In opalr: 'Opal' Data Repository Client and 'DataSHIELD' Utils

#
# Global settings
#
url <- getOption("opal.url", "https://opal-demo.obiba.org")
username <- getOption("opal.username", "administrator")
password <- getOption("opal.password", "password")
datasource <- getOption("opal.datasource", "FNAC")
table <- getOption("opal.table", "FNAC")
withStatistics <- getOption("opal.withStatistics", TRUE)
withGraphs <- getOption("opal.withGraphs", TRUE)

# set up dictionary and data
library(opalr)
o <- opal.login(username, password, url)
variables <- opal.variables(o, datasource, table)
t <- opal.table(o, datasource, table, counts=TRUE)
if (withStatistics | withGraphs) {
  opal.execute(o, 'require(e1071)')
  opal.assign(o,'D', paste0(datasource, ".", table))
}
if (withGraphs) {
  require(ggplot2)
  opal.execute(o, 'require(ggplot2)')
}

r table Data Dictionary

Name of the report | Data Dictionary for r table ---------------------- | ------------------- Project | r datasource Table | r table Number of variables | r t$variableCount Number of participants | r t$valueSetCount Date | r as.character(Sys.Date())

Variables

for (i in 1:nrow(variables)) {
  variable <- variables[i,]
  cat(paste0("* [", variable$name, "](#", gsub("\\.","_",variable$name),")\n"))
}

out <- NULL
for (i in 1:nrow(variables)) {
  variable <- variables[i,]
  out <- c(out, knitr::knit_child('opal-variable.Rmd'), sep='\n')
}

r paste(out, collapse='\n')

opal.logout(o)

opalr documentation built on Sept. 18, 2024, 9:11 a.m.