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adapr (version 1.0.2)

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. V1.02 adds parallel execution of project scripts and function map in vignette. Makes project specification argument last in order.

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Version

Install

install.packages('adapr')

Monthly Downloads

43

Version

1.0.2

License

LGPL-2

Maintainer

Jonathan Gelfond

Last Published

February 2nd, 2017

Functions in adapr (1.0.2)

Check.file.hash

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

Create source file directories
Digest

Digest files from (digest package)
create_markdown

Renders and Rmarkdown file
default.adapr.setup

Set up adapr 1st time
Create.file.info

Creates a list containing information about a file
create_program_graph_v2

Make plot of project programs only Summarize all programs.
get.project

Returns the adapr project in R option "adaprProject"
Condense.file.info

Generate condensed information about files from dependency object
get.project.path

Given Project name, Return project directory
create_program_graph

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

Given Project name, Return project publish directory
finalize_dependency

Writes dependency data to file in "Dependency" directory
get.project.swap.directory

Retrieve project swap directory
first.project

Create first project
Get.file.info

Retrieve the file info for the file by name OR from the data subdirectory data
git_provenance

Identify git provenance of file within a project
get.fs.time

Retrun time of file system
get_adapr_options

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

git add to stage the file
get_orchard

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

Checks git configuration. Requires git installation
guess.read.fcn

Return function for reading common file types
git.history.search

Performes git history search
graph.project

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

Write object and capture file information
guess.write.fcn

Return function for writing common file types
load.install.library.file

Loads librarys within the file library.list.file
Make.dependency.graph.obj

Creates an graph object from a dependency object
load.source.directory

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

Makes HTML hyper link
git.commit

git commit. Requires git installation.
id_new_libs

Captures libraries that are not loaded automatically
git.configure

Configure user.name and email for git. Requires git installation.
list.branches

Lists the branches available for loading in the adapr project
install_project_packages

Installs all packages
ID.sync

Returns the source files needed to repair synchrony
plant.orchard

Create project hub files in root directory
monitorParallelSync.project

Track parallelSync.project while in progress
open_orchard

Browses orchard in file system
plant.tree

initialize project
program.io.table

Create program io table
project_report_markdown

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

Read data and capture the file information within dependency object
get.project.info

Acquire all dependencies related to a project, Generate graph of project dependencies, Get all file information related to project
remove.program

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

Remove R package to a project
ReadTrack

Tracks files that read by functions not in adapr and captures the file information within dependency object
git_path

Find path for git executable
Harvest.trees

Collect trees from dependency directory
get.pubresults

Read result filepaths to publish
get.project.info.si

Given source_info object, retrieves project information
hashcopy

Given Project name, Return project publish directory
list.datafiles

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

Renders and Rmarkdown file
list.programs

Lists the R scripts in the adapr project
pull_source_info

Create source_info from project.id
remove.project

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

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

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

Read library file
set.project

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

Opens project directory
sync.project

Checks the synchronization project and runs scripts needed for synchronization
Sync.test_2nd

check the synchrony of source files and their created objects
Write.cap

Write data and capture the file information within dependency object
synctest.project

Tests the synchrony of files in dependency tree
show.results

Opens results directory of project or R script within a project
show.pubresults

Browses publication table for editing
scriptLoader

Initializes dependency object source_info
run.program

Run an R script within a project using devtools::clean_source
Sync.test

check the synchrony of source files and their created objects
source_sync_si_load

Synchronize project by IDENTIFYING necessary R scripts
send.branch.si

Copy dependent programs to swap directory
send.branch

Copy dependent programs to swap directory
Sync.test.OLD

check the synchrony of source files and their created objects
showProject

Opens project directory
commit2char

git2r commit class to character converter
commit.project

Git commit of project.
source.sync.si

Synchronize project by running necessary R scripts
showResults

Opens results directory
adapr-package

adapr
adaprApp

Launches Main app
git.init

Initiate git
checkAdaprHashAlgo

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

Checks whether interactive R markdown session is ON
git.info

Retrieves the information from git about a file
initialize_dependency_info

Initializes dependency object source_info
init.project

initialize project
Load.branch

Loads a single R object from file
make.program

Generates the shell of a code that is project specific
listScripts

Lists the R scripts in the adapr project
add_package

Add R package to a project
Make.summary.graph

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

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

Tests the synchrony of files in dependency tree
relocate.project

Changes project directory/publish directory or identifies imported project
redirect.tree

Changes project directory/publish directory or identifies imported project
sync.test.si

Tests the synchrony of files in dependency tree
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!
WriteTrack

Tracks files written by functions not in adapr and captures the file information within dependency object
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!
listBranches

Lists the branches available for loading in the adapr project
parallelSync.project

Uses DOSNOW package for parallel syncrhonization of project. Takes advantage of directed acyclic graph structure to run R script processes in parallel.
listDatafiles

Lists the data files available for reading in the adapr project
read.dependency

Read the dependcy data from file
path.expand.2

Swap / for \ in path expand
send.pubresults

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

Read data and capture the file information within dependency object
sprout.program

Generates the shell of a code that is project specific
set_adapr_options

Returns Modifies the primary adapr option file
swap.project.paths

Take list of dependency file data and changes the project path
write.dependency

Write the dependcy object to file
Write

Write object and capture file information
dependency-class

Dependency class