diff --git a/Documentation/.Rhistory b/Documentation/.Rhistory
new file mode 100644
index 0000000..a5ebd21
--- /dev/null
+++ b/Documentation/.Rhistory
@@ -0,0 +1,512 @@
+library(BigKnn)
+library(caret)
+2
+# general initial settings `50g' means 50GB - you may need to reduce
+options(fftempdir = "drive:/FFtemp")
+h2o.init(nthreads = -1, max_mem_size = '50g')
+dbms <- "pdw"
+user <- mblacke
+pw <- N8wgd=p34
+server <- "jrdusapsctl01"
+port <- 17001
+oracleTempSchema <- NULL
+cdmVersion <- 5
+connectionDetails <- DatabaseConnector::createConnectionDetails(dbms = dbms,
+server = server,
+user = user,
+password = pw,
+port = port)
+conn <- DatabaseConnector::connect(connectionDetails)
+dbms <- "pdw"
+user <- "mblacke"
+pw <- "N8wgd=p34"
+server <- "jrdusapsctl01"
+port <- 17001
+oracleTempSchema <- NULL
+cdmVersion <- 5
+connectionDetails <- DatabaseConnector::createConnectionDetails(dbms = dbms,
+server = server,
+user = user,
+password = pw,
+port = port)
+conn <- DatabaseConnector::connect(connectionDetails)
+dbms="pdw",
+server="JRDUSAPSCTL01",
+port="17001"
+oracleTempSchema <- NULL
+cdmVersion <- 5
+connectionDetails <- DatabaseConnector::createConnectionDetails(dbms = dbms,
+server = server,
+port = port)
+conn <- DatabaseConnector::connect(connectionDetails)
+library(DatabaseConnector)
+library(SqlRender)
+library(httr)
+library(RJSONIO)
+library(reshape2)
+library('ReporteRs')
+#=============================================================#
+#
+#      ADD THE STUDY SETTINGS HERE:
+#=============================================================#
+dir <- "\\wprdusmj12rcz\Epi\Mood_Haliperidol\project390"
+# settings:
+prior_start <- '2013-07-01'
+tab_start <- '2014-01-01'
+tab_end <- '2015-12-31'
+studytype <- 'new'
+mingap <- 182
+install.packages("ReporteRs")
+library('ReporteRs')
+getConcepts <- function(conceptSetIdentifiers) {
+results <- list()
+length(results) <- length(conceptSetIdentifiers)
+ind <- 0
+for (conceptSetIdentifier in conceptSetIdentifiers){
+ind <- ind+1
+# get the concept set expression from the webapi
+conceptSetExpressionUrl = paste("http://hix.jnj.com:8080/WebAPI/conceptset/", conceptSetIdentifier, "/expression", sep = "")
+## http://hix.jnj.com:8080/WebAPI/VOCAB/vocabulary/lookup/mapped
+expression <- httr::content(httr::GET(conceptSetExpressionUrl),"text")
+result <- RJSONIO::fromJSON(expression)
+concepts <- t(as.data.frame(lapply(result[[1]], function(x) c(x$concept$CONCEPT_ID,
+x$concept$CONCEPT_CODE,
+x$concept$CONCEPT_NAME,
+x$concept$VOCABULARY_ID,
+x$isExcluded, x$includeDescendants,
+x$includeMapped)) ))
+concepts <- as.data.frame(concepts)
+rownames(concepts) <- NULL
+colnames(concepts) <- c('concept_id','concept_code','concept_name','vocabulary_id',
+'exclude','descendants','mapped')
+concepts[,'exclude'] <- ifelse(concepts[,'exclude']=='TRUE', 1, 0)
+concepts[,'descendants'] <- ifelse(concepts[,'descendants']=='TRUE', 1, 0)
+concepts[,'mapped'] <- ifelse(concepts[,'mapped']=='TRUE', 1, 0)
+# save to temp table
+connectionDetails <- createConnectionDetails(dbms="pdw",
+server="JRDUSAPSCTL01",
+port=17001,
+user=NULL,
+password=NULL)
+conn <- connect(connectionDetails)
+DatabaseConnector::insertTable(conn, 'concepts', concepts, tempTable = T)
