## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

## ----setup--------------------------------------------------------------------
library(tidyOhdsiSolutions)

## -----------------------------------------------------------------------------
diabetes_df <- data.frame(
  concept_id       = c(201826L, 442793L),
  concept_name     = c("Type 2 diabetes mellitus",
                        "Diabetes mellitus due to insulin resistance"),
  domain_id        = c("Condition", "Condition"),
  vocabulary_id    = c("SNOMED", "SNOMED"),
  standard_concept = c("S", "S"),
  descendants      = c(TRUE, TRUE),
  excluded         = c(FALSE, FALSE)
)

hypertension_df <- data.frame(
  concept_id       = 320128L,
  concept_name     = "Essential hypertension",
  domain_id        = "Condition",
  vocabulary_id    = "SNOMED",
  standard_concept = "S",
  descendants      = TRUE,
  excluded         = FALSE
)

## -----------------------------------------------------------------------------
diabetes_cs     <- toConceptSet(diabetes_df, name = "Type 2 Diabetes")
hypertension_cs <- toConceptSet(hypertension_df, name = "Hypertension")

## -----------------------------------------------------------------------------
all_cs <- toConceptSets(list(
  "Type 2 Diabetes" = diabetes_df,
  "Hypertension"    = hypertension_df
))

## -----------------------------------------------------------------------------
cohort <- cohortFromConceptSet(
  conceptSetList = all_cs,
  limit          = "earliest",
  requiredObservation = c(365L, 0L),
  end            = "observation_period_end_date"
)

## -----------------------------------------------------------------------------
json <- cohortToJson(cohort)
cat(substr(json, 1, 300), "...\n")

## ----eval = FALSE-------------------------------------------------------------
# writeLines(json, "my_cohort.json")

## -----------------------------------------------------------------------------
cohort_obs <- cohortFromConceptSet(
  all_cs,
  end = "observation_period_end_date"
)

## -----------------------------------------------------------------------------
cohort_fixed <- cohortFromConceptSet(
  all_cs,
  end     = "fixed_exit",
  endArgs = list(index = "startDate", offsetDays = 180)
)

# Verify
cohort_fixed$EndStrategy$DateOffset

## -----------------------------------------------------------------------------
drug_df <- data.frame(
  concept_id   = 1503297L,
  concept_name = "Metformin",
  domain_id    = "Drug",
  vocabulary_id = "RxNorm",
  standard_concept = "S",
  descendants  = TRUE,
  excluded     = FALSE
)

drug_cs <- toConceptSets(list("Metformin" = drug_df))

cohort_drug <- cohortFromConceptSet(
  drug_cs,
  end     = "drug_exit",
  endArgs = list(persistenceWindow = 30, surveillanceWindow = 7)
)

# Verify
cohort_drug$EndStrategy$CustomEra

## -----------------------------------------------------------------------------
# Keep only the earliest qualifying event per person
earliest <- cohortFromConceptSet(all_cs, limit = "earliest")
earliest$PrimaryCriteria$PrimaryCriteriaLimit$Type

# Keep all qualifying events
all_events <- cohortFromConceptSet(all_cs, limit = "all")
all_events$PrimaryCriteria$PrimaryCriteriaLimit$Type

# Keep only the latest qualifying event
latest <- cohortFromConceptSet(all_cs, limit = "latest")
latest$PrimaryCriteria$PrimaryCriteriaLimit$Type

## -----------------------------------------------------------------------------
cohort_src <- cohortFromConceptSet(all_cs, addSourceCriteria = TRUE)
length(cohort_src$PrimaryCriteria$CriteriaList)

# Without source criteria
cohort_plain <- cohortFromConceptSet(all_cs, addSourceCriteria = FALSE)
length(cohort_plain$PrimaryCriteria$CriteriaList)

## -----------------------------------------------------------------------------
names(cohort)

## -----------------------------------------------------------------------------
# Number of concept sets
length(cohort$ConceptSets)

# Names of concept sets
vapply(cohort$ConceptSets, `[[`, character(1), "name")

# Observation window
cohort$PrimaryCriteria$ObservationWindow