R/getHbA1cStat.R
In rohit43/DiabetesTxPath: Learning Effective Clinical Treatment Pathways for Type-2 Diabetes from Observational Data
Defines functions
getHbA1cStat
# @file functions
#
# Copyright 2017 Observational Health Data Sciences and Informatics
#
# This file is part of:
# ----------------------------------------------
# DiabetesTxPath
# ----------------------------------------------
# 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
#
# http://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.
#
# @author Stanford University Center for Biomedical Informatics - Shah Lab
# @author Rohit Vashisht
#
#' @title
#' getAgeGender
#'
#' @author
#' Rohit Vashisht
#'
#' @details
#' This function plots the results of T2D study.
getHbA1cStat <- function(results_path){
print(paste("Getting HbA1c Stats. This might take few minutes ... "))
resFiles <- list.files(paste(results_path,"/deleteMeBeforeSharing/",sep=""))
#---------------------------------------------------------------------
#For outCome 4 representing HbA1c <= 7%, represented as HbA1c7Good
x <- grep("_o4.rds",resFiles)
resFilesOutCome4 <- resFiles[x]
#Get files sorted for t and c comparisions
#bigToSulf and bigToDpp4 (1,2)
tcOne <- grep("_t1_c2",resFilesOutCome4)
#bigToSulf and bigToThia
tcTwo <- grep("_t1_c3",resFilesOutCome4)
#bigToDpp4 and bigToThia
tcThree <- grep("_t2_c3",resFilesOutCome4)
#---- For tcOne
if(length(tcOne)!=0){
resFilesOutCome4tcOne <- resFilesOutCome4[tcOne]
#load the data
ps <- grep("Ps",resFilesOutCome4tcOne)
psScore <- readRDS(paste(results_path,"deleteMeBeforeSharing/",resFilesOutCome4tcOne[ps],sep=""))
matchPop <- grep("StratPop",resFilesOutCome4tcOne)
matchedPop <- readRDS(paste(results_path,"deleteMeBeforeSharing/",resFilesOutCome4tcOne[matchPop],sep=""))
studPop <- grep("StudyPop", resFilesOutCome4tcOne)
studyPop <- readRDS(paste(results_path,"deleteMeBeforeSharing/",resFilesOutCome4tcOne[studPop],sep=""))
bl <- grep("Bal",resFilesOutCome4tcOne)
balance <- readRDS(paste(results_path,"deleteMeBeforeSharing/",resFilesOutCome4tcOne[bl],sep=""))
remove(ps,matchPop,studPop,bl)
conn <- DatabaseConnector::connect(connectionDetails)
insertTable(conn,
"ohdsiT2DstudyPop",
studyPop,
dropTableIfExists = TRUE,
createTable = TRUE,
tempTable = TRUE,
oracleTempSchema = NULL)
sqlOne <- paste("SELECT o.treatment,
count(DISTINCT m.person_id) AS patients,
count(*)
AS records,
AVG(m.VALUE_AS_NUMBER) AS AVG,
STDEV(m.VALUE_AS_NUMBER) AS STD
FROM @cdmDatabaseSchema.MEASUREMENT m
JOIN #ohdsiT2DstudyPop o
ON m.person_id = o.SUBJECTID
WHERE m.measurement_concept_id IN (3004410,
3007263,
3003309,
3005673,
40762352,
40758583,
3034639,
4197971)
AND m.MEASUREMENT_DATE < CAST(o.COHORTSTARTDATE AS DATE)
AND m.VALUE_AS_NUMBER < 20
GROUP BY o.treatment", sep = "")
sqlOne <- SqlRender::renderSql(sqlOne, cdmDatabaseSchema = cdmDatabaseSchema)$sql
sqlOne <- SqlRender::translateSql(sqlOne, targetDialect = connectionDetails$dbms)$sql
HbA1cBefTx <- querySql(conn, sqlOne)
remove(sqlOne)
sqlOne <- paste("SELECT o.treatment,
count(DISTINCT m.person_id) AS patients,
count(*)
AS records,
AVG(m.VALUE_AS_NUMBER) AS AVG,
STDEV(m.VALUE_AS_NUMBER) AS STD
FROM @cdmDatabaseSchema.MEASUREMENT m
JOIN #ohdsiT2DstudyPop o
ON m.person_id = o.SUBJECTID
WHERE m.measurement_concept_id IN (3004410,
3007263,
3003309,
3005673,
40762352,
40758583,
3034639,
4197971)
AND m.MEASUREMENT_DATE > CAST(o.COHORTSTARTDATE AS DATE)
AND m.VALUE_AS_NUMBER < 20
GROUP BY o.treatment", sep = "")
sqlOne <- SqlRender::renderSql(sqlOne, cdmDatabaseSchema = cdmDatabaseSchema)$sql
sqlOne <- SqlRender::translateSql(sqlOne, targetDialect = connectionDetails$dbms)$sql
HbA1cAfTx <- querySql(conn, sqlOne)
remove(sqlOne)
HbA1cBefTx$TcPatients <- NA
HbA1cBefTx$TcPatients[1] <- nrow(subset(studyPop, treatment == 0))
HbA1cBefTx$TcPatients[2] <- nrow(subset(studyPop, treatment == 1))
HbA1cBefTx$Index <- c("Before")
HbA1cAfTx$TcPatients <- NA
HbA1cAfTx$TcPatients[1] <- nrow(subset(studyPop, treatment == 0))
HbA1cAfTx$TcPatients[2] <- nrow(subset(studyPop, treatment == 1))
HbA1cAfTx$Index <- c("After")
unMatchedHbA1cMeanSd <- rbind(HbA1cBefTx, HbA1cAfTx)
unMatchedHbA1cMeanSd$class <- c("unMatched")
remove(HbA1cBefTx, HbA1cAfTx)
# Matched Cohort
insertTable(conn,
"ohdsiT2DstudyPop",
matchedPop,
dropTableIfExists = TRUE,
createTable = TRUE,
tempTable = TRUE,
oracleTempSchema = NULL)
sqlOne <- paste("SELECT o.treatment,
count(DISTINCT m.person_id) AS patients,
count(*)
AS records,
AVG(m.VALUE_AS_NUMBER) AS AVG,
STDEV(m.VALUE_AS_NUMBER) AS STD
FROM @cdmDatabaseSchema.MEASUREMENT m
JOIN #ohdsiT2DstudyPop o
ON m.person_id = o.SUBJECTID
WHERE m.measurement_concept_id IN (3004410,
3007263,
3003309,
3005673,
40762352,
40758583,
3034639,
4197971)
AND m.MEASUREMENT_DATE < CAST(o.COHORTSTARTDATE AS DATE)
AND m.measurement_date >= dateadd(day,
-365,
CAST(o.COHORTSTARTDATE AS DATE)) AND m.measurement_date <= CAST(o.COHORTSTARTDATE AS DATE)
AND m.VALUE_AS_NUMBER < 20
GROUP BY o.treatment", sep = "")
sqlOne <- SqlRender::renderSql(sqlOne, cdmDatabaseSchema = cdmDatabaseSchema)$sql
sqlOne <- SqlRender::translateSql(sqlOne, targetDialect = connectionDetails$dbms)$sql
HbA1cBefTx <- querySql(conn, sqlOne)
remove(sqlOne)
sqlOne <- paste("SELECT o.treatment,
count(DISTINCT m.person_id) AS patients,
count(*)
AS records,
AVG(m.VALUE_AS_NUMBER) AS AVG,
STDEV(m.VALUE_AS_NUMBER) AS STD
FROM @cdmDatabaseSchema.MEASUREMENT m
JOIN #ohdsiT2DstudyPop o
ON m.person_id = o.SUBJECTID
WHERE m.measurement_concept_id IN (3004410,
3007263,
3003309,
3005673,
40762352,
40758583,
3034639,
4197971)
AND m.MEASUREMENT_DATE > CAST(o.COHORTSTARTDATE AS DATE)
AND m.VALUE_AS_NUMBER < 20
GROUP BY o.treatment", sep = "")
sqlOne <- SqlRender::renderSql(sqlOne, cdmDatabaseSchema = cdmDatabaseSchema)$sql
sqlOne <- SqlRender::translateSql(sqlOne, targetDialect = connectionDetails$dbms)$sql
HbA1cAfTx <- querySql(conn, sqlOne)
remove(sqlOne)
HbA1cBefTx$TcPatients <- NA
HbA1cBefTx$TcPatients[1] <- nrow(subset(matchedPop, treatment == 0))
HbA1cBefTx$TcPatients[2] <- nrow(subset(matchedPop, treatment == 1))
HbA1cBefTx$Index <- c("Before")
HbA1cAfTx$TcPatients <- NA
HbA1cAfTx$TcPatients[1] <- nrow(subset(matchedPop, treatment == 0))
HbA1cAfTx$TcPatients[2] <- nrow(subset(matchedPop, treatment == 1))
HbA1cAfTx$Index <- c("After")