+# run cocnept_extract sql using temp table
+sql <- SqlRender::readSql(file.path(dir,'concept_extract.sql'))
+sql <- SqlRender::renderSql(sql, cdm='Vocabulary')$sql
+sql <- SqlRender::translateSql(sql, sourceDialect = 'sql server', targetDialect = 'pdw')$sql
+results[[ind]] <- DatabaseConnector::querySql(conn,sql)
+}
+return(results)
+}
+conceptSetIds <- list(name=c(#'Agitation, aggression or psychotic Symptoms in dementia together',
+'Agitation, aggression or psychotic Symptoms in dementia sep',
+'Tic disorder',
+'Schizophrenia',
+'Aggression in children with autism or developmental disorders'),
+code=list(#2349,
+c(2478,2479), 2348, 2347,c(2361, 2362)
+))
+# put concept sets into inds
+inds <- lapply(conceptSetIds[[2]], getConcepts)
+names(inds) <-conceptSetIds[[1]]
+conceptSetIds
+inds <- lapply(conceptSetIds[[2]], getConcepts)
+dir <- "\\wprdusmj12rcz\Epi\Mood_Haliperidol\project390\"
+dir <- "S:Epi\Mood_Haliperidol\project390\"
+dir <- "S:Epi/Mood_Haliperidol/project390/"
+inds <- lapply(conceptSetIds[[2]], getConcepts)
+inds
+names(inds) <-conceptSetIds[[1]]
+getConcepts <- function(conceptSetIdentifiers) {
+results <- list()
+length(results) <- length(conceptSetIdentifiers)
+ind <- 0
+for (conceptSetIdentifier in conceptSetIdentifiers){
+ind <- ind+1
+# get the concept set expression from the webapi
+conceptSetExpressionUrl = paste("http://hix.jnj.com:8080/WebAPI/conceptset/", conceptSetIdentifier, "/expression", sep = "")
+## http://hix.jnj.com:8080/WebAPI/VOCAB/vocabulary/lookup/mapped
+expression <- httr::content(httr::GET(conceptSetExpressionUrl),"text")
+result <- RJSONIO::fromJSON(expression)
+concepts <- t(as.data.frame(lapply(result[[1]], function(x) c(x$concept$CONCEPT_ID,
+x$concept$CONCEPT_CODE,
+x$concept$CONCEPT_NAME,
+x$concept$VOCABULARY_ID,
+x$isExcluded, x$includeDescendants,
+x$includeMapped)) ))
+concepts <- as.data.frame(concepts)
+rownames(concepts) <- NULL
+colnames(concepts) <- c('concept_id','concept_code','concept_name','vocabulary_id',
+'exclude','descendants','mapped')
+concepts[,'exclude'] <- ifelse(concepts[,'exclude']=='TRUE', 1, 0)
+concepts[,'descendants'] <- ifelse(concepts[,'descendants']=='TRUE', 1, 0)
+concepts[,'mapped'] <- ifelse(concepts[,'mapped']=='TRUE', 1, 0)
+# save to temp table
+connectionDetails <- createConnectionDetails(dbms="pdw",
+server="JRDUSAPSCTL01",
+port=17001,
+user=NULL,
+password=NULL)
+conn <- connect(connectionDetails)
+DatabaseConnector::insertTable(conn, 'scratch.dbo.390_concepts', concepts)#, tempTable = T)
+# run cocnept_extract sql using temp table
+sql <- SqlRender::readSql(file.path(dir,'concept_extract.sql'))
+sql <- SqlRender::renderSql(sql, cdm='Vocabulary')$sql
+sql <- SqlRender::translateSql(sql, sourceDialect = 'sql server', targetDialect = 'pdw')$sql
+results[[ind]] <- DatabaseConnector::querySql(conn,sql)
+}
+return(results)
+}
+conceptSetIds <- list(name=c(#'Agitation, aggression or psychotic Symptoms in dementia together',
+'Agitation, aggression or psychotic Symptoms in dementia sep',
+'Tic disorder',
+'Schizophrenia',
+'Aggression in children with autism or developmental disorders'),
+code=list(#2349,
+c(2478,2479), 2348, 2347,c(2361, 2362)
+))
+# put concept sets into inds
