adapr: Implementation of an Accountable Data Analysis Process

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.

Install the latest version of this package by entering the following in R:
install.packages("adapr")
AuthorJon Gelfond, Martin Goros
Date of publication2017-02-02 11:23:37
MaintainerJonathan Gelfond <gelfondjal@uthscsa.edu>
LicenseLGPL-2
Version1.0.2

View on CRAN

Man pages

adaprApp: Launches Main app

adapr-package: Implementation of an Accountable Data Analysis Process

add_package: Add R package to a project

checkAdaprHashAlgo: Checks or changes the specified adapr hash algorithm...

Check.file.hash: Checks the consistency of the dependency directory with the...

Check.file.hash.source: Checks the consistency of the dependency directory with the...

Check.file.mtime.source: Checks the consistency of the dependency directory with the...

checkRmdMode: Checks whether interactive R markdown session is ON

commit2char: git2r commit class to character converter

commit.project: Git commit of project.

Condense.file.info: Generate condensed information about files from dependency...

Create.file.info: Creates a list containing information about a file

create_markdown: Renders and Rmarkdown file

create_program_graph: Make plot of project programs only Summarize all programs....

create_program_graph_v2: Make plot of project programs only Summarize all programs.

create_source_file_dir: Create source file directories

default.adapr.setup: Set up adapr 1st time

dependency-class: Dependency class

Digest: Digest files from (digest package)

finalize_dependency: Writes dependency data to file in "Dependency" directory

first.project: Create first project

get_adapr_options: Returns the primary hub file with project location and id...

Get.file.info: Retrieve the file info for the file by name OR from the data...

get.fs.time: Retrun time of file system

get_orchard: Returns the primary hub file with project location and id...

get.project: Returns the adapr project in R option "adaprProject"

get.project.info: Acquire all dependencies related to a project, Generate graph...

get.project.info.si: Given source_info object, retrieves project information

get.project.path: Given Project name, Return project directory

get.project.publish.path: Given Project name, Return project publish directory

get.project.swap.directory: Retrieve project swap directory

get.pubresults: Read result filepaths to publish

git.add: git add to stage the file

git.commit: git commit. Requires git installation.

git.configure: Configure user.name and email for git. Requires git...

git.configure.test: Checks git configuration. Requires git installation

git.history.search: Performes git history search

git.info: Retrieves the information from git about a file

git.init: Initiate git

git_path: Find path for git executable

git_provenance: Identify git provenance of file within a project

Graph: Write object and capture file information

graph.project: Make plot of project programs only Summarize all programs....

guess.read.fcn: Return function for reading common file types

guess.write.fcn: Return function for writing common file types

Harvest.trees: Collect trees from dependency directory

hashcopy: Given Project name, Return project publish directory

id_new_libs: Captures libraries that are not loaded automatically

ID.sync: Returns the source files needed to repair synchrony

initialize_dependency_info: Initializes dependency object source_info

init.project: initialize project

install_project_packages: Installs all packages

list.branches: Lists the branches available for loading in the adapr project

listBranches: Lists the branches available for loading in the adapr project

list.datafiles: Lists the data files available for reading in the adapr...

listDatafiles: Lists the data files available for reading in the adapr...

list.programs: Lists the R scripts in the adapr project

listScripts: Lists the R scripts in the adapr project

Load.branch: Loads a single R object from file

load.install.library.file: Loads librarys within the file library.list.file

load.source.directory: Runs all source files within the directory source.directory

Make.dependency.graph.obj: Creates an graph object from a dependency object

make.hyperlink: Makes HTML hyper link

make.program: Generates the shell of a code that is project specific

Make.summary.graph: Make.summary graph of projects based on files in dependency...

monitorParallelSync.project: Track parallelSync.project while in progress

open_orchard: Browses orchard in file system

parallelSync.project: Uses DOSNOW package for parallel syncrhonization of project....

path.expand.2: Swap / for \ in path expand

plant.orchard: Create project hub files in root directory

plant.tree: initialize project

program.io.table: Create program io table

project.directory.tree: Project directory tree structure contains the relative...

project_report_markdown: Make plot of network within html documents. Summarize all...

project_report_send_rmd: Make plot of network within html documents. Summarize all...

pull_source_info: Create source_info from project.id

Read: Read data and capture the file information within dependency...