matchedHbA1cMeanSd <- rbind(HbA1cBefTx, HbA1cAfTx)
matchedHbA1cMeanSd$class <- c("matched")
remove(HbA1cBefTx, HbA1cAfTx)
hbA1cStat <- rbind(unMatchedHbA1cMeanSd, matchedHbA1cMeanSd)
write.csv(hbA1cStat, file = paste(results_path,"bigToSulf_bigToDpp4_HbA1c7Good_Stat.csv",sep=""))
remove(unMatchedHbA1cMeanSd, matchedHbA1cMeanSd, hbA1cStat)
remove(psScore, matchedPop, studyPop, balance)
}else
{
print(paste("You don't seems to have results for the bigToSulf and bigToDpp4 comparision"))
}
#---- For tcTwo
if(length(tcTwo)!=0){
resFilesOutCome4tcTwo <- resFilesOutCome4[tcTwo]
#load the data
ps <- grep("Ps",resFilesOutCome4tcTwo)
psScore <- readRDS(paste(results_path,"deleteMeBeforeSharing/",resFilesOutCome4tcTwo[ps],sep=""))
matchPop <- grep("StratPop",resFilesOutCome4tcTwo)
matchedPop <- readRDS(paste(results_path,"deleteMeBeforeSharing/",resFilesOutCome4tcTwo[matchPop],sep=""))
studPop <- grep("StudyPop", resFilesOutCome4tcTwo)
studyPop <- readRDS(paste(results_path,"deleteMeBeforeSharing/",resFilesOutCome4tcTwo[studPop],sep=""))
bl <- grep("Bal",resFilesOutCome4tcTwo)
balance <- readRDS(paste(results_path,"deleteMeBeforeSharing/",resFilesOutCome4tcTwo[bl],sep=""))
remove(ps,matchPop,studPop,bl)
conn <- DatabaseConnector::connect(connectionDetails)
insertTable(conn,
"ohdsiT2DstudyPop",
studyPop,
dropTableIfExists = TRUE,
createTable = TRUE,
tempTable = TRUE,
oracleTempSchema = NULL)
sqlOne <- paste("SELECT o.treatment,
count(DISTINCT m.person_id) AS patients,
count(*)
AS records,
AVG(m.VALUE_AS_NUMBER) AS AVG,
STDEV(m.VALUE_AS_NUMBER) AS STD
FROM @cdmDatabaseSchema.MEASUREMENT m
JOIN #ohdsiT2DstudyPop o
ON m.person_id = o.SUBJECTID
WHERE m.measurement_concept_id IN (3004410,
3007263,
3003309,
3005673,
40762352,
40758583,
3034639,
4197971)
AND m.MEASUREMENT_DATE < CAST(o.COHORTSTARTDATE AS DATE)
AND m.VALUE_AS_NUMBER < 20
GROUP BY o.treatment", sep = "")
sqlOne <- SqlRender::renderSql(sqlOne, cdmDatabaseSchema = cdmDatabaseSchema)$sql
sqlOne <- SqlRender::translateSql(sqlOne, targetDialect = connectionDetails$dbms)$sql
HbA1cBefTx <- querySql(conn, sqlOne)
remove(sqlOne)
sqlOne <- paste("SELECT o.treatment,
count(DISTINCT m.person_id) AS patients,
count(*)
AS records,
AVG(m.VALUE_AS_NUMBER) AS AVG,
STDEV(m.VALUE_AS_NUMBER) AS STD
FROM @cdmDatabaseSchema.MEASUREMENT m
JOIN #ohdsiT2DstudyPop o
ON m.person_id = o.SUBJECTID
WHERE m.measurement_concept_id IN (3004410,
3007263,
3003309,
3005673,
40762352,
40758583,
3034639,
4197971)
AND m.MEASUREMENT_DATE > CAST(o.COHORTSTARTDATE AS DATE)
AND m.VALUE_AS_NUMBER < 20
GROUP BY o.treatment", sep = "")
sqlOne <- SqlRender::renderSql(sqlOne, cdmDatabaseSchema = cdmDatabaseSchema)$sql
sqlOne <- SqlRender::translateSql(sqlOne, targetDialect = connectionDetails$dbms)$sql
HbA1cAfTx <- querySql(conn, sqlOne)
remove(sqlOne)
HbA1cBefTx$TcPatients <- NA
HbA1cBefTx$TcPatients[1] <- nrow(subset(studyPop, treatment == 0))
HbA1cBefTx$TcPatients[2] <- nrow(subset(studyPop, treatment == 1))
HbA1cBefTx$Index <- c("Before")
HbA1cAfTx$TcPatients <- NA
HbA1cAfTx$TcPatients[1] <- nrow(subset(studyPop, treatment == 0))
HbA1cAfTx$TcPatients[2] <- nrow(subset(studyPop, treatment == 1))
HbA1cAfTx$Index <- c("After")
unMatchedHbA1cMeanSd <- rbind(HbA1cBefTx, HbA1cAfTx)
unMatchedHbA1cMeanSd$class <- c("unMatched")
remove(HbA1cBefTx, HbA1cAfTx)
# Matched Cohort
insertTable(conn,
"ohdsiT2DstudyPop",
matchedPop,
dropTableIfExists = TRUE,
createTable = TRUE,
tempTable = TRUE,
oracleTempSchema = NULL)
sqlOne <- paste("SELECT o.treatment,
count(DISTINCT m.person_id) AS patients,
count(*)
AS records,
AVG(m.VALUE_AS_NUMBER) AS AVG,
STDEV(m.VALUE_AS_NUMBER) AS STD
FROM @cdmDatabaseSchema.MEASUREMENT m
JOIN #ohdsiT2DstudyPop o
ON m.person_id = o.SUBJECTID
WHERE m.measurement_concept_id IN (3004410,
3007263,
3003309,
3005673,
40762352,
40758583,
3034639,
4197971)
AND m.MEASUREMENT_DATE < CAST(o.COHORTSTARTDATE AS DATE)
AND m.measurement_date >= dateadd(day,
-365,
CAST(o.COHORTSTARTDATE AS DATE)) AND m.measurement_date <= CAST(o.COHORTSTARTDATE AS DATE)
AND m.VALUE_AS_NUMBER < 20
GROUP BY o.treatment", sep = "")
sqlOne <- SqlRender::renderSql(sqlOne, cdmDatabaseSchema = cdmDatabaseSchema)$sql
sqlOne <- SqlRender::translateSql(sqlOne, targetDialect = connectionDetails$dbms)$sql
HbA1cBefTx <- querySql(conn, sqlOne)
remove(sqlOne)
sqlOne <- paste("SELECT o.treatment,
count(DISTINCT m.person_id) AS patients,
count(*)
AS records,
AVG(m.VALUE_AS_NUMBER) AS AVG,
STDEV(m.VALUE_AS_NUMBER) AS STD
FROM @cdmDatabaseSchema.MEASUREMENT m
JOIN #ohdsiT2DstudyPop o
ON m.person_id = o.SUBJECTID
WHERE m.measurement_concept_id IN (3004410,
3007263,
3003309,
3005673,
40762352,
40758583,
3034639,
4197971)
AND m.MEASUREMENT_DATE > CAST(o.COHORTSTARTDATE AS DATE)
AND m.VALUE_AS_NUMBER < 20
GROUP BY o.treatment", sep = "")
sqlOne <- SqlRender::renderSql(sqlOne, cdmDatabaseSchema = cdmDatabaseSchema)$sql
sqlOne <- SqlRender::translateSql(sqlOne, targetDialect = connectionDetails$dbms)$sql
HbA1cAfTx <- querySql(conn, sqlOne)
remove(sqlOne)
HbA1cBefTx$TcPatients <- NA
HbA1cBefTx$TcPatients[1] <- nrow(subset(matchedPop, treatment == 0))
HbA1cBefTx$TcPatients[2] <- nrow(subset(matchedPop, treatment == 1))
HbA1cBefTx$Index <- c("Before")
HbA1cAfTx$TcPatients <- NA
HbA1cAfTx$TcPatients[1] <- nrow(subset(matchedPop, treatment == 0))
HbA1cAfTx$TcPatients[2] <- nrow(subset(matchedPop, treatment == 1))
HbA1cAfTx$Index <- c("After")
matchedHbA1cMeanSd <- rbind(HbA1cBefTx, HbA1cAfTx)
matchedHbA1cMeanSd$class <- c("matched")
remove(HbA1cBefTx, HbA1cAfTx)
hbA1cStat <- rbind(unMatchedHbA1cMeanSd, matchedHbA1cMeanSd)
write.csv(hbA1cStat, file = paste(results_path,"bigToSulf_bigToThia_HbA1c7Good_Stat.csv",sep=""))
remove(unMatchedHbA1cMeanSd, matchedHbA1cMeanSd, hbA1cStat)
remove(psScore, matchedPop, studyPop, balance)
}else
{
print(paste("You don't seems to have results for the bigToSulf and bigToThia comparision"))
}
#---- For tcThree
if(length(tcThree)!=0){
resFilesOutCome4tcThree <- resFilesOutCome4[tcThree]
#load the data
ps <- grep("Ps",resFilesOutCome4tcThree)
psScore <- readRDS(paste(results_path,"deleteMeBeforeSharing/",resFilesOutCome4tcThree[ps],sep=""))
matchPop <- grep("StratPop",resFilesOutCome4tcThree)
matchedPop <- readRDS(paste(results_path,"deleteMeBeforeSharing/",resFilesOutCome4tcThree[matchPop],sep=""))