+inds <- lapply(conceptSetIds[[2]], getConcepts)
+getConcepts <- function(conceptSetIdentifiers) {
+results <- list()
+length(results) <- length(conceptSetIdentifiers)
+ind <- 0
+for (conceptSetIdentifier in conceptSetIdentifiers){
+ind <- ind+1
+# get the concept set expression from the webapi
+conceptSetExpressionUrl = paste("http://hix.jnj.com:8080/WebAPI/conceptset/", conceptSetIdentifier, "/expression", sep = "")
+## http://hix.jnj.com:8080/WebAPI/VOCAB/vocabulary/lookup/mapped
+expression <- httr::content(httr::GET(conceptSetExpressionUrl),"text")
+result <- RJSONIO::fromJSON(expression)
+concepts <- t(as.data.frame(lapply(result[[1]], function(x) c(x$concept$CONCEPT_ID,
+x$concept$CONCEPT_CODE,
+x$concept$CONCEPT_NAME,
+x$concept$VOCABULARY_ID,
+x$isExcluded, x$includeDescendants,
+x$includeMapped)) ))
+concepts <- as.data.frame(concepts)
+rownames(concepts) <- NULL
+colnames(concepts) <- c('concept_id','concept_code','concept_name','vocabulary_id',
+'exclude','descendants','mapped')
+concepts[,'exclude'] <- ifelse(concepts[,'exclude']=='TRUE', 1, 0)
+concepts[,'descendants'] <- ifelse(concepts[,'descendants']=='TRUE', 1, 0)
+concepts[,'mapped'] <- ifelse(concepts[,'mapped']=='TRUE', 1, 0)
+# save to temp table
+connectionDetails <- createConnectionDetails(dbms="pdw",
+server="JRDUSAPSCTL01",
+port=17001,
+user=NULL,
+password=NULL)
+conn <- connect(connectionDetails)
+DatabaseConnector::insertTable(conn, 'scratch.dbo.concepts_390', concepts)#, tempTable = T)
+# run cocnept_extract sql using temp table
+sql <- SqlRender::readSql(file.path(dir,'concept_extract.sql'))
+sql <- SqlRender::renderSql(sql, cdm='Vocabulary')$sql
+sql <- SqlRender::translateSql(sql, sourceDialect = 'sql server', targetDialect = 'pdw')$sql
+results[[ind]] <- DatabaseConnector::querySql(conn,sql)
+}
+return(results)
+}
+conceptSetIds <- list(name=c(#'Agitation, aggression or psychotic Symptoms in dementia together',
+'Agitation, aggression or psychotic Symptoms in dementia sep',
+'Tic disorder',
+'Schizophrenia',
+'Aggression in children with autism or developmental disorders'),
+code=list(#2349,
+c(2478,2479), 2348, 2347,c(2361, 2362)
+))
+# put concept sets into inds
+inds <- lapply(conceptSetIds[[2]], getConcepts)
+names(inds) <-conceptSetIds[[1]]
+getConcepts <- function(conceptSetIdentifiers) {
+results <- list()
+length(results) <- length(conceptSetIdentifiers)
+ind <- 0
+for (conceptSetIdentifier in conceptSetIdentifiers){
+ind <- ind+1
+# get the concept set expression from the webapi
+conceptSetExpressionUrl = paste("http://hix.jnj.com:8080/WebAPI/conceptset/", conceptSetIdentifier, "/expression", sep = "")
+## http://hix.jnj.com:8080/WebAPI/VOCAB/vocabulary/lookup/mapped
+expression <- httr::content(httr::GET(conceptSetExpressionUrl),"text")
+result <- RJSONIO::fromJSON(expression)
+concepts <- t(as.data.frame(lapply(result[[1]], function(x) c(x$concept$CONCEPT_ID,
+x$concept$CONCEPT_CODE,
+x$concept$CONCEPT_NAME,
+x$concept$VOCABULARY_ID,
+x$isExcluded, x$includeDescendants,
+x$includeMapped)) ))
+concepts <- as.data.frame(concepts)
+rownames(concepts) <- NULL
+colnames(concepts) <- c('concept_id','concept_code','concept_name','vocabulary_id',
+'exclude','descendants','mapped')
