Package: sendigR 1.0.0

Wenxian Wang

sendigR: Enable Cross-Study Analysis of 'CDISC' 'SEND' Datasets

A system enables cross study Analysis by extracting and filtering study data for control animals from 'CDISC' 'SEND' Study Repository. These data types are supported: Body Weights, Laboratory test results and Microscopic findings. These database types are supported: 'SQLite' and 'Oracle'.

Authors:Bo Larsen [aut], Yousuf Ali [aut], Kevin Snyder [aut], William Houser [aut], Brianna Paisley [aut], Cmsabbir Ahmed [aut], Susan Butler [aut], Michael Rosentreter [aut], Michael Denieu [aut], Wenxian Wang [cre, aut], BioCelerate [cph]

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sendigR.pdf |sendigR.html✨
sendigR/json (API)

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

Peer review:

Bug tracker:https://github.com/phuse-org/sendigr/issues

On CRAN:

21 exports 12 stars 1.87 score 130 dependencies 6 scripts 235 downloads

Last updated 9 months agofrom:5f21ce37fd. Checks:OK: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 13 2024
R-4.5-winWARNINGSep 13 2024
R-4.5-linuxWARNINGSep 13 2024
R-4.4-winWARNINGSep 13 2024
R-4.4-macWARNINGSep 13 2024
R-4.3-winWARNINGSep 13 2024
R-4.3-macWARNINGSep 13 2024

Exports:dbCreateIndexesdbCreateSchemadbDeleteStudiesdbImportOneStudydbImportStudiesdisconnectDBexecSendDashboardgen_vocabgenericQuerygetControlSubjgetFindingsPhasegetFindingsSubjAgegetStudiesSDESIGNgetStudiesSTSTDTCgetSubjDatagetSubjRoutegetSubjSexgetSubjSpeciesStraingetTabColLabelsinitEnvironmentstandardize_file

Dependencies:askpassassertthatbackportsbase64encbitbit64blobbootbslibcachemcellrangercheckmateciceroneclassclicliprclustercolorspacecommonmarkcpp11crayoncrosstalkcurldata.tabledatawizardDBIDescToolsdigestdplyrDTe1071evaluateExactexpmfansifarverfastmapfontawesomeforcatsforeignFormulafsgenericsggplot2gldgluegridExtragtablehavenherehighrHmischmshtmlTablehtmltoolshtmlwidgetshttpuvhttrinsightisobandjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclelmommagrittrMASSMatrixmemoisemgcvmimemunsellmvtnormnlmennetopensslparsedatepillarpkgconfigplogrplotlypngprettyunitsprogresspromisesproxypurrrR6rappdirsRColorBrewerRcppRcppTOMLreadrreadxlrematchreticulaterlangrmarkdownrootSolverpartrprojrootRSQLiterstudioapisassscalesshinyshinydashboardsjlabelledsourcetoolsstringistringrsystibbletidyrtidyselecttinytextzdbutf8vctrsviridisviridisLitevroomwithrxfunxtableyaml

Introduction to sendigR

Rendered fromIntroduction.Rmdusingknitr::rmarkdownon Sep 13 2024.

Last update: 2022-08-09
Started: 2021-03-17

Using xptcleaner

Rendered fromUsingxptcleaner.Rmdusingknitr::rmarkdownon Sep 13 2024.

Last update: 2022-07-16
Started: 2022-05-19

Readme and manuals

Help Manual

Help pageTopics
Create indexes in SEND databasedbCreateIndexes
Create a SEND schema in an open and empty databasedbCreateSchema
Delete one or more studies in SEND databasedbDeleteStudies
Import SEND study data in SAS xport format into a SEND database from a single study folderdbImportOneStudy
Import SEND study data in SAS xport format into a SEND database from a hierarchy study folders.dbImportStudies
Disconnect from the open database.disconnectDB
Execute sendDashboard appexecSendDashboard
Create json file for vocabulary mappings. Keys are synonyms and values are the CDISC Controlled Terminology Submission values. Vocabularies are defined by column values from the tab-delimited files.gen_vocab
Execute database query and returns fetched rows.genericQuery
Extract a list of control animals for a list of studiesgetControlSubj
Extract a set of findings for a specified study phase - or just add phase for each animal.getFindingsPhase
Add the subject age at finding time - and optionally extract the set of findings within a specified range of age.getFindingsSubjAge
Extract a list of SEND studies with a specified study design - or just add actual study design for each study.getStudiesSDESIGN
Extract a list of SEND studies with study start date within a specified interval - or just add actual study start date for each studygetStudiesSTSTDTC
Extract data from a subject level domain.getSubjData
Extract the set of animals of the specified route of administration - or just add actual route of administration for each animal.getSubjRoute
Extract the set of animals of the specified sex - or just add the sex of each animal.getSubjSex
Extract the set of animals of the specified species and strain - or just add the species and strain for each animal.getSubjSpeciesStrain
Get labels for columns in a data.tablegetTabColLabels
Initialize the environment.initEnvironment
Standardizes SEND xpt files using CDISC controlled terminologiesstandardize_file