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.
|Author||Jon Gelfond, Martin Goros|
|Date of publication||2016-12-30 00:13:36|
|Maintainer||Jonathan Gelfond <firstname.lastname@example.org>|
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...