+concepts[,'exclude'] <- ifelse(concepts[,'exclude']=='TRUE', 1, 0)
+concepts[,'descendants'] <- ifelse(concepts[,'descendants']=='TRUE', 1, 0)
+concepts[,'mapped'] <- ifelse(concepts[,'mapped']=='TRUE', 1, 0)
+# save to temp table
+connectionDetails <- createConnectionDetails(dbms="pdw",
+server="JRDUSAPSCTL01",
+port=17001,
+user=NULL,
+password=NULL)
+conn <- connect(connectionDetails)
+DatabaseConnector::insertTable(conn, 'scratch.dbo.concepts_390', concepts)#, tempTable = T)
+# run cocnept_extract sql using temp table
+sql <- SqlRender::readSql(file.path(dir,'concept_extract.sql'))
+sql <- SqlRender::renderSql(sql, cdm='Vocabulary')$sql
+sql <- SqlRender::translateSql(sql, sourceDialect = 'sql server', targetDialect = 'pdw')$sql
+results[[ind]] <- DatabaseConnector::querySql(conn,sql)
+}
+return(results)
+}
+conceptSetIds <- list(name=c(#'Agitation, aggression or psychotic Symptoms in dementia together',
+'Agitation, aggression or psychotic Symptoms in dementia sep',
+'Tic disorder',
+'Schizophrenia',
+'Aggression in children with autism or developmental disorders'),
+code=list(#2349,
+c(2478,2479), 2348, 2347,c(2361, 2362)
+))
+# put concept sets into inds
+inds <- lapply(conceptSetIds[[2]], getConcepts)
+names(inds) <-conceptSetIds[[1]]
+getConcepts <- function(conceptSetIdentifiers) {
+results <- list()
+length(results) <- length(conceptSetIdentifiers)
+ind <- 0
+for (conceptSetIdentifier in conceptSetIdentifiers){
+ind <- ind+1
+# get the concept set expression from the webapi
+conceptSetExpressionUrl = paste("http://hix.jnj.com:8080/WebAPI/conceptset/", conceptSetIdentifier, "/expression", sep = "")
+## http://hix.jnj.com:8080/WebAPI/VOCAB/vocabulary/lookup/mapped
+expression <- httr::content(httr::GET(conceptSetExpressionUrl),"text")
+result <- RJSONIO::fromJSON(expression)
+concepts <- t(as.data.frame(lapply(result[[1]], function(x) c(x$concept$CONCEPT_ID,
+x$concept$CONCEPT_CODE,
+x$concept$CONCEPT_NAME,
+x$concept$VOCABULARY_ID,
+x$isExcluded, x$includeDescendants,
+x$includeMapped)) ))
+concepts <- as.data.frame(concepts)
+rownames(concepts) <- NULL
+colnames(concepts) <- c('concept_id','concept_code','concept_name','vocabulary_id',
+'exclude','descendants','mapped')
+concepts[,'exclude'] <- ifelse(concepts[,'exclude']=='TRUE', 1, 0)
+concepts[,'descendants'] <- ifelse(concepts[,'descendants']=='TRUE', 1, 0)
+concepts[,'mapped'] <- ifelse(concepts[,'mapped']=='TRUE', 1, 0)
+# save to temp table
+connectionDetails <- createConnectionDetails(dbms="pdw",
+server="JRDUSAPSCTL01",
+port=17001,
+user=NULL,
+password=NULL)
+conn <- connect(connectionDetails)
+DatabaseConnector::insertTable(conn, 'concepts', concepts, tempTable = T)
+# run cocnept_extract sql using temp table
+sql <- SqlRender::readSql(file.path(dir,'concept_extract.sql'))
+sql <- SqlRender::renderSql(sql, cdm='Vocabulary')$sql
+sql <- SqlRender::translateSql(sql, sourceDialect = 'sql server', targetDialect = 'pdw')$sql
+results[[ind]] <- DatabaseConnector::querySql(conn,sql)
+}
+return(results)
+}
+conceptSetIds <- list(name=c(#'Agitation, aggression or psychotic Symptoms in dementia together',
+'Agitation, aggression or psychotic Symptoms in dementia sep',
+'Tic disorder',
+'Schizophrenia',
+'Aggression in children with autism or developmental disorders'),
