Implementation of an Accountable Data Analysis Process


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Documentation for package ‘adapr’ version 2.0.0

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A B C D F G I L M O P R S U W misc

adapr-package Implementation of an Accountable Data Analysis Process

-- A --

adapr Implementation of an Accountable Data Analysis Process
adaprApp Launches Main app
adaprDependencies Returns character string of adapr R package import dependencies
adaprHomeDir Identify adapr Home directory. Location of options file and project listing.
adaprInstall Install adapr in a library adaprInstall.R
adaprSheet Browse adapr cheat sheet
adaprUpdate Updates latest adapr from gitHub.
addPackage Add R package to a project
AppLoadFlex Loads a single R object from file for a R Shiny app
arcRead Loads R object from archivist repository within the results directory of another adapr Script
arcWrite Saves R object to archivist repository in results directory of adapr Script

-- B --

browsePubFiles Browses publication table for editing

-- C --

checkAdaprHashAlgo Checks or changes the specified adapr hash algorithm (adaprHashAlgo option)
checkFileHash Checks the consistency of the dependency directory with the files within the file system
checkFileHashSource Checks the consistency of the dependency directory with the files within the file system. Reports the source scripts that need to be updated.
checkFileMtimeSource Checks the consistency of the dependency directory with the files within the file system Reports the source scripts that need to be updated!
checkRmdMode Checks whether interactive R markdown session is ON
checkVersion Check install of package of specific version
commit2char git2r commit class to character converter
commitProject Git commit of project.
condenseFileInfo Generate condensed information about files from dependency object
createFileInfo Creates a list containing information about a file
createMarkdown Creates an Rmarkdown file in specified directory
createProgramGraph Make plot of project programs only Summarize all programs. Sync status is assessed and indicated.
create_source_file_dir Create source file directories

-- D --

dataDir Returns project's data directory, allows relative directories. Used within an R script.
defaultAdaprSetup Set up adapr 1st time
dependency Dependency class
dependency-class Dependency class
Digest Digest files from (digest package)

-- F --

fileInfoProjects List project file information disk space, modification timespan, days inactive
finalize_dependency Writes dependency data to file in "Dependency" directory
firstProject Create first project

-- G --

getAdaprOptions Returns the primary hub file with project location and id information
getDepSubgraph Produces subgraph of dependencies of R script
getFileInfo Retrieve the file info for the file by name OR from the data subdirectory data
getFileSysTime Retrun time of file system
getLibrary Get library for a project
getProject Returns the adapr project in R option "adaprProject"
getProjectInfo Acquire all dependencies related to a project, Generate graph of project dependencies, Get all file information related to project
getProjectInfoSI Given source_info object, retrieves project information
getProjectLibrary Given Project name, Return project library directory
getProjectPath Given Project id, Return project directory
getProjectPublishPath Given Project name, Return project publish directory
getProjectSwapPath Retrieve project swap directory
getPubResults Read result filepaths to publish
getSourceInfo Returns the information related to the adapr script
getUpstream Identifies dependencies in a DAG
get_orchard Returns the primary hub file with project location and id information
gitAdd git add to stage the file
gitCommit git commit. Requires git installation.
gitConfigure Configure user.name and email for git.
gitConfigureTest Checks git configuration. Requires git installation
gitHistorySearch Performes git history search
gitIgnoreLibrary Git ignore the library file
gitInfo Retrieves the information from git about a file
gitInit Initiate git
gitProvenance Identify git provenance of file within a project
git_path Find path for git executable
Graph Write object and capture file information
graphProject Make plot of project programs only Summarize all programs. Sync status is assessed and indicated.
guess.read.fcn Return function for reading common file types
guessWriteFcn Return function for writing common file types

-- I --

idPackages Lower level function that captures packages that are explicitly loaded, not loaded automatically
idSync Returns the source files needed to repair synchrony
importData Import selected file into the project data directory
initialize_dependency_info Initializes dependency object source_info
initProject initialize project
install Install package of specific version
installLibrary Install package of specific version
installProjectPackages Installs all packages

