Implementation of an Accountable Data Analysis Process

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Documentation for package ‘adapr’ version 1.0

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adapr-package Implementation of an Accountable Data Analysis Process
adapr Implementation of an Accountable Data Analysis Process
adaprApp Launches Main app
Check.file.hash Checks the consistency of the dependency directory with the files within the file system
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!
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!
checkAdaprHashAlgo Checks or changes the specified adapr hash algorithm (adaprHashAlgo option)
checkRmdMode Checks whether interactive R markdown session is ON
Condense.file.info Generate condensed information about files from dependency object
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 Dependency class
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.file.info Retrieve the file info for the file by name OR from the data subdirectory data
get.fs.time Retrun time of file system
get.project.info Acquire all dependencies related to a project, Generate graph of project dependencies, Get all file information related to project
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_adapr_options Returns the primary hub file with project location and id information
get_orchard Returns the primary hub file with project location and id information
git.add git add to stage the file
git.commit git commit
git.configure Configure user.name and email for git
git.configure.test Checks git configuration
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
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.sync Returns the source files needed to repair synchrony
id_new_libs Captures libraries that are not loaded automatically
initialize_dependency_info Initializes dependency object source_info
listBranches Lists the branches available for loading in the adapr project
listDatafiles Lists the data files available for reading 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.summary.graph Make.summary graph of projects based on files in dependency directory
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 directory structure included analysis, data, texidr, dependency.dir, support functions, and library bank locations
project_report_markdown Make plot of network within html documents. Summarize all programs. Uses pandoc unlike project_report
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
pull_source_info Create source_info from project.id
Read Read data and capture the file information within dependency object
Read.cap Read data and capture the file information within dependency object
read.dependency Read the dependcy data from file
redirect.tree Changes project directory/publish directory or identifies imported project
Render_Rmd Renders and Rmarkdown file
rework.project.path Collects all trees in dependency.dir and changes the project path
scriptLoader Initializes dependency object source_info
send.branch Copy dependent programs to swap directory
send.branch.si Copy dependent programs to swap directory
set_adapr_options Returns Modifies the primary adapr option file
showProject Opens project directory
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 path
Sync.test 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
sync.test.si Tests the synchrony of files in dependency tree
Sync.test_2nd check the synchrony of source files and their created objects
Write Write object and capture file information
Write.cap Write data and capture the file information within dependency object
write.dependency Write the dependcy object to file