studPop <- grep("StudyPop", resFilesOutCome4tcThree)
studyPop <- readRDS(paste(results_path,"deleteMeBeforeSharing/",resFilesOutCome4tcThree[studPop],sep=""))
bl <- grep("Bal",resFilesOutCome4tcThree)
balance <- readRDS(paste(results_path,"deleteMeBeforeSharing/",resFilesOutCome4tcThree[bl],sep=""))
remove(ps,matchPop,studPop,bl)
conn <- DatabaseConnector::connect(connectionDetails)
insertTable(conn,
"ohdsiT2DstudyPop",
studyPop,
dropTableIfExists = TRUE,
createTable = TRUE,
tempTable = TRUE,
oracleTempSchema = NULL)
sqlOne <- paste("SELECT o.treatment,
count(DISTINCT m.person_id) AS patients,
count(*)
AS records,
AVG(m.VALUE_AS_NUMBER) AS AVG,
STDEV(m.VALUE_AS_NUMBER) AS STD
FROM @cdmDatabaseSchema.MEASUREMENT m
JOIN #ohdsiT2DstudyPop o
ON m.person_id = o.SUBJECTID
WHERE m.measurement_concept_id IN (3004410,
3007263,
3003309,
3005673,
40762352,
40758583,
3034639,
4197971)
AND m.MEASUREMENT_DATE < CAST(o.COHORTSTARTDATE AS DATE)
AND m.VALUE_AS_NUMBER < 20
GROUP BY o.treatment", sep = "")
sqlOne <- SqlRender::renderSql(sqlOne, cdmDatabaseSchema = cdmDatabaseSchema)$sql
sqlOne <- SqlRender::translateSql(sqlOne, targetDialect = connectionDetails$dbms)$sql
HbA1cBefTx <- querySql(conn, sqlOne)
remove(sqlOne)
sqlOne <- paste("SELECT o.treatment,
count(DISTINCT m.person_id) AS patients,
count(*)
AS records,
AVG(m.VALUE_AS_NUMBER) AS AVG,
STDEV(m.VALUE_AS_NUMBER) AS STD
FROM @cdmDatabaseSchema.MEASUREMENT m
JOIN #ohdsiT2DstudyPop o
ON m.person_id = o.SUBJECTID
WHERE m.measurement_concept_id IN (3004410,
3007263,
3003309,
3005673,
40762352,
40758583,
3034639,
4197971)
AND m.MEASUREMENT_DATE > CAST(o.COHORTSTARTDATE AS DATE)
AND m.VALUE_AS_NUMBER < 20
GROUP BY o.treatment", sep = "")
sqlOne <- SqlRender::renderSql(sqlOne, cdmDatabaseSchema = cdmDatabaseSchema)$sql
sqlOne <- SqlRender::translateSql(sqlOne, targetDialect = connectionDetails$dbms)$sql
HbA1cAfTx <- querySql(conn, sqlOne)
remove(sqlOne)
HbA1cBefTx$TcPatients <- NA
HbA1cBefTx$TcPatients[1] <- nrow(subset(studyPop, treatment == 0))
HbA1cBefTx$TcPatients[2] <- nrow(subset(studyPop, treatment == 1))
HbA1cBefTx$Index <- c("Before")
HbA1cAfTx$TcPatients <- NA
HbA1cAfTx$TcPatients[1] <- nrow(subset(studyPop, treatment == 0))
HbA1cAfTx$TcPatients[2] <- nrow(subset(studyPop, treatment == 1))
HbA1cAfTx$Index <- c("After")
unMatchedHbA1cMeanSd <- rbind(HbA1cBefTx, HbA1cAfTx)
unMatchedHbA1cMeanSd$class <- c("unMatched")
remove(HbA1cBefTx, HbA1cAfTx)
# Matched Cohort
insertTable(conn,
"ohdsiT2DstudyPop",
matchedPop,
dropTableIfExists = TRUE,
createTable = TRUE,
tempTable = TRUE,
oracleTempSchema = NULL)
sqlOne <- paste("SELECT o.treatment,
count(DISTINCT m.person_id) AS patients,
count(*)
AS records,
AVG(m.VALUE_AS_NUMBER) AS AVG,
STDEV(m.VALUE_AS_NUMBER) AS STD
FROM @cdmDatabaseSchema.MEASUREMENT m
JOIN #ohdsiT2DstudyPop o
ON m.person_id = o.SUBJECTID
WHERE m.measurement_concept_id IN (3004410,
3007263,
3003309,
3005673,
40762352,
40758583,
3034639,
4197971)
AND m.MEASUREMENT_DATE < CAST(o.COHORTSTARTDATE AS DATE)
AND m.measurement_date >= dateadd(day,
-365,
CAST(o.COHORTSTARTDATE AS DATE)) AND m.measurement_date <= CAST(o.COHORTSTARTDATE AS DATE)
AND m.VALUE_AS_NUMBER < 20
GROUP BY o.treatment", sep = "")
sqlOne <- SqlRender::renderSql(sqlOne, cdmDatabaseSchema = cdmDatabaseSchema)$sql
sqlOne <- SqlRender::translateSql(sqlOne, targetDialect = connectionDetails$dbms)$sql
HbA1cBefTx <- querySql(conn, sqlOne)
remove(sqlOne)
sqlOne <- paste("SELECT o.treatment,
count(DISTINCT m.person_id) AS patients,
count(*)
AS records,
AVG(m.VALUE_AS_NUMBER) AS AVG,
STDEV(m.VALUE_AS_NUMBER) AS STD
FROM @cdmDatabaseSchema.MEASUREMENT m
JOIN #ohdsiT2DstudyPop o
ON m.person_id = o.SUBJECTID
WHERE m.measurement_concept_id IN (3004410,
3007263,
3003309,
3005673,
40762352,
40758583,
3034639,
4197971)
AND m.MEASUREMENT_DATE > CAST(o.COHORTSTARTDATE AS DATE)
AND m.VALUE_AS_NUMBER < 20
GROUP BY o.treatment", sep = "")
sqlOne <- SqlRender::renderSql(sqlOne, cdmDatabaseSchema = cdmDatabaseSchema)$sql
sqlOne <- SqlRender::translateSql(sqlOne, targetDialect = connectionDetails$dbms)$sql
HbA1cAfTx <- querySql(conn, sqlOne)
remove(sqlOne)
HbA1cBefTx$TcPatients <- NA
HbA1cBefTx$TcPatients[1] <- nrow(subset(matchedPop, treatment == 0))
HbA1cBefTx$TcPatients[2] <- nrow(subset(matchedPop, treatment == 1))
HbA1cBefTx$Index <- c("Before")
HbA1cAfTx$TcPatients <- NA
HbA1cAfTx$TcPatients[1] <- nrow(subset(matchedPop, treatment == 0))
HbA1cAfTx$TcPatients[2] <- nrow(subset(matchedPop, treatment == 1))
HbA1cAfTx$Index <- c("After")
matchedHbA1cMeanSd <- rbind(HbA1cBefTx, HbA1cAfTx)
matchedHbA1cMeanSd$class <- c("matched")
remove(HbA1cBefTx, HbA1cAfTx)
hbA1cStat <- rbind(unMatchedHbA1cMeanSd, matchedHbA1cMeanSd)
write.csv(hbA1cStat, file = paste(results_path,"bigToDpp4_bigToThia_HbA1c7Good_Stat.csv",sep=""))
remove(unMatchedHbA1cMeanSd, matchedHbA1cMeanSd, hbA1cStat)
remove(psScore, matchedPop, studyPop, balance)
}else
{
print(paste("You don't seems to have results for the bigToDpp4 and bigToThia comparision"))
}
#----------------------------------------------------------------------
#---------------------------------------------------------------------
#For outCome 5 representing HbA1c <= 8%, represented as HbA1c7Good
x <- grep("_o5.rds",resFiles)
resFilesOutCome5 <- resFiles[x]
#Get files sorted for t and c comparisions
#bigToSulf and bigToDpp4 (1,2)
tcOne <- grep("_t1_c2",resFilesOutCome5)
#bigToSulf and bigToThia
tcTwo <- grep("_t1_c3",resFilesOutCome5)
#bigToDpp4 and bigToThia
tcThree <- grep("_t2_c3",resFilesOutCome5)
#---- For tcOne
if(length(tcOne)!=0){
resFilesOutCome5tcOne <- resFilesOutCome5[tcOne]
#load the data
ps <- grep("Ps",resFilesOutCome5tcOne)
psScore <- readRDS(paste(results_path,"deleteMeBeforeSharing/",resFilesOutCome5tcOne[ps],sep=""))
matchPop <- grep("StratPop",resFilesOutCome5tcOne)
matchedPop <- readRDS(paste(results_path,"deleteMeBeforeSharing/",resFilesOutCome5tcOne[matchPop],sep=""))
studPop <- grep("StudyPop", resFilesOutCome5tcOne)
studyPop <- readRDS(paste(results_path,"deleteMeBeforeSharing/",resFilesOutCome5tcOne[studPop],sep=""))
bl <- grep("Bal",resFilesOutCome5tcOne)
balance <- readRDS(paste(results_path,"deleteMeBeforeSharing/",resFilesOutCome5tcOne[bl],sep=""))
remove(ps,matchPop,studPop,bl)
