R/Helpers.R

In OHDSI/SkeletonPredictionStudy: A Skeleton for Prediction Development Studies that use the PatientLevelPrediction Framework

# Borrowed from devtools: https://github.com/hadley/devtools/blob/ba7a5a4abd8258c52cb156e7b26bb4bf47a79f0b/R/utils.r#L44
is_installed <- function (pkg, version = 0) {
  installed_version <- tryCatch(utils::packageVersion(pkg), 
                                error = function(e) NA)
  !is.na(installed_version) && installed_version >= version
}

# Borrowed and adapted from devtools: https://github.com/hadley/devtools/blob/ba7a5a4abd8258c52cb156e7b26bb4bf47a79f0b/R/utils.r#L74
ensure_installed <- function(pkg) {
  if (!is_installed(pkg)) {
    msg <- paste0(sQuote(pkg), " must be installed for this functionality.")
    if (interactive()) {
      message(msg, "\nWould you like to install it?")
      if (utils::menu(c("Yes", "No")) == 1) {
        if(pkg%in%c('Hydra', 'CirceR')){
          if(!is_installed('devtools')){
            utils::install.packages('devtools')
          }
          devtools::install_github(paste0('OHDSI/',pkg))
        }else{
          utils::install.packages(pkg)
        }
      } else {
        stop(msg, call. = FALSE)
      }
    } else {
      stop(msg, call. = FALSE)
    }
  }
}



addCohortSettings <- function(
  covariateSettings, 
  cohortDatabaseSchema, 
  cohortTable
){
  
  if(class(covariateSettings) == 'covariateSettings'){
    covariateSettings <- list(covariateSettings)
  }
  
  # set the cohort table and database to the settings where the cohorts were generated
  for(i in 1:length(covariateSettings)){
    
    if('cohortTable' %in% names(covariateSettings[[i]])){
      covariateSettings[[i]]$cohortTable <- cohortTable
    }
    
    if('cohortDatabaseSchema' %in% names(covariateSettings[[i]])){
      covariateSettings[[i]]$cohortDatabaseSchema <- cohortDatabaseSchema
    }
    
  }
  
  return(covariateSettings)
}