+code=list(#2349,
+c(2478,2479), 2348, 2347,c(2361, 2362)
+))
+# put concept sets into inds
+inds <- lapply(conceptSetIds[[2]], getConcepts)
+getConcepts <- function(conceptSetIdentifiers) {
+results <- list()
+length(results) <- length(conceptSetIdentifiers)
+ind <- 0
+for (conceptSetIdentifier in conceptSetIdentifiers){
+ind <- ind+1
+# get the concept set expression from the webapi
+conceptSetExpressionUrl = paste("http://hix.jnj.com:8080/WebAPI/conceptset/", conceptSetIdentifier, "/expression", sep = "")
+## http://hix.jnj.com:8080/WebAPI/VOCAB/vocabulary/lookup/mapped
+expression <- httr::content(httr::GET(conceptSetExpressionUrl),"text")
+result <- RJSONIO::fromJSON(expression)
+concepts <- t(as.data.frame(lapply(result[[1]], function(x) c(x$concept$CONCEPT_ID,
+x$concept$CONCEPT_CODE,
+x$concept$CONCEPT_NAME,
+x$concept$VOCABULARY_ID,
+x$isExcluded, x$includeDescendants,
+x$includeMapped)) ))
+concepts <- as.data.frame(concepts)
+rownames(concepts) <- NULL
+colnames(concepts) <- c('concept_id','concept_code','concept_name','vocabulary_id',
+'exclude','descendants','mapped')
+concepts[,'exclude'] <- ifelse(concepts[,'exclude']=='TRUE', 1, 0)
+concepts[,'descendants'] <- ifelse(concepts[,'descendants']=='TRUE', 1, 0)
+concepts[,'mapped'] <- ifelse(concepts[,'mapped']=='TRUE', 1, 0)
+# save to temp table
+connectionDetails <- createConnectionDetails(dbms="pdw",
+server="JRDUSAPSCTL01",
+port=17001,
+user=NULL,
+password=NULL)
+conn <- connect(connectionDetails)
+DatabaseConnector::insertTable(conn, 'scratch.dbo.concepts_390', concepts)#, tempTable = T)
+# run cocnept_extract sql using temp table
+sql <- SqlRender::readSql(file.path(dir,'concept_extract.sql'))
+sql <- SqlRender::renderSql(sql, cdm='Vocabulary')$sql
+sql <- SqlRender::translateSql(sql, sourceDialect = 'sql server', targetDialect = 'pdw')$sql
+results[[ind]] <- DatabaseConnector::querySql(conn,sql)
+}
+return(results)
+}
+conceptSetIds <- list(name=c(#'Agitation, aggression or psychotic Symptoms in dementia together',
+'Agitation, aggression or psychotic Symptoms in dementia sep',
+'Tic disorder',
+'Schizophrenia',
+'Aggression in children with autism or developmental disorders'),
+code=list(#2349,
+c(2478,2479), 2348, 2347,c(2361, 2362)
+))
+# put concept sets into inds
+inds <- lapply(conceptSetIds[[2]], getConcepts)
+library(SqlRender)
+library(DatabaseConnector)
+library(stringr)
+library(openxlsx)
+cohortIds <- c(2520, 2521)
+buildDatabase <- function(id, name, schema)
+{
+dataSource <- {};
+dataSource$id = id;
+dataSource$name = name;
+dataSource$schema = schema;
+return(dataSource);
+}
+dbList <- list(
+buildDatabase("CPRD_V423", "CDM_CPRD_V423", "dbo"),
+buildDatabase("JMDC_V429", "CDM_JMDC_V429", "dbo"),
+buildDatabase("OPTUMEXTSES_V427", "CDM_OPTUM_EXTENDED_SES_V427", "dbo"),
+buildDatabase("PREMIER_V428", "CDM_PREMIER_V428", "dbo"),
+buildDatabase("TRUVENCCAE_V418", "CDM_TRUVEN_CCAE_V418", "dbo"),
+buildDatabase("TRUVENMDCD_V432", "CDM_TRUVEN_MDCD_V432", "dbo"),
+buildDatabase("TRUVENMDCR_V415", "CDM_TRUVEN_MDCR_V415", "dbo")
+);
+connectionDetails <- createConnectionDetails(dbms = "pdw", server = "JRDUSAPSCTL01",
+port = 17001, user = "hix_reader", password = "reader1!")