conn <- DatabaseConnector::connect(connectionDetails)
insertTable(conn,
"ohdsiT2DstudyPop",
studyPop,
dropTableIfExists = TRUE,
createTable = TRUE,
tempTable = TRUE,
oracleTempSchema = NULL)
sqlOne <- paste("SELECT o.treatment,
count(DISTINCT m.person_id) AS patients,
count(*)
AS records,
AVG(m.VALUE_AS_NUMBER) AS AVG,
STDEV(m.VALUE_AS_NUMBER) AS STD
FROM @cdmDatabaseSchema.MEASUREMENT m
JOIN #ohdsiT2DstudyPop o
ON m.person_id = o.SUBJECTID
WHERE m.measurement_concept_id IN (3004410,
3007263,
3003309,
3005673,
40762352,
40758583,
3034639,
4197971)
AND m.MEASUREMENT_DATE < CAST(o.COHORTSTARTDATE AS DATE)
AND m.VALUE_AS_NUMBER < 20
GROUP BY o.treatment", sep = "")
sqlOne <- SqlRender::renderSql(sqlOne, cdmDatabaseSchema = cdmDatabaseSchema)$sql
sqlOne <- SqlRender::translateSql(sqlOne, targetDialect = connectionDetails$dbms)$sql
HbA1cBefTx <- querySql(conn, sqlOne)
remove(sqlOne)
sqlOne <- paste("SELECT o.treatment,
count(DISTINCT m.person_id) AS patients,
count(*)
AS records,
AVG(m.VALUE_AS_NUMBER) AS AVG,
STDEV(m.VALUE_AS_NUMBER) AS STD
FROM @cdmDatabaseSchema.MEASUREMENT m
JOIN #ohdsiT2DstudyPop o
ON m.person_id = o.SUBJECTID
WHERE m.measurement_concept_id IN (3004410,
3007263,
3003309,
3005673,
40762352,
40758583,
3034639,
4197971)
AND m.MEASUREMENT_DATE > CAST(o.COHORTSTARTDATE AS DATE)
AND m.VALUE_AS_NUMBER < 20
GROUP BY o.treatment", sep = "")
sqlOne <- SqlRender::renderSql(sqlOne, cdmDatabaseSchema = cdmDatabaseSchema)$sql
sqlOne <- SqlRender::translateSql(sqlOne, targetDialect = connectionDetails$dbms)$sql
HbA1cAfTx <- querySql(conn, sqlOne)
remove(sqlOne)
HbA1cBefTx$TcPatients <- NA
HbA1cBefTx$TcPatients[1] <- nrow(subset(studyPop, treatment == 0))
HbA1cBefTx$TcPatients[2] <- nrow(subset(studyPop, treatment == 1))
HbA1cBefTx$Index <- c("Before")
HbA1cAfTx$TcPatients <- NA
HbA1cAfTx$TcPatients[1] <- nrow(subset(studyPop, treatment == 0))
HbA1cAfTx$TcPatients[2] <- nrow(subset(studyPop, treatment == 1))
HbA1cAfTx$Index <- c("After")
unMatchedHbA1cMeanSd <- rbind(HbA1cBefTx, HbA1cAfTx)
unMatchedHbA1cMeanSd$class <- c("unMatched")
remove(HbA1cBefTx, HbA1cAfTx)
# Matched Cohort
insertTable(conn,
"ohdsiT2DstudyPop",
matchedPop,
dropTableIfExists = TRUE,
createTable = TRUE,
tempTable = TRUE,
oracleTempSchema = NULL)
sqlOne <- paste("SELECT o.treatment,
count(DISTINCT m.person_id) AS patients,
count(*)
AS records,
AVG(m.VALUE_AS_NUMBER) AS AVG,
STDEV(m.VALUE_AS_NUMBER) AS STD
FROM @cdmDatabaseSchema.MEASUREMENT m
JOIN #ohdsiT2DstudyPop o
ON m.person_id = o.SUBJECTID
WHERE m.measurement_concept_id IN (3004410,
3007263,
3003309,
3005673,
40762352,
40758583,
3034639,
4197971)
AND m.MEASUREMENT_DATE < CAST(o.COHORTSTARTDATE AS DATE)
AND m.measurement_date >= dateadd(day,
-365,
CAST(o.COHORTSTARTDATE AS DATE)) AND m.measurement_date <= CAST(o.COHORTSTARTDATE AS DATE)
AND m.VALUE_AS_NUMBER < 20
GROUP BY o.treatment", sep = "")
sqlOne <- SqlRender::renderSql(sqlOne, cdmDatabaseSchema = cdmDatabaseSchema)$sql
sqlOne <- SqlRender::translateSql(sqlOne, targetDialect = connectionDetails$dbms)$sql
HbA1cBefTx <- querySql(conn, sqlOne)
remove(sqlOne)
sqlOne <- paste("SELECT o.treatment,
count(DISTINCT m.person_id) AS patients,
count(*)
AS records,
AVG(m.VALUE_AS_NUMBER) AS AVG,
STDEV(m.VALUE_AS_NUMBER) AS STD
FROM @cdmDatabaseSchema.MEASUREMENT m
JOIN #ohdsiT2DstudyPop o
ON m.person_id = o.SUBJECTID
WHERE m.measurement_concept_id IN (3004410,
3007263,
3003309,
3005673,
40762352,
40758583,
3034639,
4197971)
AND m.MEASUREMENT_DATE > CAST(o.COHORTSTARTDATE AS DATE)
AND m.VALUE_AS_NUMBER < 20
GROUP BY o.treatment", sep = "")
sqlOne <- SqlRender::renderSql(sqlOne, cdmDatabaseSchema = cdmDatabaseSchema)$sql
sqlOne <- SqlRender::translateSql(sqlOne, targetDialect = connectionDetails$dbms)$sql
HbA1cAfTx <- querySql(conn, sqlOne)
remove(sqlOne)
HbA1cBefTx$TcPatients <- NA
HbA1cBefTx$TcPatients[1] <- nrow(subset(matchedPop, treatment == 0))
HbA1cBefTx$TcPatients[2] <- nrow(subset(matchedPop, treatment == 1))
HbA1cBefTx$Index <- c("Before")
HbA1cAfTx$TcPatients <- NA
HbA1cAfTx$TcPatients[1] <- nrow(subset(matchedPop, treatment == 0))
HbA1cAfTx$TcPatients[2] <- nrow(subset(matchedPop, treatment == 1))
HbA1cAfTx$Index <- c("After")
matchedHbA1cMeanSd <- rbind(HbA1cBefTx, HbA1cAfTx)
matchedHbA1cMeanSd$class <- c("matched")
remove(HbA1cBefTx, HbA1cAfTx)
hbA1cStat <- rbind(unMatchedHbA1cMeanSd, matchedHbA1cMeanSd)
write.csv(hbA1cStat, file = paste(results_path,"bigToSulf_bigToDpp4_HbA1c8Moderate_Stat.csv",sep=""))
remove(unMatchedHbA1cMeanSd, matchedHbA1cMeanSd, hbA1cStat)
remove(psScore, matchedPop, studyPop, balance)
}else
{
print(paste("You don't seems to have results for the bigToSulf and bigToDpp4 comparision"))
}
#---- For tcTwo
if(length(tcTwo)!=0){
resFilesOutCome5tcTwo <- resFilesOutCome5[tcTwo]
#load the data
ps <- grep("Ps",resFilesOutCome5tcTwo)
psScore <- readRDS(paste(results_path,"deleteMeBeforeSharing/",resFilesOutCome5tcTwo[ps],sep=""))
matchPop <- grep("StratPop",resFilesOutCome5tcTwo)
matchedPop <- readRDS(paste(results_path,"deleteMeBeforeSharing/",resFilesOutCome5tcTwo[matchPop],sep=""))
studPop <- grep("StudyPop", resFilesOutCome5tcTwo)
studyPop <- readRDS(paste(results_path,"deleteMeBeforeSharing/",resFilesOutCome5tcTwo[studPop],sep=""))
bl <- grep("Bal",resFilesOutCome5tcTwo)
balance <- readRDS(paste(results_path,"deleteMeBeforeSharing/",resFilesOutCome5tcTwo[bl],sep=""))
remove(ps,matchPop,studPop,bl)
conn <- DatabaseConnector::connect(connectionDetails)
insertTable(conn,
"ohdsiT2DstudyPop",
studyPop,
dropTableIfExists = TRUE,
createTable = TRUE,
tempTable = TRUE,
oracleTempSchema = NULL)
sqlOne <- paste("SELECT o.treatment,
count(DISTINCT m.person_id) AS patients,
count(*)
AS records,
AVG(m.VALUE_AS_NUMBER) AS AVG,
STDEV(m.VALUE_AS_NUMBER) AS STD
FROM @cdmDatabaseSchema.MEASUREMENT m
JOIN #ohdsiT2DstudyPop o
ON m.person_id = o.SUBJECTID
WHERE m.measurement_concept_id IN (3004410,
3007263,
3003309,
3005673,
40762352,
40758583,
3034639,
4197971)
AND m.MEASUREMENT_DATE < CAST(o.COHORTSTARTDATE AS DATE)
AND m.VALUE_AS_NUMBER < 20
GROUP BY o.treatment", sep = "")
sqlOne <- SqlRender::renderSql(sqlOne, cdmDatabaseSchema = cdmDatabaseSchema)$sql
sqlOne <- SqlRender::translateSql(sqlOne, targetDialect = connectionDetails$dbms)$sql
HbA1cBefTx <- querySql(conn, sqlOne)
remove(sqlOne)
sqlOne <- paste("SELECT o.treatment,
