This package contains functions for extracting characterization, estimation and prediction results from the OHDSI result database (see https://ohdsi.github.io/Strategus/results-schema/index.html).
It also contains codes to create useful plots, presentations templates and report templates.
Download this repository and using RStudio, install the package. Then you can make use of the report generator by running:
# Install OhdsiReportGenerator using remotes}
install.packages('remotes')
remotes::install_github('OHDSI/OhdsiReportGenerator')
# Load the library to start using it
library(OhdsiReportGenerator)
# to run the report generator with a demo set of results
conDet <- OhdsiReportGenerator:::getExampleConnectionDetails()
# render a quarto template report with the results in the
# example database for targetId 1 and outcomeId 3.
generatePresentation(
server = conDet$server(),
username = conDet$user(),
password = conDet$password(),
dbms = conDet$dbms,
resultsSchema = 'main',
dbDetails = NULL,
lead = 'John Doe',
team = 'name 1, name 2',
trigger = 'A signal was found in spontaneous reports',
safetyQuestion = '',
objective = '',
date = as.character(Sys.Date()),
targetId = 1,
outcomeIds = 3,
cohortNames = c('target','outcome'),
cohortIds = c(1,3),
covariateIds = NULL,
details = list(
studyPeriod = 'All Time',
restrictions = "Age - None"
),
evaluationText = '',
includeCI = TRUE,
includeCharacterization = TRUE,
includeCM = TRUE,
includeSCCS = TRUE,
includePLP = FALSE,
outputLocation = file.path(getwd(), "extras/reportTest"),
outputName = paste0('presentation_', gsub(':', '_',gsub(' ','_',as.character(date()))),'.html')
intermediateDir = tempdir()
)
OhdsiReportGenerator is an R package.
Running the package requires R and Java.
OhdsiReportGenerator is licensed under Apache License 2.0.
OhdsiReportGenerator is being developed in R Studio.
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