v0.1

DESCRIPTION

@@ -1,10 +1,22 @@
 Package: CohortSurvival
-Title: What the Package Does (One Line, Title Case)
-Version: 0.0.0.9000
-Authors@R: 
-    person("First", "Last", , "[email protected]", role = c("aut", "cre"),
-           comment = c(ORCID = "YOUR-ORCID-ID"))
-Description: What the package does (one paragraph).
+Title: Estimate survival using the OMOP Common Data Model
+Version: 0.1
+Authors@R: c(
+    person("Edward", "Burn", email = "[email protected]", 
+    role = c("aut", "cre"), 
+    comment = c(ORCID = "0000-0002-9286-1128")), 
+    person("Kim", "Lopez", email = "[email protected]", role = c("ctb"),
+    comment = c(ORCID = "0000-0002-8462-8668")),
+    person("Marti", "Catala", email = "[email protected]", 
+    role = c("ctb"), 
+    comment = c(ORCID = "0000-0003-3308-9905")),
+    person("Xintong", "Li", email = "[email protected]", 
+    role = c("ctb"), 
+    comment = c(ORCID = "0000-0003-3308-9905")),
+    person("Danielle", "Newby", email = "[email protected]", 
+    role = c("ctb"), 
+    comment = c(ORCID = "0000-0002-3001-1478")))
+Description: Estimate survival using data mapped to the Observational Medical Outcomes Partnership (OMOP) common data model. Survival can be estimated based on user-defined study cohorts.
 License: Apache License (>= 2)
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)

R/generateDeathCohort.R

@@ -8,6 +8,7 @@
 #' @param name name for the created death cohort table
 #' @param cohortTable name of the cohort table to create a death cohort for
 #' @param cohortId name of the cohort table to create a death cohort for
+#' @param overwrite	Should the cohort table be overwritten if it already exists?
 #'
 #' @return A cohort table with a death cohort in cdm
 #' @export
@@ -18,7 +19,8 @@ generateDeathCohortSet <- function(
     deathInObservation = FALSE,
     name = "death_cohort",
     cohortTable = NULL,
-    cohortId = NULL){
+    cohortId = NULL,
+    overwrite = FALSE){
 
   # 0. validate inputs...
   checkCdm(cdm, tables = c(
@@ -80,7 +82,9 @@ generateDeathCohortSet <- function(
     ) %>%
     CDMConnector::computeQuery(
       name = paste0(attr(cdm, "write_prefix"), name),
-      FALSE, attr(cdm, "write_schema"), TRUE
+      temporary = FALSE,
+      schema =  attr(cdm, "write_schema"),
+      overwrite = overwrite
     )
 
   cohortSetRef <- cohortRef %>%
@@ -89,7 +93,9 @@ generateDeathCohortSet <- function(
     dplyr::mutate(cohort_name = "death_cohort") %>%
     CDMConnector::computeQuery(
       name = paste0(attr(cdm, "write_prefix"), name, "_set"),
-      FALSE, attr(cdm, "write_schema"), TRUE
+      temporary = FALSE,
+      schema = attr(cdm, "write_schema"),
+      overwrite = overwrite
     )
 
   cohortCountRef <-  cohortRef %>%
@@ -101,15 +107,17 @@ generateDeathCohortSet <- function(
     ) %>%
     CDMConnector::computeQuery(
       name = paste0(attr(cdm, "write_prefix"), name, "_count"),
-      FALSE, attr(cdm, "write_schema"), TRUE
+      temporary = FALSE,
+      schema =  attr(cdm, "write_schema"),
+      overwrite = overwrite
     )
 
-
+  if(cohortRef %>% utils::head(5) %>% dplyr::tally() %>% dplyr::pull("n") > 0){
   cdm[[name]] <- CDMConnector::newGeneratedCohortSet(
     cohortRef = cohortRef,
     cohortSetRef = cohortSetRef,
     cohortCountRef = cohortCountRef
-  )
+  )}
 
   attr(cdm[[name]], "cohort_attrition") <- tibble::tibble(
     "reason" = "Qualifying initial records",

R/suppressSurvivalCounts.R

@@ -27,15 +27,15 @@ for(i in seq_along(toObscure$group_name)){
       .data$strata_name == toObscure$strata_name[i]  &
       .data$strata_level == toObscure$strata_level[i]  &
       .data$variable_type == "n_start", paste0("<", minCellCount),
-      as.character(estimate))) %>%
+      as.character(.data$estimate))) %>%
     dplyr::mutate(estimate = dplyr::if_else(
       .data$group_name == toObscure$group_name[i] &
         .data$group_level == toObscure$group_level[i] &
         .data$strata_name == toObscure$strata_name[i]  &
         .data$strata_level == toObscure$strata_level[i]  &
         .data$variable_type != "n_start",
       as.character(NA),
-      as.character(estimate)))
+      as.character(.data$estimate)))
 }
   }