Read.cap: Read data and capture the file information within dependency...

read.dependency: Read the dependcy data from file

read_library: Read library file

ReadTrack: Tracks files that read by functions not in adapr and captures...

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

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

remove_package: Remove R package to a project

remove.program: Remove an R script from a project. Removes program,...

remove.project: Removes project from orchard, but doesn't delete project from...

Render_Rmd: Renders and Rmarkdown file

report.project: Make plot of network within html documents. Summarize all...

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

run.program: Run an R script within a project using devtools::clean_source

scriptLoader: Initializes dependency object source_info

send.branch: Copy dependent programs to swap directory

send.branch.si: Copy dependent programs to swap directory

send.pubresults: Read in results to publish & Copies results to the project's...

set_adapr_options: Returns Modifies the primary adapr option file

set.project: Checks or changes the specified adapr project in R option...

show.project: Opens project directory

showProject: Opens project directory

show.pubresults: Browses publication table for editing

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

showResults: Opens results directory

source.sync.si: Synchronize project by running necessary R scripts

source_sync_si_load: Synchronize project by IDENTIFYING necessary R scripts

sprout.program: Generates the shell of a code that is project specific

swap.project.paths: Take list of dependency file data and changes the project...

sync.project: Checks the synchronization project and runs scripts needed...

Sync.test: check the synchrony of source files and their created objects

Sync.test_2nd: check the synchrony of source files and their created objects

Sync.test.OLD: check the synchrony of source files and their created objects

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

synctest.project: Tests the synchrony of files in dependency tree

sync.test.si: Tests the synchrony of files in dependency tree

Write: Write object and capture file information

Write.cap: Write data and capture the file information within dependency...

write.dependency: Write the dependcy object to file

WriteTrack: Tracks files written by functions not in adapr and captures...

Functions

adapr Man page
adaprApp Man page
adapr-package Man page
add_package Man page
checkAdaprHashAlgo Man page
Check.file.hash Man page
Check.file.hash.source Man page
Check.file.mtime.source Man page
checkRmdMode Man page
commit2char Man page
commit.project Man page
Condense.file.info Man page
Create.file.info Man page
create_markdown Man page
create_program_graph Man page
create_program_graph_v2 Man page
create_source_file_dir Man page
default.adapr.setup Man page
dependency Man page
dependency-class Man page
Digest Man page
finalize_dependency Man page
first.project Man page
get_adapr_options Man page
Get.file.info Man page
get.fs.time Man page
get_orchard Man page
get.project Man page
get.project.info Man page
get.project.info.si Man page
get.project.path Man page
get.project.publish.path Man page
get.project.swap.directory Man page
get.pubresults Man page
git.add Man page
git.commit Man page
git.configure Man page
git.configure.test Man page
git.history.search Man page
git.info Man page
git.init Man page
git_path Man page
git_provenance Man page
Graph Man page
graph.project Man page
guess.read.fcn Man page
guess.write.fcn Man page
Harvest.trees Man page
hashcopy Man page
id_new_libs Man page
ID.sync Man page
initialize_dependency_info Man page
init.project Man page
install_project_packages Man page
list.branches Man page
listBranches Man page
list.datafiles Man page
listDatafiles Man page
list.programs Man page
listScripts Man page
Load.branch Man page
load.install.library.file Man page
load.source.directory Man page
Make.dependency.graph.obj Man page
make.hyperlink Man page
make.program Man page
Make.summary.graph Man page
monitorParallelSync.project Man page
open_orchard Man page
parallelSync.project Man page
path.expand.2 Man page
plant.orchard Man page
plant.tree Man page
program.io.table Man page
project.directory.tree Man page
project_report_markdown Man page
project_report_send_rmd Man page
pull_source_info Man page
Read Man page
Read.cap Man page
read.dependency Man page
read_library Man page
ReadTrack Man page
redirect.tree Man page
relocate.project Man page
remove_package Man page
remove.program Man page
remove.project Man page
Render_Rmd Man page
report.project Man page
rework.project.path Man page
run.program Man page
scriptLoader Man page
send.branch Man page
send.branch.si Man page
send.pubresults Man page
set_adapr_options Man page
set.project Man page
show.project Man page
showProject Man page
show.pubresults Man page
show.results Man page
showResults Man page
source.sync.si Man page
source_sync_si_load Man page
sprout.program Man page
swap.project.paths Man page
sync.project Man page
Sync.test Man page
Sync.test_2nd Man page
Sync.test.OLD Man page
Sync.test.pi Man page
synctest.project Man page
sync.test.si Man page
Write Man page
Write.cap Man page
write.dependency Man page
WriteTrack Man page

