Merge branch 'develop'

OHDSI · Jan 21, 2022 · 0dbfe63 · 0dbfe63
2 parents 674c3d6 + f13c882
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diff --git a/.gitignore b/.gitignore
@@ -10,3 +10,5 @@
 # RStudio files
 .Rproj.user/
 .Rproj.user
+
+SignalInjectionTemp
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,47 +1,50 @@
-Package: MethodEvaluation
-Type: Package
-Title: Package for Evaluation of Estimation Methods
-Version: 2.1.0
-Date: 2021-03-19
-Authors@R: c(
-  person("Martijn", "Schuemie", , "[email protected]", role = c("aut", "cre"))
-  )
-Maintainer: Martijn Schuemie <[email protected]>
-Description: Resources for the evaluation of the
-	performance of methods that aim to estimate the magnitude (relative risk) of
-	the effect of a drug on an outcome. These resources include reference sets for
-	evaluating methods on real data, as well as functions for inserting simulated
-	effects in real data based on negative control drug-outcome pairs. Further
-	included are functions for the computation of the minimum detectable relative
-	risks and functions for computing performance statistics such as predictive
-	accuracy, error and bias.
-License: Apache License 2.0
-VignetteBuilder: knitr
-URL: https://github.com/OHDSI/MethodEvaluation
-BugReports: https://github.com/OHDSI/MethodEvaluation/issues
-Depends:
-  R (>= 3.2.0),
-  DatabaseConnector (>= 3.0.0),
-  FeatureExtraction (>= 3.0.0),
-  Cyclops (>= 3.0.0)
-Imports:
-  dplyr,
-  bit64,
-  readr,
-  purrr,
-  rlang,
-  SqlRender (>= 1.6.5),
-  pROC,
-  ggplot2,
-  ParallelLogger (>= 2.0.0),
-  methods,
-  EmpiricalCalibration
-Suggests:
-  testthat,
-  DT,
-  shiny,
-  knitr
-Remotes:
-  ohdsi/FeatureExtraction
-RoxygenNote: 7.1.1
-Encoding: UTF-8
+Package: MethodEvaluation
+Type: Package
+Title: Package for Evaluation of Estimation Methods
+Version: 2.2.0
+Date: 2022-01-21
+Authors@R: c(
+  person("Martijn", "Schuemie", , "[email protected]", role = c("aut", "cre"))
+  )
+Maintainer: Martijn Schuemie <[email protected]>
+Description: Resources for the evaluation of the
+	performance of methods that aim to estimate the magnitude (relative risk) of
+	the effect of a drug on an outcome. These resources include reference sets for
+	evaluating methods on real data, as well as functions for inserting simulated
+	effects in real data based on negative control drug-outcome pairs. Further
+	included are functions for the computation of the minimum detectable relative
+	risks and functions for computing performance statistics such as predictive
+	accuracy, error and bias.
+License: Apache License 2.0
+VignetteBuilder: knitr
+URL: https://github.com/OHDSI/MethodEvaluation
+BugReports: https://github.com/OHDSI/MethodEvaluation/issues
+Depends:
+  R (>= 3.2.0),
+  DatabaseConnector (>= 4.0.2),
+  FeatureExtraction (>= 3.0.0),
+  Cyclops (>= 3.0.0)
+Imports:
+  dplyr,
+  bit64,
+  readr,
+  purrr,
+  rlang,
+  SqlRender (>= 1.7.0),
+  pROC,
+  ggplot2,
+  ParallelLogger (>= 2.0.0),
+  methods,
+  EmpiricalCalibration
+Suggests:
+  Eunomia,
+  testthat,
+  DT,
+  shiny,
+  knitr,
+  rmarkdown
+Remotes:
+  ohdsi/FeatureExtraction,
+  ohdsi/Eunomia
+RoxygenNote: 7.1.2
+Encoding: UTF-8
diff --git a/MethodEvaluation.Rproj b/MethodEvaluation.Rproj
@@ -1,17 +1,17 @@
-Version: 1.0
-
-RestoreWorkspace: No
-SaveWorkspace: No
-AlwaysSaveHistory: No
-
-EnableCodeIndexing: Yes
-UseSpacesForTab: Yes
-NumSpacesForTab: 2
-Encoding: UTF-8
-
-RnwWeave: Sweave
-LaTeX: pdfLaTeX
-
-BuildType: Package
-PackageInstallArgs: --no-multiarch --with-keep.source
-PackageRoxygenize: rd,namespace
+Version: 1.0
+
+RestoreWorkspace: No
+SaveWorkspace: No
+AlwaysSaveHistory: No
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+BuildType: Package
+PackageInstallArgs: --no-multiarch --with-keep.source
+PackageRoxygenize: rd,namespace
diff --git a/NEWS.md b/NEWS.md
@@ -3,6 +3,16 @@ MethodEvaluation 2.1.0
 
 Changes:
 
+1. Updating from 'oracleTempSchema' to 'tempEmulationSchema' for newer versions of SqlRender.
+
+2. Added unit tests.
+
+
+MethodEvaluation 2.1.0
+======================
+
+Changes:
+
 1. Added 'ohdsiDevelopment' reference set, intended to be used when developing methods. This set is based on 76 negative controls from the LEGEND Hypertension study.
 
