Merge pull request #769 from 1Anuar/add-dbSummary

Add db summary

NAMESPACE

@@ -23,6 +23,7 @@ export(exportToAres)
 export(exportToJson)
 export(exportVisitDetailToJson)
 export(exportVisitToJson)
+export(generateDbSummary)
 export(getAnalysisDetails)
 export(getSeasonalityScore)
 export(getTemporalData)

R/generateDbSummary.R

@@ -0,0 +1,124 @@
+# @file generateDbSummary
+#
+# Copyright 2021 Observational Health Data Sciences and Informatics
+#
+# This file is part of Achilles
+# 
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+# 
+#     https://www.apache.org/licenses/LICENSE-2.0
+# 
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
+#' @title
+#' generateDbSummary
+#'
+#' @description
+#' \code{generateDbSummary} can be run after the Achilles analyses are complete 
+#' to create a high-level database summary.
+#'
+#' @details
+#' Used to generate a high-level database summary consisting of earliest date available, latest
+#' date available, median age at first observation, total persons, etc. This function
+#' creates a summary table meant for a manuscript detailing the network of databases
+#' used in an analysis
+#'
+#' @param connectionDetails       An R object of type \code{connectionDetails} created using the
+#'                                function \code{createConnectionDetails} in the
+#'                                \code{DatabaseConnector} package.
+#' @param cdmDatabaseSchema       Fully qualified name of database schema that contains OMOP CDM
+#'                                schema. On SQL Server, this should specifiy both the database and the
+#'                                schema, so for example, on SQL Server, 'cdm_instance.dbo'.
+#' @param resultsDatabaseSchema   Fully qualified name of database schema that we can write final
+#'                                results to. Default is cdmDatabaseSchema. On SQL Server, this should
+#'                                specifiy both the database and the schema, so for example, on SQL
+#'                                Server, 'cdm_results.dbo'.
+#' @param country                 The country of origin of the database
+#' @param provenance              The provenance of the data (EHR, claims, registry, etc)
+#'
+#' @return
+#' none
+#'
+#' @examples
+#' \dontrun{
+#' connectionDetails <- DatabaseConnector::createConnectionDetails(dbms = "sql server",
+#'                                                                 server = "yourserver")
+#' dbSummary <- generateDbSummary(connectionDetails,
+#'                                cdmDatabaseSchema = "cdm_schema",
+#'                                resultsDatabaseSchema = "results_schema",
+#'                                country = "Country of Origin",
+#'                                provenance = "Provenance of data")
+#' }
+#' @export
+
+generateDbSummary <- function (connectionDetails,
+                               cdmDatabaseSchema,
+                               resultsDatabaseSchema,
+                               country,
+                               provenance){
+
+  conn <- DatabaseConnector::connect(connectionDetails)
+
+  sql <-
+    SqlRender::loadRenderTranslateSql(
+      sqlFilename = "summary/generateDbSummary.sql",
+      packageName = "Achilles",
+      dbms = connectionDetails$dbms,
+      warnOnMissingParameters = FALSE,
+      cdm_database_schema = cdmDatabaseSchema,
+      results_database_schema = resultsDatabaseSchema,
+      country = country,
+      provenance = provenance
+    )
+
+  dbSummary <- DatabaseConnector::querySql(conn, sql)
+
+  sql <-
+    SqlRender::loadRenderTranslateSql(
+      sqlFilename = "summary/dbSourceVocabs.sql",
+      packageName = "Achilles",
+      dbms = connectionDetails$dbms,
+      warnOnMissingParameters = FALSE,
+      cdm_database_schema = cdmDatabaseSchema,
+      results_database_schema = resultsDatabaseSchema,
+      country = country,
+      provenance = provenance
+    )
+
+  dbSourceVocabs <- DatabaseConnector::querySql(conn, sql)
+
+  sql <-
+    SqlRender::loadRenderTranslateSql(
+      sqlFilename = "summary/dbVisitDist.sql",
+      packageName = "Achilles",
+      dbms = connectionDetails$dbms,
+      warnOnMissingParameters = FALSE,
+      cdm_database_schema = cdmDatabaseSchema,
+      results_database_schema = resultsDatabaseSchema,
+      country = country,
+      provenance = provenance
+    )
+
+  dbVisitDist <- DatabaseConnector::querySql(conn, sql)
+
+  DatabaseConnector::dbDisconnect(conn)
+
+  # extract columns and pivot
+  dbInfo <- dbSummary[1,c(1,2,3,4)]
+  row.names(dbSummary) <- dbSummary$ATTRIBUTE_NAME
+  df <- dbSummary[,c('ATTRIBUTE_VALUE')]
+  df_t <- t(df)
+  colnames(df_t) <- rownames(dbSummary)
+  dbSummaryFinal <- cbind(dbInfo, df_t)
+
+  colnames(dbSummaryFinal)[1:4] <- c("Data Source Name", "Data Source Abbreviation", "Source Country", "Data Provenance")
+
+  return(list(summary=dbSummaryFinal, visitDist=dbVisitDist, sourceVocabs = dbSourceVocabs))
+}

extras/GenerateDatabaseSummary.R

@@ -6,12 +6,31 @@ options(connectionObserver = NULL)
 
 demoCountry <- "United States"
 demoProvenance <- "Synthetic"
+connectionDetails <- Eunomia::getEunomiaConnectionDetails()
 
-dbSummary <- generateDbSummary(connectionDetails, cdmDatabaseSchema, resultsDatabaseSchema,demoCountry,demoProvenance)
+cdmDatabaseSchema <- "main"
+resultsDatabaseSchema <- "main"
+
+cdmVersion <- "5.3"
+
+Achilles::achilles(
+  cdmVersion = cdmVersion,
+  connectionDetails = connectionDetails,
+  cdmDatabaseSchema = cdmDatabaseSchema,
+  resultsDatabaseSchema = cdmDatabaseSchema,
+  smallCellCount = 0,
+  createTable = TRUE,
+  createIndices = FALSE,
+  sqlOnly = FALSE
+)
+
+dbSummary <- Achilles::generateDbSummary(connectionDetails, cdmDatabaseSchema, resultsDatabaseSchema,demoCountry,demoProvenance)
 
 tableOutput <- dbSummary$summary
 tableOutput$"Source Vocabularies" <- paste(dbSummary$sourceVocabs$VOCABULARY_ID, collapse="<br>")
 tableOutput$"Visits" <- paste(dbSummary$visitDist$CONCEPT_NAME, collapse="<br>")
 
+
 # this will open results in the RStudio Viewer which can then be exported to image or html.
-kable(tableOutput,escape=F) %>% kableExtra::kable_styling()
+kbl(tableOutput,escape=F) %>% kableExtra::kable_styling()
+