Package: TAF 4.4.0

Arni Magnusson

TAF: Transparent Assessment Framework for Reproducible Research

General framework to organize data, methods, and results used in reproducible scientific analyses. A TAF analysis consists of four scripts (data.R, model.R, output.R, report.R) that are run sequentially. Each script starts by reading files from a previous step and ends with writing out files for the next step. Convenience functions are provided to version control the required data and software, run analyses, clean residues from previous runs, manage files, manipulate tables, and produce figures. With a focus on stability and reproducible analyses, the TAF package comes with no dependencies. TAF forms a base layer for the 'icesTAF' package and other scientific applications.

Authors:Arni Magnusson [aut, cre], Colin Millar [aut], Iago Mosqueira [aut], Alexandros Kokkalis [ctb], Ibrahim Umar [ctb], Hjalte Parner [ctb]

TAF_4.4.0.tar.gz
TAF_4.4.0.zip(r-4.7)TAF_4.4.0.zip(r-4.6)TAF_4.4.0.zip(r-4.5)
TAF_4.4.0.tgz(r-4.6-any)TAF_4.4.0.tgz(r-4.5-any)
TAF_4.4.0.tar.gz(r-4.7-any)TAF_4.4.0.tar.gz(r-4.6-any)
TAF_4.4.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
TAF/json (API)
NEWS

# Install 'TAF' in R:
install.packages('TAF', repos = c('https://ices-tools-prod.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/ices-tools-prod/taf/issues

Datasets:

On CRAN:

Conda:

7.13 score 3 stars 2 packages 416 scripts 445 downloads 98 exports 1 dependencies

Last updated from:54ea855fc7. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK108
source / vignettesOK128
linux-release-x86_64OK97
macos-release-arm64OK86
macos-oldrel-arm64OK106
windows-develOK124
windows-releaseOK71
windows-oldrelOK64
wasm-releaseOK87

Exports:already.in.taf.libraryboot.dirboot.dir.insideboot.existscheck.datacheck.softwarecleanclean.bootclean.dataclean.libraryclean.softwareconvert.spacescpddimdepsdetach.packagesdir.treedivdos2unixdownloaddownload.githubdraft.datadraft.readmedraft.softwareds.fileds.packageextract.subdirfile.encodingflr2tafget.remote.shagit.repoinstall.depsis.r.packagelatin1.to.utf8limline.endingslong2taflong2xtabmakemake.allmake.tafmakeAllmakeTAFmkdirmodel.dirmodel.scriptmsgosos.linuxos.macosos.unixos.windowsparse.repopdepsperiodplusprocess.bibfileprocess.entryread.bibread.tafrmdirrndsam2tafsource.allsource.dirsource.tafsourceAllsourceDirsourceTAFstamp.descriptiontaf.boottaf.boot.pathtaf.bootstraptaf.data.pathtaf.exampletaf.installtaf.libPathstaf.librariestaf.librarytaf.pkgtaf.pngtaf.sessiontaf.skeletontaf.sourcestaf.unziptaf2htmltaf2longtaf2xtabtafpngttunix2dosutf8.to.latin1wide2longwrite.tafxtab2longxtab2tafzoomzoom.trellis

Dependencies:lattice

Readme and manuals

Help Manual

Help pageTopics
Transparent Assessment Framework for Reproducible ResearchTAF-package TAF
Catch at Age in Long Formatcatage.long
Catch at Age in TAF Formatcatage.taf
Catch at Age in Wide Formatcatage.wide
Catch at Age in Crosstab Formatcatage.xtab
Check DATA.bib Entriescheck.data
Check SOFTWARE.bib Against Global Packagescheck.software
Clean TAF Directoriesclean
Clean Boot Directoryclean.boot
Clean Dataclean.data
Clean TAF Libraryclean.library
Clean TAF Softwareclean.software
Convert Spacesconvert.spaces
Copy Filescp
Data Dimensionsddim
Dependencies of a Workflowdeps
Detach Packagesdetach.packages
Directory Treedir.tree
Divide Columnsdiv
Convert Line Endingsdos2unix unix2dos
Download Filedownload
Download GitHub Repositorydownload.github
Draft DATA.bibdraft.data
Draft Readmedraft.readme
Draft SOFTWARE.bibdraft.software
File Encodingfile.encoding
Convert FLR Table to TAF Formatflr2taf
Get Remote SHAget.remote.sha
Git Repogit.repo
Install Dependenciesinstall.deps
Is R Packageis.r.package
Convert File Encodinglatin1.to.utf8 utf8.to.latin1
Axis Limitslim
Line Endingsline.endings
Linear Regressionlinreg
Convert Long Table to TAF Formatlong2taf
Convert Long Table to Crosstab Formatlong2xtab
Run R Script if Neededmake
Run All TAF Scripts as Neededmake.all makeAll
Run TAF Script if Neededmake.taf makeTAF
Create Directorymkdir
Show Messagemsg
Operating Systemos os.linux os.macos os.unix os.windows
Dependencies of a Packagepdeps
Periodperiod
Rename Plus Group Columnplus
Read Metadata Entriesread.bib
Read TAF Tableread.taf
Remove Empty Directoryrmdir
Round Columnsrnd
Convert SAM Table to TAF Formatsam2taf
Run All TAF Scriptssource.all sourceAll
Source Directorysource.dir sourceDir
Run TAF Scriptsource.taf sourceTAF
Summary Results in TAF Formatsummary.taf
Boot TAF Analysistaf.boot taf.bootstrap
Construct Boot Pathtaf.boot.path
TAF Colorstaf.blue taf.colors taf.dark taf.green taf.light taf.orange
Construct Boot Data Pathtaf.data.path
TAF Exampletaf.example
TAF Installtaf.install
Add TAF Library Pathtaf.libPaths
TAF Librariestaf.libraries
TAF Librarytaf.library
PNG Devicetaf.png tafpng
TAF Sessiontaf.session
TAF Skeletontaf.skeleton
List Sourcestaf.sources
Unzip Filetaf.unzip
Convert TAF Table to HTMLtaf2html
Convert TAF Table to Long Formattaf2long
Convert TAF Table to Crosstab Formattaf2xtab
TAF Transposett
Convert Wide Table to Long Formatwide2long
Write TAF Tablewrite.taf
Convert Crosstab Table to Long Formatxtab2long
Convert Crosstab Table to TAF Formatxtab2taf
Zoomzoom zoom.trellis