Files

inst
inst/adapr_options.csv
inst/doc
inst/doc/ADAPRVignette.Rmd
inst/doc/ADAPRVignette.html
inst/adapr21
inst/adapr21/ui.R inst/adapr21/server.R
inst/adapr21/www
inst/adapr21/www/makeProgramPic.jpg
inst/adapr21/www/graftBranch.jpg
inst/adapr21/www/tree_logo.png
inst/adapr21/www/projectReport.jpg
inst/adapr21/www/sendBranch.jpg
inst/adapr21/www/configure.jpg
inst/adapr21/www/style.css
inst/adapr21/www/treePic.jpg
inst/adapr21/www/syncTree.jpg
inst/adapr21/helpers.R inst/adapr21/global.R
NAMESPACE
data
R
R/sync_test_2.R R/parallelsync_project.R R/project_directory_tree.R R/sync_test_3.R R/Read_cap.R R/finalize_dependency.R R/add_library.R R/git_init.R R/dependency_class.R R/git_add.R R/git_info.R R/Check_file_hash_source.R R/create_program_graph_2.R R/commit_project.R R/create_file_info.R R/plant_tree.R R/swap_project_paths.R R/sync_test.R R/Make_dependency_graph.R R/script_loader.R R/guess_write_fnc.R R/Graph.R R/git.commit.R R/id_new_libs.R R/ID_sync.R R/source_sync_si.R R/get_project_info_si.R R/hashcopy.R R/shinyTree.R R/Render.R R/Harvest_trees.R R/write_cap.R R/hashtags.R R/make_summary_graph.R R/list_files.R R/make_source_info.R R/Sync_test_pi.R R/get.orchard.R R/Condense_file_info.R R/Check_file_hash.R R/default_setup.R R/project_report_markdown.R R/Write.R R/git_config_test.R R/project_report_send_rmd.R R/create_markdown.R R/path_expand.2.R R/send_branch_si.R R/create_program_graph.R R/git_configure.R R/sync_test_si.R R/get_project_swap_directory.R R/Digest.R R/git_path.R R/source_sync_si_load.R R/get.fs.time.R R/plant_orchard.R R/create_source_file_dir.R R/get_project_info.R R/Get.file.info.R R/load_source_directory.R R/write_dependency.R R/publishers.R R/run_Program.R R/Check_file_mtime_source.R R/git_history_search.R R/sprout_program.R R/read_dependency.R R/git_provenance.R R/program_io_table.R R/intialize.dependency.info.R R/get_project_path.R R/send_branch.R R/guress_read_fcn.R R/get.adapr.options.R R/Read.R R/file_delay.R R/rework_project_path.R R/load_install_library_file.R R/make_hyperlink.R R/load_branch.R
vignettes
vignettes/program_tab.png
vignettes/function_maps.pdf
vignettes/report_tab.png
vignettes/send_tab.png
vignettes/configure_tab.png
vignettes/ADAPRVignette.Rmd
vignettes/function_maps.png
vignettes/project_tab.png
vignettes/project_report_tab.png
vignettes/synchronize_tab.png
MD5
build
build/vignette.rds
build/partial.rdb
DESCRIPTION
man
