Package: sendigR 1.0.2

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]

sendigR_1.0.2.tar.gz
sendigR_1.0.2.zip(r-4.7-any)sendigR_1.0.2.zip(r-4.6-any)sendigR_1.0.2.zip(r-4.5-any)
sendigR_1.0.2.tgz(r-4.6-any)sendigR_1.0.2.tgz(r-4.5-any)
sendigR_1.0.2.tar.gz(r-4.7-any)sendigR_1.0.2.tar.gz(r-4.6-any)
sendigR_1.0.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
sendigR/json (API)

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

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

On CRAN:

Conda:

5.62 score 14 stars 8 scripts 313 downloads 21 exports 129 dependencies

Last updated from:beb4a17066. Checks:7 WARNING, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64WARNING229
source / vignettesOK199
linux-release-x86_64WARNING178
macos-release-arm64WARNING127
macos-oldrel-arm64WARNING74
windows-develWARNING99
windows-releaseWARNING91
windows-oldrelWARNING96
wasm-releaseOK175

Exports:dbCreateIndexesdbCreateSchemadbDeleteStudiesdbImportOneStudydbImportStudiesdisconnectDBexecSendDashboardgen_vocabgenericQuerygetControlSubjgetFindingsPhasegetFindingsSubjAgegetStudiesSDESIGNgetStudiesSTSTDTCgetSubjDatagetSubjRoutegetSubjSexgetSubjSpeciesStraingetTabColLabelsinitEnvironmentstandardize_file

Dependencies:askpassassertthatbackportsbase64encbitbit64blobbootbslibcachemcellrangercheckmateciceroneclassclicliprclustercolorspacecommonmarkcpp11crayoncrosstalkcurldata.tabledatawizardDBIDescToolsdigestdplyrDTe1071evaluateExactexpmfarverfastmapfontawesomeforcatsforeignFormulafsgenericsggplot2gldgluegridExtragtablehavenherehighrHmischmshtmlTablehtmltoolshtmlwidgetshttpuvhttrinsightisobandjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclelmomlubridatemagrittrMASSMatrixmemoisemimemvtnormnnetopensslotelparsedatepillarpkgconfigplotlypngprettyunitsprogresspromisesproxypurrrR6rappdirsRColorBrewerRcppRcppTOMLreadrreadxlrematchreticulaterlangrmarkdownrootSolverpartRPostgresrprojrootRSQLiterstudioapiS7sassscalesshinyshinydashboardsjlabelledsourcetoolsstringistringrsystibbletidyrtidyselecttimechangetinytextzdbutf8vctrsviridisLitevroomwithrxfunxtableyaml

Introduction to sendigR
Getting started | Package dependencies | Database | Study data to import | SEND controlled terminology | Function overview. | Initiation and closure of SEND environment | Build a SQLite SEND database | Examples | Extract and filter SEND data | Example | Execute sendDashboard app
Rendered fromIntroduction.Rmdusingknitr::rmarkdown

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

Using xptcleaner
Description of Vignette | Getting started | xptcleaner python package and sendigR R package installation | Python and R installation | xptcleaner python package installation | Using pip | Using source archive or using wheel file. | sendigR R package installation | Locating the scripts | Creating the JSON for Vocabulary Mapping | Standardize xpt files with the json file created
Rendered fromUsingxptcleaner.Rmdusingknitr::rmarkdown

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