Package: D4TAlink.light 2.1.22

Gregoire Thomas

D4TAlink.light: GDP - Workflow Management

Tools, methods and processes for the management of analysis workflows. These lightweight solutions facilitate structuring R&D activities. These solutions were developed to comply with Good Documentation Practice (GDP), with ALCOA+ principles as proposed by the U.S. FDA, and with FAIR principles as discussed by Jacobsen et al. (2017) <doi:10.1162/dint_r_00024>.

Authors:Gregoire Thomas [aut, cre, cph], Metabolomic Diagnostics Ltd. [fnd]

D4TAlink.light_2.1.22.tar.gz
D4TAlink.light_2.1.22.tar.gz(r-4.7-any)D4TAlink.light_2.1.22.tar.gz(r-4.6-any)
D4TAlink.light_2.1.22.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
D4TAlink.light/json (API)

# Install 'D4TAlink.light' in R:
install.packages('D4TAlink.light', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://bitbucket.org/sq4/d4talink.light

On CRAN:

Conda:

quarto

2.68 score 12 scripts 331 downloads 70 exports 83 dependencies

Last updated from:8607501707. Checks:4 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK205
source / vignettesOK240
linux-release-x86_64OK202
wasm-releaseOK146

Exports:archiveTaskbinaryDirbinaryFncatReportdatasourceDirdatasourceFndocDirdocFnDTxgetTaskAuthorgetTaskEnckeygetTaskFilepathgetTaskPathsgetTaskQmdTemplategetTaskRmdTemplategetTaskRootgetTaskRscriptTemplategetTaskSponsorgetTaskStructureinitTaskinitTaskQmdinitTaskRmdinitTaskRscriptjpegReportjpegReportFnlistTaskFileslistTasksloadTaskpathsDefaultpathsGLPGpathsPMSpdfReportpdfReportFnpngReportpngReportFnprogDirqmdFnquerySQLitereadBinaryreadFeatherreadPicklereadReportJSONreadReportTablereadSQLiterenderTaskQmdrenderTaskRmdreportDirreportFnreportXlsFnrestoreTaskrmdFnrscriptFnsaveBinarysaveBinaryEsaveFeathersavePicklesaveReportJSONsaveReportTablesaveReportXlssaveSQLitescanReportsetTaskAuthorsetTaskEnckeysetTaskQmdTemplatesetTaskRmdTemplatesetTaskRootsetTaskRscriptTemplatesetTaskSponsorsetTaskStructuretaskID

Dependencies:arrowaskpassassertthatbase64encBiobaseBiocGenericsbitbit64blobbslibcachemclicpp11DBIdigestdplyrevaluatefastmapfeatherfontawesomefontBitstreamVerafontLiberationfontquiverfsgdtoolsgenericsgetPassglueherehighrhtmltoolsjquerylibjsonliteknitrlaterlatticelifecyclemagrittrMatrixmemoisemimeofficedownofficeropensslopenxlsxpillarpkgconfigpngprocessxpspurrrquartoR6raggrappdirsRcppRcppTOMLreticulaterjsonrlangrmarkdownrprojrootRSQLiterstudioapirvgsassstringistringrsyssystemfontstextshapingtibbletidyrtidyselecttinytexutf8uuidvctrswithrxfunxml2yamlzip

D4TAlink.light - Manual
1. Introduction | 2. Installation | 3. Quick start | 4. Usage | 4.1. Parametrisation | 4.2. Analysis task | 4.3. Task content | 4.4. Create and render an R markdown file | 4.5. Create an R script | 4.6. Report data | 4.7. Transfer data between tasks | 4.8. Share a task | 4.9. R markdown and script templates | 4.10. Change directory structure
Rendered fromD4TAlink_basics.Rmdusingknitr::rmarkdown

Last update: 2024-12-02
Started: 2022-08-26

D4TAlink.light - Quick start
Rendered fromD4TAlink_quickstart.Rmdusingknitr::rmarkdown