 2. Now generating cohort counts when generating reference set cohorts.

diff --git a/R/CreateReferenceSetCohorts.R b/R/CreateReferenceSetCohorts.R
diff --git a/R/Mdrr.R b/R/Mdrr.R
@@ -1,6 +1,6 @@
 # @file Mdrr.R
 #
-# Copyright 2021 Observational Health Data Sciences and Informatics
+# Copyright 2022 Observational Health Data Sciences and Informatics
 #
 # This file is part of MethodEvaluation
 # 
@@ -28,9 +28,10 @@
 #'                                 function \code{createConnectionDetails} in the
 #'                                 \code{DatabaseConnector} package.
 #' @param cdmDatabaseSchema        Name of database schema that contains OMOP CDM and vocabulary.
-#' @param oracleTempSchema         For Oracle only: the name of the database schema where you want all
-#'                                 temporary tables to be managed. Requires create/insert permissions
-#'                                 to this database.
+#' @param oracleTempSchema    DEPRECATED: use `tempEmulationSchema` instead.
+#' @param tempEmulationSchema Some database platforms like Oracle and Impala do not truly support temp tables. To
+#'                            emulate temp tables, provide a schema with write privileges where temp tables
+#'                            can be created.
 #' @param exposureOutcomePairs     A data frame with at least two columns:
 #'                                 \itemize{
 #'                                   \item {"exposureId" or "targetId" containing the drug_concept_ID or
@@ -80,13 +81,18 @@
 #' @export
 computeMdrr <- function(connectionDetails,
                         cdmDatabaseSchema,
-                        oracleTempSchema = cdmDatabaseSchema,
+                        oracleTempSchema = NULL,
+                        tempEmulationSchema = getOption("sqlRenderTempEmulationSchema"),
                         exposureOutcomePairs,
                         exposureDatabaseSchema = cdmDatabaseSchema,
                         exposureTable = "drug_era",
                         outcomeDatabaseSchema = cdmDatabaseSchema,
                         outcomeTable = "condition_era",
                         cdmVersion = "5") {
+  if (!is.null(oracleTempSchema) && oracleTempSchema != "") {
+    warning("The 'oracleTempSchema' argument is deprecated. Use 'tempEmulationSchema' instead.")
+    tempEmulationSchema <- oracleTempSchema
+  }
   if (is.null(exposureOutcomePairs$exposureId) && !is.null(exposureOutcomePairs$targetId))
     exposureOutcomePairs$exposureId <- exposureOutcomePairs$targetId
   if (is.null(exposureOutcomePairs$exposureId))
@@ -138,7 +144,7 @@ computeMdrr <- function(connectionDetails,
   renderedSql <- SqlRender::loadRenderTranslateSql("MDRR.sql",
                                                    packageName = "MethodEvaluation",
                                                    dbms = connectionDetails$dbms,
-                                                   oracleTempSchema = oracleTempSchema,
+                                                   tempEmulationSchema = tempEmulationSchema,
                                                    cdm_database_schema = cdmDatabaseSchema,
                                                    exposures_of_interest = unique(exposureOutcomePairs$exposureId),
                                                    outcomes_of_interest = unique(exposureOutcomePairs$outcomeId),
@@ -161,13 +167,13 @@ computeMdrr <- function(connectionDetails,
   sql <- "SELECT * FROM #mdrr"
   sql <- SqlRender::translate(sql,
                               targetDialect = connectionDetails$dbms,
-                              oracleTempSchema = oracleTempSchema)
+                              tempEmulationSchema = tempEmulationSchema)
   mdrr <- DatabaseConnector::querySql(conn, sql, snakeCaseToCamelCase = TRUE)
 
   renderedSql <- SqlRender::loadRenderTranslateSql("MDRR_Drop_temp_tables.sql",
                                                    packageName = "MethodEvaluation",
                                                    dbms = connectionDetails$dbms,
-                                                   oracleTempSchema = oracleTempSchema)
+                                                   tempEmulationSchema = tempEmulationSchema)
   DatabaseConnector::executeSql(conn, renderedSql, progressBar = FALSE, reportOverallTime = FALSE)
 
   mdrr <- data.frame(exposureId = mdrr$drugConceptId,

diff --git a/R/MethodEvaluation.R b/R/MethodEvaluation.R
@@ -1,6 +1,6 @@
 # @file MethodEvaluation.R
 #
-# Copyright 2021 Observational Health Data Sciences and Informatics
+# Copyright 2022 Observational Health Data Sciences and Informatics
 #
 # This file is part of MethodEvaluation
 # 

diff --git a/R/Metrics.R b/R/Metrics.R
@@ -1,6 +1,6 @@
 # @file Metrics.R
 #
-# Copyright 2021 Observational Health Data Sciences and Informatics
+# Copyright 2022 Observational Health Data Sciences and Informatics
 #
 # This file is part of MethodEvaluation
 # 

diff --git a/R/Plots.R b/R/Plots.R
@@ -1,6 +1,6 @@
 # @file Plots.R
 #
-# Copyright 2021 Observational Health Data Sciences and Informatics
+# Copyright 2022 Observational Health Data Sciences and Informatics
 #
 # This file is part of MethodEvaluation
 #