+outputExcel <- "Output/ExcelFiles/PP_Atlas"
+for (cohortId in cohortIds)
+{
+filePath <- paste(paste(outputExcel, cohortId, sep="/", collapse=""), ".xlsx", sep="", collapse="")
+if (file.exists(filePath))
+{
+file.remove(filePath)
+}
+wb <- createWorkbook()
+for (db in dbList)
+{
+addWorksheet(wb, db$id)
+pp_sql <- readSql("sql/PP_Atlas.sql");
+pp_sql <- renderSql(pp_sql, cdmDatabaseSchema = paste(db$name, db$schema, sep=".", collapse=""), cohort_definition_id = cohortId,
+urlPrefix = paste("'http://hix.jnj.com/atlas/#/profiles",
+db$id, cohortId, "'", sep="/", collapse=""))$sql;
+conn <- connect(connectionDetails)
+pp_data <- querySql(conn, pp_sql)
+hs <- createStyle(textDecoration = "Bold")
+writeData(wb, sheet=db$id, pp_data,
+startCol = 1, startRow = 1, colNames = TRUE, rowNames = FALSE, headerStyle = hs)
+setColWidths(wb, sheet = db$id, cols = 1:5, widths = "auto")
+}
+saveWorkbook(wb, filePath, overwrite = TRUE)
+}
+install_github("ohdsi/Aphrodite")
+install_github("ohdsi/Aphrodite")
+library(OhdsiRTools)
+install_github("ohdsi/Aphrodite")
+install.packages("ohdsi/Aphrodite")
+install.packages("devtools")
+library("devtools")
+install_github("ohdsi/Aphrodite")
+install.packages(chron)
+install.packages("chron")
+install_github("ohdsi/Aphrodite")
+install_github("OHDSI/CdmAtlasCutover")
+library(devtools)
+install_github("OHDSI/CdmAtlasCutover")
+repoConnectionDetails <- createConnectionDetails(dbms = "sql server",
+server = "rndusrdhit01",
+port = 1433, schema = "ohdsi_repository.dbo")
+oldCdmSources <- list(
+buildCdmSource(sourceKey = "DEATHSUBSET_CCAE")
+)
+newCdmSources <- list(
+buildCdmSource(sourceKey = "DEATHSUBSET_CCAE", sourceName = "Death Subset - Truven CCAE",
+dbms = "pdw",
+connectionString = "jdbc:sqlserver://JRDUSAPSCTL01:17001;databaseName=CDM_DEATH_SUBSET;user=hix_writer;password=writer1!",
+cdmDatabaseSchema = "CDM_DEATH_SUBSET.truven_ccae", resultsDatabaseSchema = "CDM_DEATH_SUBSET.truven_ccae",
+vocabDatabaseSchema = "CDM_DEATH_SUBSET.truven_ccae"),
+buildCdmSource(sourceKey = "DEATHSUBSET_MDCR", sourceName = "Death Subset - Truven MDCR",
+dbms = "pdw",
+connectionString = "jdbc:sqlserver://JRDUSAPSCTL01:17001;databaseName=CDM_DEATH_SUBSET;user=hix_writer;password=writer1!",
+cdmDatabaseSchema = "CDM_DEATH_SUBSET.truven_mdcr",
+resultsDatabaseSchema = "CDM_DEATH_SUBSET.truven_mdcr",
+vocabDatabaseSchema = "VOCABULARY_20161218.dbo"),
+buildCdmSource(sourceKey = "DEATHSUBSET_OPTUM", sourceName = "Death Subset - Optum Extended DOD",
+dbms = "pdw",
+connectionString = "jdbc:sqlserver://JRDUSAPSCTL01:17001;databaseName=CDM_DEATH_SUBSET;user=hix_writer;password=writer1!",
+cdmDatabaseSchema = "CDM_DEATH_SUBSET.optum_extended_dod",
+resultsDatabaseSchema = "CDM_DEATH_SUBSET.optum_extended_dod",
+vocabDatabaseSchema = "VOCABULARY_20161218.dbo")
+)
+library(CdmAtlasCutover)
+oldCdmSources <- list(
+buildCdmSource(sourceKey = "DEATHSUBSET_CCAE")
+)
+newCdmSources <- list(
+buildCdmSource(sourceKey = "DEATHSUBSET_CCAE", sourceName = "Death Subset - Truven CCAE",
+dbms = "pdw",
+connectionString = "jdbc:sqlserver://JRDUSAPSCTL01:17001;databaseName=CDM_DEATH_SUBSET;user=hix_writer;password=writer1!",
+cdmDatabaseSchema = "CDM_DEATH_SUBSET.truven_ccae", resultsDatabaseSchema = "CDM_DEATH_SUBSET.truven_ccae",
+vocabDatabaseSchema = "CDM_DEATH_SUBSET.truven_ccae"),
+buildCdmSource(sourceKey = "DEATHSUBSET_MDCR", sourceName = "Death Subset - Truven MDCR",
+dbms = "pdw",
