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adapr (version 1.0.1)

Implementation of an Accountable Data Analysis Process

Description

Tracks reading and writing within R scripts that are organized into a directed acyclic graph. Contains an interactive shiny application adaprApp(). Uses git2r package, Git and file hashes to track version histories of input and output. See package vignette for how to get started.

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Version

Install

install.packages('adapr')

Monthly Downloads

43

Version

1.0.1

License

LGPL-2

Maintainer

Jonathan Gelfond

Last Published

December 30th, 2016

Functions in adapr (1.0.1)

checkAdaprHashAlgo

Checks or changes the specified adapr hash algorithm (adaprHashAlgo option)
add_package

Add R package to a project
commit2char

git2r commit class to character converter
commit.project

Git commit of project.
checkRmdMode

Checks whether interactive R markdown session is ON
adapr-package

\Sexpr[results=rd,stage=build]{tools:::Rd_package_title("#1")}adaprImplementation of an Accountable Data Analysis Process
Check.file.mtime.source

Checks the consistency of the dependency directory with the files within the file system Reports the source scripts that need to be updated!
adaprApp

Launches Main app
first.project

Create first project
finalize_dependency

Writes dependency data to file in "Dependency" directory
default.adapr.setup

Set up adapr 1st time
create_program_graph_v2

Make plot of project programs only Summarize all programs.
Digest

Digest files from (digest package)
create_source_file_dir

Create source file directories
Create.file.info

Creates a list containing information about a file
create_markdown

Renders and Rmarkdown file
Condense.file.info

Generate condensed information about files from dependency object
get_adapr_options

Returns the primary hub file with project location and id information
get_orchard

Returns the primary hub file with project location and id information
git.commit

git commit. Requires git installation.
git.configure

Configure user.name and email for git. Requires git installation.
guess.write.fcn

Return function for writing common file types
guess.read.fcn

Return function for reading common file types
load.source.directory

Runs all source files within the directory source.directory
make.program

Generates the shell of a code that is project specific
load.install.library.file

Loads librarys within the file library.list.file
Check.file.hash.source

Checks the consistency of the dependency directory with the files within the file system Reports the source scripts that need to be updated!
get.project.publish.path

Given Project name, Return project publish directory
get.project.swap.directory

Retrieve project swap directory
git_provenance

Identify git provenance of file within a project
graph.project

Make plot of project programs only Summarize all programs. Sync status is assessed and indicated.
git.add

git add to stage the file
Graph

Write object and capture file information
install_project_packages

Installs all packages
get.project

Returns the adapr project in R option "adaprProject"
open_orchard

Browses orchard in file system
list.branches

Lists the branches available for loading in the adapr project
get.project.path

Given Project name, Return project directory
Harvest.trees

Collect trees from dependency directory
hashcopy

Given Project name, Return project publish directory
ReadTrack

Tracks files that read by functions not in adapr and captures the file information within dependency object
send.branch.si

Copy dependent programs to swap directory
listDatafiles

Lists the data files available for reading in the adapr project
listBranches

Lists the branches available for loading in the adapr project
Read

Read data and capture the file information within dependency object
send.branch

Copy dependent programs to swap directory
Check.file.hash

Checks the consistency of the dependency directory with the files within the file system
create_program_graph

Make plot of project programs only Summarize all programs. Sync status is assessed and indicated.
get.project.info

Acquire all dependencies related to a project, Generate graph of project dependencies, Get all file information related to project
get.project.info.si

Given source_info object, retrieves project information
git_path

Find path for git executable
Make.dependency.graph.obj

Creates an graph object from a dependency object
make.hyperlink

Makes HTML hyper link
get.pubresults

Read result filepaths to publish
list.datafiles

Lists the data files available for reading in the adapr project
list.programs

Lists the R scripts in the adapr project
scriptLoader

Initializes dependency object source_info
run.program

Run an R script within a project using devtools::clean_source
showProject

Opens project directory
Make.summary.graph

Make.summary graph of projects based on files in dependency directory
sync.project

Checks the synchronization project and runs scripts needed for synchronization
path.expand.2

Swap / for \ in path expand
showResults

Opens results directory
project_report_send_rmd

Make plot of network within html documents. Summarize all programs. Make a readme file at top project directory copy to target.directory Uses pander and pandoc unlike project_report
project.directory.tree

Project directory tree structure contains the relative directory structure included analysis, data, texidr, dependency.dir, support functions, and library bank locations
set.project

Checks or changes the specified adapr project in R option "adaprProject"
Render_Rmd

Renders and Rmarkdown file
remove.project

Removes project from orchard, but doesn't delete project from file system
show.project

Opens project directory
git.info

Retrieves the information from git about a file
initialize_dependency_info

Initializes dependency object source_info
init.project

initialize project
git.init

Initiate git
listScripts

Lists the R scripts in the adapr project
Load.branch

Loads a single R object from file
plant.orchard

Create project hub files in root directory
swap.project.paths

Take list of dependency file data and changes the project path
WriteTrack

Tracks files written by functions not in adapr and captures the file information within dependency object
sprout.program

Generates the shell of a code that is project specific
plant.tree

initialize project
read_library

Read library file
pull_source_info

Create source_info from project.id
show.pubresults

Browses publication table for editing
Get.file.info

Retrieve the file info for the file by name OR from the data subdirectory data
show.results

Opens results directory of project or R script within a project
git.configure.test

Checks git configuration. Requires git installation
git.history.search

Performes git history search
get.fs.time

Retrun time of file system
id_new_libs

Captures libraries that are not loaded automatically
ID.sync

Returns the source files needed to repair synchrony
program.io.table

Create program io table
redirect.tree

Changes project directory/publish directory or identifies imported project
relocate.project

Changes project directory/publish directory or identifies imported project
send.pubresults

Read in results to publish & Copies results to the project's publication directory
set_adapr_options

Returns Modifies the primary adapr option file
synctest.project

Tests the synchrony of files in dependency tree
remove.program

Remove an R script from a project. Removes program, dependency, and results.
remove_package

Remove R package to a project
Write.cap

Write data and capture the file information within dependency object
write.dependency

Write the dependcy object to file
project_report_markdown

Make plot of network within html documents. Summarize all programs.
Write

Write object and capture file information
Read.cap

Read data and capture the file information within dependency object
read.dependency

Read the dependcy data from file
source_sync_si_load

Synchronize project by IDENTIFYING necessary R scripts
report.project

Make plot of network within html documents. Summarize all programs.
rework.project.path

Collects all trees in dependency.dir and changes the project path
Sync.test_2nd

check the synchrony of source files and their created objects
source.sync.si

Synchronize project by running necessary R scripts
Sync.test

check the synchrony of source files and their created objects
sync.test.si

Tests the synchrony of files in dependency tree
Sync.test.pi

Tests the synchrony of files in dependency tree
Sync.test.OLD

check the synchrony of source files and their created objects