man/get.project.swap.directory.Rd man/get.project.Rd man/send.pubresults.Rd man/Get.file.info.Rd man/remove.program.Rd man/run.program.Rd man/project_report_send_rmd.Rd man/list.datafiles.Rd man/Harvest.trees.Rd man/Render_Rmd.Rd man/get_orchard.Rd man/open_orchard.Rd man/showProject.Rd man/initialize_dependency_info.Rd man/read_library.Rd man/get.project.path.Rd man/git_provenance.Rd man/create_program_graph_v2.Rd man/read.dependency.Rd man/install_project_packages.Rd man/Make.dependency.graph.obj.Rd man/remove.project.Rd man/guess.write.fcn.Rd man/Check.file.hash.source.Rd man/listScripts.Rd man/git.configure.test.Rd man/get.project.info.si.Rd man/git.info.Rd man/commit.project.Rd man/report.project.Rd man/monitorParallelSync.project.Rd man/get.project.publish.path.Rd man/create_markdown.Rd man/sprout.program.Rd man/Make.summary.graph.Rd man/list.programs.Rd man/sync.project.Rd man/init.project.Rd man/scriptLoader.Rd man/guess.read.fcn.Rd man/list.branches.Rd man/graph.project.Rd man/commit2char.Rd man/synctest.project.Rd man/source_sync_si_load.Rd man/write.dependency.Rd man/project.directory.tree.Rd man/path.expand.2.Rd man/make.hyperlink.Rd man/load.source.directory.Rd man/send.branch.si.Rd man/project_report_markdown.Rd man/get_adapr_options.Rd man/id_new_libs.Rd man/Create.file.info.Rd man/checkRmdMode.Rd man/program.io.table.Rd man/hashcopy.Rd man/ID.sync.Rd man/make.program.Rd man/plant.tree.Rd man/parallelSync.project.Rd man/add_package.Rd man/Read.Rd man/send.branch.Rd man/finalize_dependency.Rd man/Graph.Rd man/default.adapr.setup.Rd man/dependency-class.Rd man/Read.cap.Rd man/git.add.Rd man/set_adapr_options.Rd man/show.results.Rd man/sync.test.si.Rd man/set.project.Rd man/show.project.Rd man/first.project.Rd man/Sync.test_2nd.Rd man/Write.Rd man/git_path.Rd man/rework.project.path.Rd man/relocate.project.Rd man/listBranches.Rd man/create_source_file_dir.Rd man/Condense.file.info.Rd man/showResults.Rd man/adapr-package.Rd man/Sync.test.pi.Rd man/Check.file.mtime.source.Rd man/WriteTrack.Rd man/show.pubresults.Rd man/Load.branch.Rd man/get.pubresults.Rd man/redirect.tree.Rd man/git.init.Rd man/swap.project.paths.Rd man/adaprApp.Rd man/Write.cap.Rd man/pull_source_info.Rd man/git.history.search.Rd man/checkAdaprHashAlgo.Rd man/listDatafiles.Rd man/plant.orchard.Rd man/git.commit.Rd man/get.fs.time.Rd man/Digest.Rd man/ReadTrack.Rd man/Sync.test.OLD.Rd man/remove_package.Rd man/get.project.info.Rd man/source.sync.si.Rd man/load.install.library.file.Rd man/Sync.test.Rd man/Check.file.hash.Rd man/create_program_graph.Rd man/git.configure.Rd

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