DownloadCohorts.R

################################################################################
# INSTRUCTIONS: This script assumes you have cohorts you would like to use in an
# ATLAS instance. Please note you will need to update the baseUrl to match
# the settings for your enviroment. You will also want to change the 
# CohortGenerator::saveCohortDefinitionSet() function call arguments to identify
# a folder to store your cohorts. This code will store the cohorts in 
# "inst/sampleStudy" as part of the template for reference. You should store
# your settings in the root of the "inst" folder and consider removing the 
# "inst/sampleStudy" resources when you are ready to release your study.
# 
# See the Download cohorts section
# of the UsingThisTemplate.md for more details.
# ##############################################################################

# remotes::install_github("OHDSI/ROhdsiWebApi")
library(dplyr)
# baseUrl <- "https://atlas-demo.ohdsi.org/WebAPI"
baseUrl <- Sys.getenv("baseUrl")
# Use this if your WebAPI instance has security enables
ROhdsiWebApi::authorizeWebApi(
  baseUrl = baseUrl,
  authMethod = "windows"
)
cohortDefinitionSet <- ROhdsiWebApi::exportCohortDefinitionSet(
  baseUrl = baseUrl,
  cohortIds = c(
     19018, # GLP-1
     19019, # DPP-4
     16968  # ALI
  ),
  generateStats = TRUE
)
readr::write_csv(cohortDefinitionSet, "inst/Cohorts.csv")

# 
# # Rename cohorts
# cohortDefinitionSet[cohortDefinitionSet$cohortId == 467,]$cohortName <- "GLP-1"
# cohortDefinitionSet[cohortDefinitionSet$cohortId == 468,]$cohortName <- "DPP-4"
# cohortDefinitionSet[cohortDefinitionSet$cohortId == 475,]$cohortName <- "GLP1R user (vs SGLT2i)"
# cohortDefinitionSet[cohortDefinitionSet$cohortId == 477,]$cohortName <- "SGLT2i user (vs GLR1Ra)"
# 
# #### Re-number cohorts####
# # GLP1Ra vs DPP4i
# cohortDefinitionSet[cohortDefinitionSet$cohortId == 467,]$cohortId <- 11
# cohortDefinitionSet[cohortDefinitionSet$cohortId == 468,]$cohortId <- 12
# 
# # GLP1Ra vs DPP4i
# cohortDefinitionSet[cohortDefinitionSet$cohortId == 475,]$cohortId <- 21
# cohortDefinitionSet[cohortDefinitionSet$cohortId == 477,]$cohortId <- 22
# 
# # outcomes
# cohortDefinitionSet[cohortDefinitionSet$cohortId == 469,]$cohortId <- 101
# cohortDefinitionSet[cohortDefinitionSet$cohortId == 480,]$cohortId <- 102
# cohortDefinitionSet[cohortDefinitionSet$cohortId == 484,]$cohortId <- 103
# 
# cohortDefinitionSet[cohortDefinitionSet$cohortId == 471,]$cohortId <- 201
# cohortDefinitionSet[cohortDefinitionSet$cohortId == 472,]$cohortId <- 202
# cohortDefinitionSet[cohortDefinitionSet$cohortId == 473,]$cohortId <- 301
# 
# # Save the cohort definition set
# # NOTE: Update settingsFileName, jsonFolder and sqlFolder
# # for your study.
# CohortGenerator::saveCohortDefinitionSet(
#   cohortDefinitionSet = cohortDefinitionSet,
#   settingsFileName = "inst/Cohorts.csv",
#   jsonFolder = "inst/cohorts",
#   sqlFolder = "inst/sql/sql_server",
# )

# Download and save the covariates to exclude
covariatesToExcludeConceptSet <- ROhdsiWebApi::getConceptSetDefinition(
  conceptSetId = 436,
  baseUrl = baseUrl
) %>%
  ROhdsiWebApi::resolveConceptSet(
    baseUrl = baseUrl
  ) %>%
  ROhdsiWebApi::getConcepts(
    baseUrl = baseUrl
  ) # %>%
#   rename(outcomeConceptId = "conceptId",
#          cohortName = "conceptName") %>%
#   mutate(cohortId = row_number() + 100) %>%
#   select(cohortId, cohortName, outcomeConceptId)

# NOTE: Update file location for your study.
CohortGenerator::writeCsv(
  x = covariatesToExcludeConceptSet,
  file = "inst/excludedCovariateConcepts.csv",
  warnOnFileNameCaseMismatch = F
)

# Download and save the negative control outcomes
negativeControlOutcomeCohortSet <- ROhdsiWebApi::getConceptSetDefinition(
  conceptSetId = 437,
  baseUrl = baseUrl
) %>%
  ROhdsiWebApi::resolveConceptSet(
    baseUrl = baseUrl
  ) %>%
  ROhdsiWebApi::getConcepts(
    baseUrl = baseUrl
  ) %>%
  rename(outcomeConceptId = "conceptId",
         cohortName = "conceptName") %>%
  mutate(cohortId = row_number() + 10000) %>%
  select(cohortId, cohortName, outcomeConceptId)

# NOTE: Update file location for your study.
CohortGenerator::writeCsv(
  x = negativeControlOutcomeCohortSet,
  file = "inst/negativeControlOutcomes.csv",
  warnOnFileNameCaseMismatch = F
)