Update docs for aggregated setting (#243)

R/GetCovariates.R

@@ -58,8 +58,12 @@
 #' @param covariateSettings      Either an object of type \code{covariateSettings} as created using one
 #'                               of the createCovariate functions, or a list of such objects.
 #' @param aggregated             Should aggregate statistics be computed instead of covariates per
-#'                               cohort entry?
-#' @param minCharacterizationMean The minimum mean value for characterization output. Values below this will be cut off from output. This
+#'                               cohort entry? If aggregated is set to FALSE, the results returned will be based 
+#'                               on each subject_id and cohort_start_date in your cohort table. If your cohort 
+#'                               contains multiple entries for the same subject_id (due to different cohort_start_date values), 
+#'                               you must carefully set the rowIdField so you can identify the patients properly.
+#'                               See issue #229 for more discussion on this parameter.
+#' @param minCharacterizationMean The minimum mean value for characterization output. Values below this will be cut off from output. This 
 #'                                will help reduce the file size of the characterization output, but will remove information
 #'                                on covariates that have very low values. The default is 0.
 #'

tests/testOracle.R

@@ -3,4 +3,4 @@ options(dbms = "oracle")
 runTestsOnOracle <- !(Sys.getenv("CDM5_ORACLE_USER") == "" & Sys.getenv("CDM5_ORACLE_PASSWORD") == "" & Sys.getenv("CDM5_ORACLE_SERVER") == "" & Sys.getenv("CDM5_ORACLE_CDM_SCHEMA") == "" & Sys.getenv("CDM5_ORACLE_OHDSI_SCHEMA") == "")
 if (runTestsOnOracle) {
   test_check("FeatureExtraction")
-}
+}

tests/testPostgres.R

@@ -3,4 +3,4 @@ options(dbms = "postgresql")
 runTestsOnPostgreSQL <- !(Sys.getenv("CDM5_POSTGRESQL_USER") == "" & Sys.getenv("CDM5_POSTGRESQL_PASSWORD") == "" & Sys.getenv("CDM5_POSTGRESQL_SERVER") == "" & Sys.getenv("CDM5_POSTGRESQL_CDM_SCHEMA") == "" & Sys.getenv("CDM5_POSTGRESQL_OHDSI_SCHEMA") == "")
 if (runTestsOnPostgreSQL) {
   test_check("FeatureExtraction")
-}
+}

tests/testRedshift.R

@@ -1,6 +1,6 @@
 library(testthat)
 options(dbms = "redshift")
-runTestsOnRedshift <- FALSE # !(Sys.getenv("CDM5_REDSHIFT_USER") == "" & Sys.getenv("CDM5_REDSHIFT_PASSWORD") == "" & Sys.getenv("CDM5_REDSHIFT_SERVER") == "" & Sys.getenv("CDM5_REDSHIFT_CDM_SCHEMA") == "" & Sys.getenv("CDM5_REDSHIFT_OHDSI_SCHEMA") == "")
-if (runTestsOnRedshift) {
+runTestsOnRedshift <- FALSE #!(Sys.getenv("CDM5_REDSHIFT_USER") == "" & Sys.getenv("CDM5_REDSHIFT_PASSWORD") == "" & Sys.getenv("CDM5_REDSHIFT_SERVER") == "" & Sys.getenv("CDM5_REDSHIFT_CDM_SCHEMA") == "" & Sys.getenv("CDM5_REDSHIFT_OHDSI_SCHEMA") == "")
+if (runTestsOnRedshift) {  
   test_check("FeatureExtraction")
-}
+}

tests/testSqlServer.R

@@ -3,4 +3,4 @@ options(dbms = "sql server")
 runTestsOnSQLServer <- !(Sys.getenv("CDM5_SQL_SERVER_USER") == "" & Sys.getenv("CDM5_SQL_SERVER_PASSWORD") == "" & Sys.getenv("CDM5_SQL_SERVER_SERVER") == "" & Sys.getenv("CDM5_SQL_SERVER_CDM_SCHEMA") == "" & Sys.getenv("CDM5_SQL_SERVER_OHDSI_SCHEMA") == "")
 if (runTestsOnSQLServer) {
   test_check("FeatureExtraction")
-}
+}