count(DISTINCT m.person_id) AS patients,
count(*)
AS records,
AVG(m.VALUE_AS_NUMBER) AS AVG,
STDEV(m.VALUE_AS_NUMBER) AS STD
FROM @cdmDatabaseSchema.MEASUREMENT m
JOIN #ohdsiT2DstudyPop o
ON m.person_id = o.SUBJECTID
WHERE m.measurement_concept_id IN (3004410,
3007263,
3003309,
3005673,
40762352,
40758583,
3034639,
4197971)
AND m.MEASUREMENT_DATE > CAST(o.COHORTSTARTDATE AS DATE)
AND m.VALUE_AS_NUMBER < 20
GROUP BY o.treatment", sep = "")
sqlOne <- SqlRender::renderSql(sqlOne, cdmDatabaseSchema = cdmDatabaseSchema)$sql
sqlOne <- SqlRender::translateSql(sqlOne, targetDialect = connectionDetails$dbms)$sql
HbA1cAfTx <- querySql(conn, sqlOne)
remove(sqlOne)
HbA1cBefTx$TcPatients <- NA
HbA1cBefTx$TcPatients[1] <- nrow(subset(studyPop, treatment == 0))
HbA1cBefTx$TcPatients[2] <- nrow(subset(studyPop, treatment == 1))
HbA1cBefTx$Index <- c("Before")
HbA1cAfTx$TcPatients <- NA
HbA1cAfTx$TcPatients[1] <- nrow(subset(studyPop, treatment == 0))
HbA1cAfTx$TcPatients[2] <- nrow(subset(studyPop, treatment == 1))
HbA1cAfTx$Index <- c("After")
unMatchedHbA1cMeanSd <- rbind(HbA1cBefTx, HbA1cAfTx)
unMatchedHbA1cMeanSd$class <- c("unMatched")
remove(HbA1cBefTx, HbA1cAfTx)
# Matched Cohort
insertTable(conn,
"ohdsiT2DstudyPop",
matchedPop,
dropTableIfExists = TRUE,
createTable = TRUE,
tempTable = TRUE,
oracleTempSchema = NULL)
sqlOne <- paste("SELECT o.treatment,
count(DISTINCT m.person_id) AS patients,
count(*)
AS records,
AVG(m.VALUE_AS_NUMBER) AS AVG,
STDEV(m.VALUE_AS_NUMBER) AS STD
FROM @cdmDatabaseSchema.MEASUREMENT m
JOIN #ohdsiT2DstudyPop o
ON m.person_id = o.SUBJECTID
WHERE m.measurement_concept_id IN (3004410,
3007263,
3003309,
3005673,
40762352,
40758583,
3034639,
4197971)
AND m.MEASUREMENT_DATE < CAST(o.COHORTSTARTDATE AS DATE)
AND m.measurement_date >= dateadd(day,
-365,
CAST(o.COHORTSTARTDATE AS DATE)) AND m.measurement_date <= CAST(o.COHORTSTARTDATE AS DATE)
AND m.VALUE_AS_NUMBER < 20
GROUP BY o.treatment", sep = "")
sqlOne <- SqlRender::renderSql(sqlOne, cdmDatabaseSchema = cdmDatabaseSchema)$sql
sqlOne <- SqlRender::translateSql(sqlOne, targetDialect = connectionDetails$dbms)$sql
HbA1cBefTx <- querySql(conn, sqlOne)
remove(sqlOne)
sqlOne <- paste("SELECT o.treatment,
count(DISTINCT m.person_id) AS patients,
count(*)
AS records,
AVG(m.VALUE_AS_NUMBER) AS AVG,
STDEV(m.VALUE_AS_NUMBER) AS STD
FROM @cdmDatabaseSchema.MEASUREMENT m
JOIN #ohdsiT2DstudyPop o
ON m.person_id = o.SUBJECTID
WHERE m.measurement_concept_id IN (3004410,
3007263,
3003309,
3005673,
40762352,
40758583,
3034639,
4197971)
AND m.MEASUREMENT_DATE > CAST(o.COHORTSTARTDATE AS DATE)
AND m.VALUE_AS_NUMBER < 20
GROUP BY o.treatment", sep = "")
sqlOne <- SqlRender::renderSql(sqlOne, cdmDatabaseSchema = cdmDatabaseSchema)$sql
sqlOne <- SqlRender::translateSql(sqlOne, targetDialect = connectionDetails$dbms)$sql
HbA1cAfTx <- querySql(conn, sqlOne)
remove(sqlOne)
HbA1cBefTx$TcPatients <- NA
HbA1cBefTx$TcPatients[1] <- nrow(subset(matchedPop, treatment == 0))
HbA1cBefTx$TcPatients[2] <- nrow(subset(matchedPop, treatment == 1))
HbA1cBefTx$Index <- c("Before")
HbA1cAfTx$TcPatients <- NA
HbA1cAfTx$TcPatients[1] <- nrow(subset(matchedPop, treatment == 0))
HbA1cAfTx$TcPatients[2] <- nrow(subset(matchedPop, treatment == 1))
HbA1cAfTx$Index <- c("After")
matchedHbA1cMeanSd <- rbind(HbA1cBefTx, HbA1cAfTx)
matchedHbA1cMeanSd$class <- c("matched")
remove(HbA1cBefTx, HbA1cAfTx)
hbA1cStat <- rbind(unMatchedHbA1cMeanSd, matchedHbA1cMeanSd)
write.csv(hbA1cStat, file = paste(results_path,"bigToSulf_bigToThia_HbA1c8Moderate_Stat.csv",sep=""))
remove(unMatchedHbA1cMeanSd, matchedHbA1cMeanSd, hbA1cStat)
remove(psScore, matchedPop, studyPop, balance)
}else
{
print(paste("You don't seems to have results for the bigToSulf and bigToThia comparision"))
}
#---- For tcThree
if(length(tcThree)!=0){
resFilesOutCome5tcThree <- resFilesOutCome5[tcThree]
#load the data
ps <- grep("Ps",resFilesOutCome5tcThree)
psScore <- readRDS(paste(results_path,"deleteMeBeforeSharing/",resFilesOutCome5tcThree[ps],sep=""))
matchPop <- grep("StratPop",resFilesOutCome5tcThree)
matchedPop <- readRDS(paste(results_path,"deleteMeBeforeSharing/",resFilesOutCome5tcThree[matchPop],sep=""))
studPop <- grep("StudyPop", resFilesOutCome5tcThree)
studyPop <- readRDS(paste(results_path,"deleteMeBeforeSharing/",resFilesOutCome5tcThree[studPop],sep=""))
bl <- grep("Bal",resFilesOutCome5tcThree)
balance <- readRDS(paste(results_path,"deleteMeBeforeSharing/",resFilesOutCome5tcThree[bl],sep=""))
remove(ps,matchPop,studPop,bl)
conn <- DatabaseConnector::connect(connectionDetails)
insertTable(conn,
"ohdsiT2DstudyPop",
studyPop,
dropTableIfExists = TRUE,
createTable = TRUE,
tempTable = TRUE,
oracleTempSchema = NULL)
sqlOne <- paste("SELECT o.treatment,
count(DISTINCT m.person_id) AS patients,
count(*)
AS records,
AVG(m.VALUE_AS_NUMBER) AS AVG,
STDEV(m.VALUE_AS_NUMBER) AS STD
FROM @cdmDatabaseSchema.MEASUREMENT m
JOIN #ohdsiT2DstudyPop o
ON m.person_id = o.SUBJECTID
WHERE m.measurement_concept_id IN (3004410,
3007263,
3003309,
3005673,
40762352,
40758583,
3034639,
4197971)
AND m.MEASUREMENT_DATE < CAST(o.COHORTSTARTDATE AS DATE)
AND m.VALUE_AS_NUMBER < 20
GROUP BY o.treatment", sep = "")
sqlOne <- SqlRender::renderSql(sqlOne, cdmDatabaseSchema = cdmDatabaseSchema)$sql
sqlOne <- SqlRender::translateSql(sqlOne, targetDialect = connectionDetails$dbms)$sql
HbA1cBefTx <- querySql(conn, sqlOne)
remove(sqlOne)
sqlOne <- paste("SELECT o.treatment,
count(DISTINCT m.person_id) AS patients,
count(*)
AS records,
AVG(m.VALUE_AS_NUMBER) AS AVG,
STDEV(m.VALUE_AS_NUMBER) AS STD
FROM @cdmDatabaseSchema.MEASUREMENT m
JOIN #ohdsiT2DstudyPop o
ON m.person_id = o.SUBJECTID
WHERE m.measurement_concept_id IN (3004410,
3007263,
3003309,
3005673,
40762352,
40758583,
3034639,
4197971)
AND m.MEASUREMENT_DATE > CAST(o.COHORTSTARTDATE AS DATE)
AND m.VALUE_AS_NUMBER < 20
GROUP BY o.treatment", sep = "")
sqlOne <- SqlRender::renderSql(sqlOne, cdmDatabaseSchema = cdmDatabaseSchema)$sql
sqlOne <- SqlRender::translateSql(sqlOne, targetDialect = connectionDetails$dbms)$sql
HbA1cAfTx <- querySql(conn, sqlOne)
remove(sqlOne)
HbA1cBefTx$TcPatients <- NA
HbA1cBefTx$TcPatients[1] <- nrow(subset(studyPop, treatment == 0))
HbA1cBefTx$TcPatients[2] <- nrow(subset(studyPop, treatment == 1))
HbA1cBefTx$Index <- c("Before")
