Function reference • sendigR

Database

Create database, add and delete studies

initEnvironment(): Initialize the environment.

dbCreateIndexes(): Create indexes in SEND database

dbCreateSchema(): Create a SEND schema in an open and empty database

dbDeleteStudies(): Delete one or more studies in SEND database

dbImportOneStudy(): Import SEND study data in SAS xport format into a SEND database from a single study folder

dbImportStudies(): Import SEND study data in SAS xport format into a SEND database from a hierarchy study folders.

disconnectDB(): Disconnect from the open database.

Query Control Animal

Get control animal information

genericQuery(): Execute database query and returns fetched rows.

getControlSubj(): Extract a list of control animals for a list of studies

getFindingsPhase(): Extract a set of findings for a specified study phase - or just add phase for each animal.

getFindingsSubjAge(): Add the subject age at finding time - and optionally extract the set of findings within a specified range of age.

getStudiesSDESIGN(): Extract a list of SEND studies with a specified study design - or just add actual study design for each study.

getStudiesSTSTDTC(): Extract a list of SEND studies with study start date within a specified interval - or just add actual study start date for each study

getSubjData(): Extract data from a subject level domain.

getSubjRoute(): Extract the set of animals of the specified route of administration - or just add actual route of administration for each animal.

getSubjSex(): Extract the set of animals of the specified sex - or just add the sex of each animal.

getSubjSpeciesStrain(): Extract the set of animals of the specified species and strain - or just add the species and strain for each animal.

Shiny App

Run shiny app

execSendDashboard(): Execute sendDashboard app

xptcleaner

Clean xpt files

gen_vocab(): 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.

standardize_file(): Standardizes SEND xpt files using CDISC controlled terminologies

Helper

Helper functions

getTabColLabels(): Get labels for columns in a data.table