Last update: 2024-12-02
Started: 2022-10-22

Readme and manuals

Help Manual

Help pageTopics
Create an archive containing the files of a given task.archiveTask
Get path of binary directory.binaryDir
Get path of binary file.binaryFn
Output R object using function cat.catReport
Get env var.D4getenv
Arguments used across the functions of the D4TAlink package.D4TAlink-common-args D4TAlink_common_args
'D4TAlinkTask' Documentation of the D4TAlinkTask classD4TAlinkTask
Get path of data source directory.datasourceDir
Get path of data source file.datasourceFn
Get path of documentation directory.docDir
Get path of documentation file.docFn
Generic function.DTx
Replace default task fields in 'docx' file.formatTaskDocx
Get the name of the task author.getTaskAuthor
Get the encryption key for binary data files.getTaskEnckey
Get the path of a file.getTaskFilepath
Get the paths of the task.getTaskPaths
Get the path to the Quarto task template.getTaskQmdTemplate
Get the path to the Rmd task template.getTaskRmdTemplate
Get the root of the task repository.getTaskRoot
Get the path to the R script task template.getTaskRscriptTemplate
Get the name of the task sponsor.getTaskSponsor
Get repository directory structure.getTaskStructure
Initialize a taskinitTask
Create task template in Quarto format.initTaskQmd
Create task template in Rmd format.initTaskRmd
Create task R script.initTaskRscript
Graphics devices for 'JPEG' format bitmap files.jpegReport
Get path of 'jpeg' output file.jpegReportFn
List the files associated to a task.listTaskFiles
List details of all tasks stored in the root directory.listTasks
Load a task.loadTask
Task paths generator.pathsDefault
Task paths generator.pathsGLPG
Task paths generator.pathsPMS
Graphics devices for 'pdf' format bitmap files.pdfReport
Get path of 'pdf' output file.pdfReportFn
Graphics devices for 'PNG' format bitmap files.pngReport
Get path of 'png' output file.pngReportFn
Get path of scripts directory.progDir
Get path of R script file name.qmdFn
Load data frame by querying an SQLite database. This function executes a SQL query on an SQLite database file created with 'saveSQLite'.querySQLite
Restore R object from binary file.readBinary
Restore R data.frame from Apache Arrow feather file.readFeather
Restore R data.frame from a Python pickle file.readPickle
Read JSON data into R object.readReportJSON
Read data into vector or list using function 'scan'.readReportTable
Load data frame from SQLite. This function reads a data frame from an SQLite database file created with 'saveSQLite'.readSQLite
Render the task from the Qmd filerenderTaskQmd
Render the task from the Rmd filerenderTaskRmd
Get path of report directory.reportDir
Get path of output file.reportFn
Get path of 'xlsx' output file.reportXlsFn
Restore an archive containing the files of a given task from a file created with archiveTask.restoreTask
Get path of R script file name.rmdFn
Get path of R script file name.rscriptFn
Save R object in binary file.saveBinary
Save R object in encrypted binary file.saveBinaryE
Save R object in Apache Arrow feather file.saveFeather
Save R object in Python pickle file.savePickle
Output R object in JSON format.saveReportJSON
Output R object using function 'write.csv'.saveReportTable
Save R object in binary file.saveReportXls
Save R data frame to SQLite file. This function saves a data frame to an SQLite database file. It can create indices on specified columns for faster querying. The database file is stored in the task's binary directory.saveSQLite
Read data into vector or list using function 'scan'.scanReport
Set the name of the tasks author.setTaskAuthor
Set the encryption key for binary data files.setTaskEnckey
Set the path to the Quarto task template.setTaskQmdTemplate
Set the path to the Rmd task template.setTaskRmdTemplate
Set the root of the task repository.setTaskRoot
Set the path to the R script task template.setTaskRscriptTemplate
Set the name of the tasks sponsor.setTaskSponsor
Set task repository directory structure.setTaskStructure
Get task identifier string.taskID