HbA1cAfTx$TcPatients <- NA
HbA1cAfTx$TcPatients[1] <- nrow(subset(studyPop, treatment == 0))
HbA1cAfTx$TcPatients[2] <- nrow(subset(studyPop, treatment == 1))
HbA1cAfTx$Index <- c("After")
unMatchedHbA1cMeanSd <- rbind(HbA1cBefTx, HbA1cAfTx)
unMatchedHbA1cMeanSd$class <- c("unMatched")
remove(HbA1cBefTx, HbA1cAfTx)
# Matched Cohort
insertTable(conn,
"ohdsiT2DstudyPop",
matchedPop,
dropTableIfExists = TRUE,
createTable = TRUE,
tempTable = TRUE,
oracleTempSchema = NULL)
sqlOne <- paste("SELECT o.treatment,
count(DISTINCT m.person_id) AS patients,
count(*)
AS records,
AVG(m.VALUE_AS_NUMBER) AS AVG,
STDEV(m.VALUE_AS_NUMBER) AS STD
FROM @cdmDatabaseSchema.MEASUREMENT m
JOIN #ohdsiT2DstudyPop o
ON m.person_id = o.SUBJECTID
WHERE m.measurement_concept_id IN (3004410,
3007263,
3003309,
3005673,
40762352,
40758583,
3034639,
4197971)
AND m.MEASUREMENT_DATE < CAST(o.COHORTSTARTDATE AS DATE)
AND m.measurement_date >= dateadd(day,
-365,
CAST(o.COHORTSTARTDATE AS DATE)) AND m.measurement_date <= CAST(o.COHORTSTARTDATE AS DATE)
AND m.VALUE_AS_NUMBER < 20
GROUP BY o.treatment", sep = "")
sqlOne <- SqlRender::renderSql(sqlOne, cdmDatabaseSchema = cdmDatabaseSchema)$sql
sqlOne <- SqlRender::translateSql(sqlOne, targetDialect = connectionDetails$dbms)$sql
HbA1cBefTx <- querySql(conn, sqlOne)
remove(sqlOne)
sqlOne <- paste("SELECT o.treatment,
count(DISTINCT m.person_id) AS patients,
count(*)
AS records,
AVG(m.VALUE_AS_NUMBER) AS AVG,
STDEV(m.VALUE_AS_NUMBER) AS STD
FROM @cdmDatabaseSchema.MEASUREMENT m
JOIN #ohdsiT2DstudyPop o
ON m.person_id = o.SUBJECTID
WHERE m.measurement_concept_id IN (3004410,
3007263,
3003309,
3005673,
40762352,
40758583,
3034639,
4197971)
AND m.MEASUREMENT_DATE > CAST(o.COHORTSTARTDATE AS DATE)
AND m.VALUE_AS_NUMBER < 20
GROUP BY o.treatment", sep = "")
sqlOne <- SqlRender::renderSql(sqlOne, cdmDatabaseSchema = cdmDatabaseSchema)$sql
sqlOne <- SqlRender::translateSql(sqlOne, targetDialect = connectionDetails$dbms)$sql
HbA1cAfTx <- querySql(conn, sqlOne)
remove(sqlOne)
HbA1cBefTx$TcPatients <- NA
HbA1cBefTx$TcPatients[1] <- nrow(subset(matchedPop, treatment == 0))
HbA1cBefTx$TcPatients[2] <- nrow(subset(matchedPop, treatment == 1))
HbA1cBefTx$Index <- c("Before")
HbA1cAfTx$TcPatients <- NA
HbA1cAfTx$TcPatients[1] <- nrow(subset(matchedPop, treatment == 0))
HbA1cAfTx$TcPatients[2] <- nrow(subset(matchedPop, treatment == 1))
HbA1cAfTx$Index <- c("After")
matchedHbA1cMeanSd <- rbind(HbA1cBefTx, HbA1cAfTx)
matchedHbA1cMeanSd$class <- c("matched")
remove(HbA1cBefTx, HbA1cAfTx)
hbA1cStat <- rbind(unMatchedHbA1cMeanSd, matchedHbA1cMeanSd)
write.csv(hbA1cStat, file = paste(results_path,"bigToDpp4_bigToThia_HbA1c8Moderate_Stat.csv",sep=""))
remove(unMatchedHbA1cMeanSd, matchedHbA1cMeanSd, hbA1cStat)
remove(psScore, matchedPop, studyPop, balance)
}else
{
print(paste("You don't seems to have results for the bigToDpp4 and bigToThia comparision"))
}
#----------------------------------------------------------------------
}
rohit43/DiabetesTxPath documentation built on May 27, 2019, 1:46 p.m.
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Defines functions getHbA1cStat
# @file functions
#
# Copyright 2017 Observational Health Data Sciences and Informatics
#
# This file is part of:
# ----------------------------------------------
# DiabetesTxPath
# ----------------------------------------------
# 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
#
# http://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.
#
# @author Stanford University Center for Biomedical Informatics - Shah Lab
# @author Rohit Vashisht
#
#' @title
#' getAgeGender
#'
#' @author
#' Rohit Vashisht
#'
#' @details
#' This function plots the results of T2D study.
getHbA1cStat <- function(results_path){
print(paste("Getting HbA1c Stats. This might take few minutes ... "))
resFiles <- list.files(paste(results_path,"/deleteMeBeforeSharing/",sep=""))
#---------------------------------------------------------------------
#For outCome 4 representing HbA1c <= 7%, represented as HbA1c7Good
x <- grep("_o4.rds",resFiles)
resFilesOutCome4 <- resFiles[x]
#Get files sorted for t and c comparisions
#bigToSulf and bigToDpp4 (1,2)
tcOne <- grep("_t1_c2",resFilesOutCome4)
#bigToSulf and bigToThia
tcTwo <- grep("_t1_c3",resFilesOutCome4)
#bigToDpp4 and bigToThia
tcThree <- grep("_t2_c3",resFilesOutCome4)
#---- For tcOne
if(length(tcOne)!=0){
resFilesOutCome4tcOne <- resFilesOutCome4[tcOne]
#load the data
ps <- grep("Ps",resFilesOutCome4tcOne)
psScore <- readRDS(paste(results_path,"deleteMeBeforeSharing/",resFilesOutCome4tcOne[ps],sep=""))
matchPop <- grep("StratPop",resFilesOutCome4tcOne)
matchedPop <- readRDS(paste(results_path,"deleteMeBeforeSharing/",resFilesOutCome4tcOne[matchPop],sep=""))
studPop <- grep("StudyPop", resFilesOutCome4tcOne)
studyPop <- readRDS(paste(results_path,"deleteMeBeforeSharing/",resFilesOutCome4tcOne[studPop],sep=""))
bl <- grep("Bal",resFilesOutCome4tcOne)
balance <- readRDS(paste(results_path,"deleteMeBeforeSharing/",resFilesOutCome4tcOne[bl],sep=""))
remove(ps,matchPop,studPop,bl)
conn <- DatabaseConnector::connect(connectionDetails)
insertTable(conn,
"ohdsiT2DstudyPop",
studyPop,
dropTableIfExists = TRUE,
createTable = TRUE,
tempTable = TRUE,
oracleTempSchema = NULL)
sqlOne <- paste("SELECT o.treatment,
count(DISTINCT m.person_id) AS patients,
count(*)
AS records,
AVG(m.VALUE_AS_NUMBER) AS AVG,
STDEV(m.VALUE_AS_NUMBER) AS STD
FROM @cdmDatabaseSchema.MEASUREMENT m
JOIN #ohdsiT2DstudyPop o
ON m.person_id = o.SUBJECTID
WHERE m.measurement_concept_id IN (3004410,
3007263,
3003309,
3005673,
40762352,
40758583,
3034639,
4197971)
AND m.MEASUREMENT_DATE < CAST(o.COHORTSTARTDATE AS DATE)
AND m.VALUE_AS_NUMBER < 20
GROUP BY o.treatment", sep = "")
sqlOne <- SqlRender::renderSql(sqlOne, cdmDatabaseSchema = cdmDatabaseSchema)$sql
sqlOne <- SqlRender::translateSql(sqlOne, targetDialect = connectionDetails$dbms)$sql
HbA1cBefTx <- querySql(conn, sqlOne)
remove(sqlOne)
sqlOne <- paste("SELECT o.treatment,
count(DISTINCT m.person_id) AS patients,
count(*)
AS records,
AVG(m.VALUE_AS_NUMBER) AS AVG,
STDEV(m.VALUE_AS_NUMBER) AS STD
FROM @cdmDatabaseSchema.MEASUREMENT m
JOIN #ohdsiT2DstudyPop o
ON m.person_id = o.SUBJECTID
WHERE m.measurement_concept_id IN (3004410,
3007263,
3003309,
3005673,
