.remove() which is no longer needed in TAF scripts.

o Added example data frames catage.long, catage.taf, and catage.xtab to demonstrate different table formats.

icesTAF 1.1-0 (2017-04-27)

o Added functions flr2taf() and taf2long() to convert between table formats.

icesTAF 1.0-0 (2017-02-17)

o Initial release, with five functions: dir.remove(), dos2unix(), readDLS(), unix2dos(), and writeDLS().

Reference manual

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3.1-1 by Arni Magnusson, 25 days ago

Browse source code at

Authors: Arni Magnusson [aut, cre] , Colin Millar [aut] , Alexandros Kokkalis [ctb]

Documentation:   PDF Manual  

GPL (>= 2) license

Imports grDevices, lattice, stats, tools, utils, bibtex, remotes

See at CRAN