-- L --

Library Installs and loads library specific to a project
listBranches Lists the branches available for loading in the adapr project
listDatafiles Lists the data files available for reading in the adapr project
listProjects List projects
listScripts Lists the R scripts in the adapr project
Load.branch Loads a single R object from file
loadAdaprTest Create adaprTest example project
loadFlex Loads a single R object from file, more flexible than Load.branch or base::load
loadInstallLibraryFile This function is no longer supported. Loads libraries within the file library.list.file

-- M --

makeDependencyGraphObj Creates an graph object from a dependency object
makeFunction Generates the shell of a R function that is project specific in support_functions folder
makeHyperlink Makes HTML hyper link
makeScript Generates the shell of a code that is project specific
makeSummaryGraph Make.summary graph of projects based on files in dependency directory
monitorParallelSync Experimental (use with caution) track parallelSync while in progress

-- O --

openProjectList Browses orchard in file system
openScript Opens script from a project with default R program. Can open markdown files as well.

-- P --

parallelSync Experimental (use with caution) parallel syncrhonization of project. Takes advantage of directed acyclic graph structure to run R script processes in parallel.
path.expand.2 Location of options file and project listing. Swap / for \ in path expand.
plantOrchard Create project hub files in root directory
plantTree initialize project
programIOTable Create program io table
project.directory.tree Project directory tree structure contains the relative directory structure included analysis, data, texidr, dependency.dir, support functions, and library bank locations
projectReportMarkdown Make plot of network within html documents. Summarize all programs.
projectReportSend 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
publishResults Read in results to publish & Copies results to the project's publication directory
pullSourceInfo Create source_info from project.id

-- R --

rapidPlot Make project graph with sync status already computed.
Read Read data and capture the file information within dependency object
Read.cap Lower level function that reads data and capture the file information within dependency object
read.dependency Lower level function that reads the script dependcy data from file
readDependency Collect trees from dependency directory
readLibrary Read library file
ReadTrack Tracks files that read by functions not in adapr and captures the file information within dependency object
redirectTree Lower level function that that changes project directory/publish directory or identifies imported project
relocateProject changes project directory/publish directory/library locataion or identifies imported project
removePackage Remove R package to a project
removeProject Removes project from orchard, but doesn't delete project from file system
removeScript Remove an R script from a project. Removes program, dependency, and results.
renderRmd Renders and Rmarkdown file
reportProject Make plot of network within html documents. Summarize all programs.
resultsDir Returns project's results directory, allows relative directories. Only used within an R script, after create_source_file_dir.
reworkProjectPath Lower level function that collects all trees in dependency.dir and changes the project path
runScript Run an R script within a project using devtools::clean_source
runSourceDirectory Runs all source files within the directory source.directory

-- S --

scriptLoader Initializes dependency object source_info
scriptSubgraph Produces script only subgraph
searchScripts Searches R scripts and R markdown files within a project.
sendBranch Copy dependent programs to swap directory
sendBranchSI Copy dependent programs to swap directory
setAdaprOptions Returns Modifies the primary adapr option file
setProject Checks or changes the specified adapr project in R option "adaprProject"
showProject Opens project directory
showResults Opens results directory of project or R script within a project
sourceSyncSI Lower level function that synchronizes project by running necessary R scripts. Loads from source_info list.
sourceSyncSILoad Synchronize project by IDENTIFYING necessary R scripts
sproutProgram Lower level function that generates the shell of a code that is project specific
swapProjectPath Lower level function that takes list of dependency file data and changes the project path
syncProject Checks the synchronization project and runs scripts needed for synchronization
syncTest Lower level function that checks the synchrony of source files and their created objects
syncTestPI Lower level function that tests the synchrony of files in dependency tree given project information.
syncTestProject Tests the synchrony of files in dependency tree
syncTestSI Tests the synchrony of files in dependency tree
syncTrunk Partial project synchronization of dependencies to an Rscript. Runs only scripts needed for synchronization.

-- U --

updateAdaprConfig Updates the project list file to include project specific libraries.

-- W --

Write Write object and capture file information
Write.cap Lower level function that writes data and captures the file information within dependency object
write.dependency Lower level function that writes the dependency object to file
WriteTrack Tracks files written by functions not in adapr and captures the file information within dependency object

-- misc --

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