40762352,
40758583,
3034639,
4197971)
AND m.MEASUREMENT_DATE > CAST(o.COHORTSTARTDATE AS DATE)
AND m.VALUE_AS_NUMBER < 20
GROUP BY o.treatment", sep = "")
sqlOne <- SqlRender::renderSql(sqlOne, cdmDatabaseSchema = cdmDatabaseSchema)$sql
sqlOne <- SqlRender::translateSql(sqlOne, targetDialect = connectionDetails$dbms)$sql
HbA1cAfTx <- querySql(conn, sqlOne)
remove(sqlOne)
HbA1cBefTx$TcPatients <- NA
HbA1cBefTx$TcPatients[1] <- nrow(subset(studyPop, treatment == 0))
HbA1cBefTx$TcPatients[2] <- nrow(subset(studyPop, treatment == 1))
HbA1cBefTx$Index <- c("Before")
HbA1cAfTx$TcPatients <- NA
HbA1cAfTx$TcPatients[1] <- nrow(subset(studyPop, treatment == 0))
HbA1cAfTx$TcPatients[2] <- nrow(subset(studyPop, treatment == 1))
HbA1cAfTx$Index <- c("After")
unMatchedHbA1cMeanSd <- rbind(HbA1cBefTx, HbA1cAfTx)
unMatchedHbA1cMeanSd$class <- c("unMatched")
remove(HbA1cBefTx, HbA1cAfTx)
# Matched Cohort
insertTable(conn,
"ohdsiT2DstudyPop",
matchedPop,
dropTableIfExists = TRUE,
createTable = TRUE,
tempTable = TRUE,
oracleTempSchema = NULL)
sqlOne <- paste("SELECT o.treatment,
count(DISTINCT m.person_id) AS patients,
count(*)
AS records,
AVG(m.VALUE_AS_NUMBER) AS AVG,
STDEV(m.VALUE_AS_NUMBER) AS STD
FROM @cdmDatabaseSchema.MEASUREMENT m
JOIN #ohdsiT2DstudyPop o
ON m.person_id = o.SUBJECTID
WHERE m.measurement_concept_id IN (3004410,
3007263,
3003309,
3005673,
40762352,
40758583,
3034639,
4197971)
AND m.MEASUREMENT_DATE < CAST(o.COHORTSTARTDATE AS DATE)
AND m.measurement_date >= dateadd(day,
-365,
CAST(o.COHORTSTARTDATE AS DATE)) AND m.measurement_date <= CAST(o.COHORTSTARTDATE AS DATE)
AND m.VALUE_AS_NUMBER < 20
GROUP BY o.treatment", sep = "")
sqlOne <- SqlRender::renderSql(sqlOne, cdmDatabaseSchema = cdmDatabaseSchema)$sql
sqlOne <- SqlRender::translateSql(sqlOne, targetDialect = connectionDetails$dbms)$sql
HbA1cBefTx <- querySql(conn, sqlOne)
remove(sqlOne)
sqlOne <- paste("SELECT o.treatment,
count(DISTINCT m.person_id) AS patients,
count(*)
AS records,
AVG(m.VALUE_AS_NUMBER) AS AVG,
STDEV(m.VALUE_AS_NUMBER) AS STD
FROM @cdmDatabaseSchema.MEASUREMENT m
JOIN #ohdsiT2DstudyPop o
ON m.person_id = o.SUBJECTID
WHERE m.measurement_concept_id IN (3004410,
3007263,
3003309,
3005673,
40762352,
40758583,
3034639,
4197971)
AND m.MEASUREMENT_DATE > CAST(o.COHORTSTARTDATE AS DATE)
AND m.VALUE_AS_NUMBER < 20
GROUP BY o.treatment", sep = "")
sqlOne <- SqlRender::renderSql(sqlOne, cdmDatabaseSchema = cdmDatabaseSchema)$sql
sqlOne <- SqlRender::translateSql(sqlOne, targetDialect = connectionDetails$dbms)$sql
HbA1cAfTx <- querySql(conn, sqlOne)
remove(sqlOne)
HbA1cBefTx$TcPatients <- NA
HbA1cBefTx$TcPatients[1] <- nrow(subset(matchedPop, treatment == 0))
HbA1cBefTx$TcPatients[2] <- nrow(subset(matchedPop, treatment == 1))
HbA1cBefTx$Index <- c("Before")
HbA1cAfTx$TcPatients <- NA
HbA1cAfTx$TcPatients[1] <- nrow(subset(matchedPop, treatment == 0))
HbA1cAfTx$TcPatients[2] <- nrow(subset(matchedPop, treatment == 1))
HbA1cAfTx$Index <- c("After")
matchedHbA1cMeanSd <- rbind(HbA1cBefTx, HbA1cAfTx)
matchedHbA1cMeanSd$class <- c("matched")
remove(HbA1cBefTx, HbA1cAfTx)
hbA1cStat <- rbind(unMatchedHbA1cMeanSd, matchedHbA1cMeanSd)
write.csv(hbA1cStat, file = paste(results_path,"bigToSulf_bigToDpp4_HbA1c7Good_Stat.csv",sep=""))
remove(unMatchedHbA1cMeanSd, matchedHbA1cMeanSd, hbA1cStat)
remove(psScore, matchedPop, studyPop, balance)
}else
{
print(paste("You don't seems to have results for the bigToSulf and bigToDpp4 comparision"))
}
#---- For tcTwo
if(length(tcTwo)!=0){
resFilesOutCome4tcTwo <- resFilesOutCome4[tcTwo]
#load the data
ps <- grep("Ps",resFilesOutCome4tcTwo)
psScore <- readRDS(paste(results_path,"deleteMeBeforeSharing/",resFilesOutCome4tcTwo[ps],sep=""))
matchPop <- grep("StratPop",resFilesOutCome4tcTwo)
matchedPop <- readRDS(paste(results_path,"deleteMeBeforeSharing/",resFilesOutCome4tcTwo[matchPop],sep=""))
studPop <- grep("StudyPop", resFilesOutCome4tcTwo)
studyPop <- readRDS(paste(results_path,"deleteMeBeforeSharing/",resFilesOutCome4tcTwo[studPop],sep=""))
bl <- grep("Bal",resFilesOutCome4tcTwo)
balance <- readRDS(paste(results_path,"deleteMeBeforeSharing/",resFilesOutCome4tcTwo[bl],sep=""))
remove(ps,matchPop,studPop,bl)
conn <- DatabaseConnector::connect(connectionDetails)
insertTable(conn,
"ohdsiT2DstudyPop",
studyPop,
dropTableIfExists = TRUE,
createTable = TRUE,
tempTable = TRUE,
oracleTempSchema = NULL)
sqlOne <- paste("SELECT o.treatment,
count(DISTINCT m.person_id) AS patients,
count(*)
AS records,
AVG(m.VALUE_AS_NUMBER) AS AVG,
STDEV(m.VALUE_AS_NUMBER) AS STD
FROM @cdmDatabaseSchema.MEASUREMENT m
JOIN #ohdsiT2DstudyPop o
ON m.person_id = o.SUBJECTID
WHERE m.measurement_concept_id IN (3004410,
3007263,
3003309,
3005673,
40762352,
40758583,
3034639,
4197971)
AND m.MEASUREMENT_DATE < CAST(o.COHORTSTARTDATE AS DATE)
AND m.VALUE_AS_NUMBER < 20
GROUP BY o.treatment", sep = "")
sqlOne <- SqlRender::renderSql(sqlOne, cdmDatabaseSchema = cdmDatabaseSchema)$sql
sqlOne <- SqlRender::translateSql(sqlOne, targetDialect = connectionDetails$dbms)$sql
HbA1cBefTx <- querySql(conn, sqlOne)
remove(sqlOne)
sqlOne <- paste("SELECT o.treatment,
count(DISTINCT m.person_id) AS patients,
count(*)
AS records,
AVG(m.VALUE_AS_NUMBER) AS AVG,
STDEV(m.VALUE_AS_NUMBER) AS STD
FROM @cdmDatabaseSchema.MEASUREMENT m
JOIN #ohdsiT2DstudyPop o
ON m.person_id = o.SUBJECTID
WHERE m.measurement_concept_id IN (3004410,
3007263,
3003309,
3005673,
40762352,
40758583,
3034639,
4197971)
AND m.MEASUREMENT_DATE > CAST(o.COHORTSTARTDATE AS DATE)
AND m.VALUE_AS_NUMBER < 20
GROUP BY o.treatment", sep = "")
sqlOne <- SqlRender::renderSql(sqlOne, cdmDatabaseSchema = cdmDatabaseSchema)$sql
sqlOne <- SqlRender::translateSql(sqlOne, targetDialect = connectionDetails$dbms)$sql
HbA1cAfTx <- querySql(conn, sqlOne)
remove(sqlOne)
HbA1cBefTx$TcPatients <- NA
HbA1cBefTx$TcPatients[1] <- nrow(subset(studyPop, treatment == 0))
HbA1cBefTx$TcPatients[2] <- nrow(subset(studyPop, treatment == 1))
HbA1cBefTx$Index <- c("Before")
HbA1cAfTx$TcPatients <- NA
HbA1cAfTx$TcPatients[1] <- nrow(subset(studyPop, treatment == 0))
HbA1cAfTx$TcPatients[2] <- nrow(subset(studyPop, treatment == 1))
HbA1cAfTx$Index <- c("After")
unMatchedHbA1cMeanSd <- rbind(HbA1cBefTx, HbA1cAfTx)
unMatchedHbA1cMeanSd$class <- c("unMatched")
remove(HbA1cBefTx, HbA1cAfTx)
