TAF4.3.1 package

Transparent Assessment Framework for Reproducible Research

check.software

Check SOFTWARE.bib Against Global Packages

clean.boot

Clean Boot Directory

clean.data

Clean Data

clean.library

Clean TAF Library

clean

Clean TAF Directories

clean.software

Clean TAF Software

convert.spaces

Convert Spaces

cp

Copy Files

ddim

Data Dimensions

deps

Dependencies of a Workflow

detach.packages

Detach Packages

dir.tree

Directory Tree

div

Divide Columns

dos2unix

Convert Line Endings

download.github

Download GitHub Repository

download

Download File

draft.data

Draft DATA.bib

draft.readme

Draft Readme

draft.software

Draft SOFTWARE.bib

file.encoding

File Encoding

flr2taf

Convert FLR Table to TAF Format

get.remote.sha

Get Remote SHA

git.repo

Git Repo

install.deps

Install Dependencies

is.r.package

Is R Package

latin1.to.utf8

Convert File Encoding

lim

Axis Limits

line.endings

Line Endings

linreg

Linear Regression

long2taf

Convert Long Table to TAF Format

long2xtab

Convert Long Table to Crosstab Format

make.all

Run All TAF Scripts as Needed

make

Run R Script if Needed

make.taf

Run TAF Script if Needed

mkdir

Create Directory

msg

Show Message

os

Operating System

pdeps

Dependencies of a Package

period

Period

plus

Rename Plus Group Column

read.bib

Read Metadata Entries

read.taf

Read TAF Table

rmdir

Remove Empty Directory

rnd

Round Columns

sam2taf

Convert SAM Table to TAF Format

source.all

Run All TAF Scripts

source.dir

Source Directory

source.taf

Run TAF Script

TAF-internal

Various TAF Helper Functions

TAF-package

Transparent Assessment Framework for Reproducible Research

taf.boot.path

Construct Boot Path

taf.boot

Boot TAF Analysis

taf.data.path

Construct Boot Data Path

taf.example

TAF Example

taf.install

TAF Install

taf.libPaths

Add TAF Library Path

taf.libraries

TAF Libraries

taf.library

TAF Library

taf.png

PNG Device

taf.session

TAF Session

taf.skeleton

TAF Skeleton

taf.sources

List Sources

taf.unzip

Unzip File

taf2html

Convert TAF Table to HTML

taf2long

Convert TAF Table to Long Format

taf2xtab

Convert TAF Table to Crosstab Format

tt

TAF Transpose

wide2long

Convert Wide Table to Long Format

write.taf

Write TAF Table

xtab2long

Convert Crosstab Table to Long Format

xtab2taf

Convert Crosstab Table to TAF Format

zoom

Zoom

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.