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.

AuthorJon Gelfond, Martin Goros
Date of publication2016-12-30 00:13:36
MaintainerJonathan Gelfond <gelfondjal@uthscsa.edu>
LicenseLGPL-2
Version1.0.1

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...

open_orchard: Browses orchard in file system

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...

Files in this package

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

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