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 |
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 |
browsePubFiles | Browses publication table for editing |
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 |
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) |
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 |
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 |
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 |
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 |
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 |
openProjectList | Browses orchard in file system |
openScript | Opens script from a project with default R program. Can open markdown files as well. |
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 |
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 |
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. |
updateAdaprConfig | Updates the project list file to include project specific libraries. |
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 |
{run.program} | Run an R script within a project using devtools::clean_source |