+connectionString = "jdbc:sqlserver://JRDUSAPSCTL01:17001;databaseName=CDM_DEATH_SUBSET;user=hix_writer;password=writer1!",
+cdmDatabaseSchema = "CDM_DEATH_SUBSET.truven_mdcr",
+resultsDatabaseSchema = "CDM_DEATH_SUBSET.truven_mdcr",
+vocabDatabaseSchema = "VOCABULARY_20161218.dbo"),
+buildCdmSource(sourceKey = "DEATHSUBSET_OPTUM", sourceName = "Death Subset - Optum Extended DOD",
+dbms = "pdw",
+connectionString = "jdbc:sqlserver://JRDUSAPSCTL01:17001;databaseName=CDM_DEATH_SUBSET;user=hix_writer;password=writer1!",
+cdmDatabaseSchema = "CDM_DEATH_SUBSET.optum_extended_dod",
+resultsDatabaseSchema = "CDM_DEATH_SUBSET.optum_extended_dod",
+vocabDatabaseSchema = "VOCABULARY_20161218.dbo")
+)
+removeCdmSources(repoConnectionDetails = repoConnectionDetails, cdmSources = oldCdmSources, sqlOnly = TRUE)
+createOhdsiResultsTables(cdmSources = newCdmSources, sqlOnly = TRUE)
+insertCdmSources(repoConnectionDetails = repoConnectionDetails, cdmSources = newCdmSources, sourceIdx = TRUE,
+daimonIdx = TRUE, sqlOnly = TRUE)
+repoConnectionDetails <- createConnectionDetails(dbms = "sql server",
+server = "rndusrdhit01",
+port = 1433, schema = "ohdsi_repository.dbo")
+removeCdmSources(repoConnectionDetails = repoConnectionDetails, cdmSources = oldCdmSources, sqlOnly = TRUE)
+removeCdmSources(repoConnectionDetails = repoConnectionDetails, cdmSources = oldCdmSources, sqlOnly = TRUE)
+insertCdmSources(repoConnectionDetails = repoConnectionDetails, cdmSources = newCdmSources, sourceIdx = TRUE,
+daimonIdx = TRUE, sqlOnly = TRUE)
+install_github("OHDSI/CdmAtlasCutover", force=TRUE)
+library(CdmAtlasCutover)
+# Initialize CDM database list, with all the CDMs to be cut over
+repoConnectionDetails <- createConnectionDetails(dbms = "sql server",
+server = "rndusrdhit01",
+port = 1433, schema = "ohdsi_repository.dbo")
+oldCdmSources <- list(
+buildCdmSource(sourceKey = "DEATHSUBSET_CCAE")
+)
+removeCdmSources(repoConnectionDetails = repoConnectionDetails, cdmSources = oldCdmSources, sqlOnly = TRUE)
+createOhdsiResultsTables(cdmSources = newCdmSources, sqlOnly = TRUE)
+insertCdmSources(repoConnectionDetails = repoConnectionDetails, cdmSources = newCdmSources, sourceIdx = TRUE,
+daimonIdx = TRUE, sqlOnly = TRUE)
+getwd()
+setwd("C:/Git/CommonDataModel/Documentation")
+library(rmarkdown)
+render("GlossaryofTerms.md","pdf_document")
+render("GlossaryofTerms.md","pdf_document", template = "default")
+render("GlossaryofTerms.md",pdf_document(template = "default"))
diff --git a/Documentation/report.Rmd b/Documentation/report.Rmd
index 88d29d9..cfc600b 100644
--- a/Documentation/report.Rmd
+++ b/Documentation/report.Rmd
@@ -1,5 +1,5 @@
 ---
-title: "OMOP Common Data Model Specifications"
+title: "OMOP Common Data Model v5.1 Specifications"
 author: "Christian Reich, Patrick Ryan, Rimma Belenkaya, Karthik Natarajan and Clair Blacketer"
 date: "`r Sys.Date()`"
 output:
@@ -9,10 +9,11 @@ output:
 linkcolor: blue
 ---
 
-```{r child = 'License.md'}
+# License
+
+```{r child = 'C:/Git/CommonDataModel.wiki/License.md'}
 ```
 
-```{r child = 'Background/TheRoleoftheCommonDataModel.md'}
+# The Role of the Common Data Model
+```{r child = 'C:/Git/CommonDataModel.wiki/Background/The-Role-of-the-Common-Data-Model.md'}
 ```
-
-Will it add the footer?
\ No newline at end of file
diff --git a/Documentation/report.pdf b/Documentation/report.pdf
new file mode 100644
index 0000000..d344ba6
Binary files /dev/null and b/Documentation/report.pdf differ