# Matched Cohort
insertTable(conn,
"ohdsiT2DstudyPop",
matchedPop,
dropTableIfExists = TRUE,
createTable = TRUE,
tempTable = TRUE,
oracleTempSchema = NULL)
sqlOne <- paste("SELECT o.treatment,
count(DISTINCT m.person_id) AS patients,
count(*)
AS records,
AVG(m.VALUE_AS_NUMBER) AS AVG,
STDEV(m.VALUE_AS_NUMBER) AS STD
FROM @cdmDatabaseSchema.MEASUREMENT m
JOIN #ohdsiT2DstudyPop o
ON m.person_id = o.SUBJECTID
WHERE m.measurement_concept_id IN (3004410,
3007263,
3003309,
3005673,
40762352,
40758583,
3034639,
4197971)
AND m.MEASUREMENT_DATE < CAST(o.COHORTSTARTDATE AS DATE)
AND m.measurement_date >= dateadd(day,
-365,
CAST(o.COHORTSTARTDATE AS DATE)) AND m.measurement_date <= CAST(o.COHORTSTARTDATE AS DATE)
AND m.VALUE_AS_NUMBER < 20
GROUP BY o.treatment", sep = "")
sqlOne <- SqlRender::renderSql(sqlOne, cdmDatabaseSchema = cdmDatabaseSchema)$sql
sqlOne <- SqlRender::translateSql(sqlOne, targetDialect = connectionDetails$dbms)$sql
HbA1cBefTx <- querySql(conn, sqlOne)
remove(sqlOne)
sqlOne <- paste("SELECT o.treatment,
count(DISTINCT m.person_id) AS patients,
count(*)
AS records,
AVG(m.VALUE_AS_NUMBER) AS AVG,
STDEV(m.VALUE_AS_NUMBER) AS STD
FROM @cdmDatabaseSchema.MEASUREMENT m
JOIN #ohdsiT2DstudyPop o
ON m.person_id = o.SUBJECTID
WHERE m.measurement_concept_id IN (3004410,
3007263,
3003309,
3005673,
40762352,
40758583,
3034639,
4197971)
AND m.MEASUREMENT_DATE > CAST(o.COHORTSTARTDATE AS DATE)
AND m.VALUE_AS_NUMBER < 20
GROUP BY o.treatment", sep = "")
sqlOne <- SqlRender::renderSql(sqlOne, cdmDatabaseSchema = cdmDatabaseSchema)$sql
sqlOne <- SqlRender::translateSql(sqlOne, targetDialect = connectionDetails$dbms)$sql
HbA1cAfTx <- querySql(conn, sqlOne)
remove(sqlOne)
HbA1cBefTx$TcPatients <- NA
HbA1cBefTx$TcPatients[1] <- nrow(subset(matchedPop, treatment == 0))
HbA1cBefTx$TcPatients[2] <- nrow(subset(matchedPop, treatment == 1))
HbA1cBefTx$Index <- c("Before")
HbA1cAfTx$TcPatients <- NA
HbA1cAfTx$TcPatients[1] <- nrow(subset(matchedPop, treatment == 0))
HbA1cAfTx$TcPatients[2] <- nrow(subset(matchedPop, treatment == 1))
HbA1cAfTx$Index <- c("After")
matchedHbA1cMeanSd <- rbind(HbA1cBefTx, HbA1cAfTx)
matchedHbA1cMeanSd$class <- c("matched")
remove(HbA1cBefTx, HbA1cAfTx)
hbA1cStat <- rbind(unMatchedHbA1cMeanSd, matchedHbA1cMeanSd)
write.csv(hbA1cStat, file = paste(results_path,"bigToSulf_bigToThia_HbA1c7Good_Stat.csv",sep=""))
remove(unMatchedHbA1cMeanSd, matchedHbA1cMeanSd, hbA1cStat)
remove(psScore, matchedPop, studyPop, balance)
}else
{
print(paste("You don't seems to have results for the bigToSulf and bigToThia comparision"))
}
#---- For tcThree
if(length(tcThree)!=0){
resFilesOutCome4tcThree <- resFilesOutCome4[tcThree]
#load the data
ps <- grep("Ps",resFilesOutCome4tcThree)
psScore <- readRDS(paste(results_path,"deleteMeBeforeSharing/",resFilesOutCome4tcThree[ps],sep=""))
matchPop <- grep("StratPop",resFilesOutCome4tcThree)
matchedPop <- readRDS(paste(results_path,"deleteMeBeforeSharing/",resFilesOutCome4tcThree[matchPop],sep=""))
studPop <- grep("StudyPop", resFilesOutCome4tcThree)
studyPop <- readRDS(paste(results_path,"deleteMeBeforeSharing/",resFilesOutCome4tcThree[studPop],sep=""))
bl <- grep("Bal",resFilesOutCome4tcThree)
balance <- readRDS(paste(results_path,"deleteMeBeforeSharing/",resFilesOutCome4tcThree[bl],sep=""))
remove(ps,matchPop,studPop,bl)
conn <- DatabaseConnector::connect(connectionDetails)
insertTable(conn,
"ohdsiT2DstudyPop",
studyPop,
dropTableIfExists = TRUE,
createTable = TRUE,
tempTable = TRUE,
oracleTempSchema = NULL)
sqlOne <- paste("SELECT o.treatment,
count(DISTINCT m.person_id) AS patients,
count(*)
AS records,
AVG(m.VALUE_AS_NUMBER) AS AVG,
STDEV(m.VALUE_AS_NUMBER) AS STD
FROM @cdmDatabaseSchema.MEASUREMENT m
JOIN #ohdsiT2DstudyPop o
ON m.person_id = o.SUBJECTID
WHERE m.measurement_concept_id IN (3004410,
3007263,
3003309,
3005673,
40762352,
40758583,
3034639,
4197971)
AND m.MEASUREMENT_DATE < CAST(o.COHORTSTARTDATE AS DATE)
AND m.VALUE_AS_NUMBER < 20
GROUP BY o.treatment", sep = "")
sqlOne <- SqlRender::renderSql(sqlOne, cdmDatabaseSchema = cdmDatabaseSchema)$sql
sqlOne <- SqlRender::translateSql(sqlOne, targetDialect = connectionDetails$dbms)$sql
HbA1cBefTx <- querySql(conn, sqlOne)
remove(sqlOne)
sqlOne <- paste("SELECT o.treatment,
count(DISTINCT m.person_id) AS patients,
count(*)
AS records,
AVG(m.VALUE_AS_NUMBER) AS AVG,
STDEV(m.VALUE_AS_NUMBER) AS STD
FROM @cdmDatabaseSchema.MEASUREMENT m
JOIN #ohdsiT2DstudyPop o
ON m.person_id = o.SUBJECTID
WHERE m.measurement_concept_id IN (3004410,
3007263,
3003309,
3005673,
40762352,
40758583,
3034639,
4197971)
AND m.MEASUREMENT_DATE > CAST(o.COHORTSTARTDATE AS DATE)
AND m.VALUE_AS_NUMBER < 20
GROUP BY o.treatment", sep = "")
sqlOne <- SqlRender::renderSql(sqlOne, cdmDatabaseSchema = cdmDatabaseSchema)$sql
sqlOne <- SqlRender::translateSql(sqlOne, targetDialect = connectionDetails$dbms)$sql
HbA1cAfTx <- querySql(conn, sqlOne)
remove(sqlOne)
HbA1cBefTx$TcPatients <- NA
HbA1cBefTx$TcPatients[1] <- nrow(subset(studyPop, treatment == 0))
HbA1cBefTx$TcPatients[2] <- nrow(subset(studyPop, treatment == 1))
HbA1cBefTx$Index <- c("Before")
HbA1cAfTx$TcPatients <- NA
HbA1cAfTx$TcPatients[1] <- nrow(subset(studyPop, treatment == 0))
HbA1cAfTx$TcPatients[2] <- nrow(subset(studyPop, treatment == 1))
HbA1cAfTx$Index <- c("After")
unMatchedHbA1cMeanSd <- rbind(HbA1cBefTx, HbA1cAfTx)
unMatchedHbA1cMeanSd$class <- c("unMatched")
remove(HbA1cBefTx, HbA1cAfTx)
# Matched Cohort
insertTable(conn,
"ohdsiT2DstudyPop",
matchedPop,
dropTableIfExists = TRUE,
createTable = TRUE,
tempTable = TRUE,
oracleTempSchema = NULL)
sqlOne <- paste("SELECT o.treatment,
count(DISTINCT m.person_id) AS patients,
count(*)
AS records,
AVG(m.VALUE_AS_NUMBER) AS AVG,
STDEV(m.VALUE_AS_NUMBER) AS STD
FROM @cdmDatabaseSchema.MEASUREMENT m
JOIN #ohdsiT2DstudyPop o
ON m.person_id = o.SUBJECTID
WHERE m.measurement_concept_id IN (3004410,
3007263,
3003309,
3005673,
40762352,
40758583,
3034639,
4197971)
AND m.MEASUREMENT_DATE < CAST(o.COHORTSTARTDATE AS DATE)
AND m.measurement_date >= dateadd(day,
-365,
CAST(o.COHORTSTARTDATE AS DATE)) AND m.measurement_date <= CAST(o.COHORTSTARTDATE AS DATE)
AND m.VALUE_AS_NUMBER < 20
GROUP BY o.treatment", sep = "")
sqlOne <- SqlRender::renderSql(sqlOne, cdmDatabaseSchema = cdmDatabaseSchema)$sql
sqlOne <- SqlRender::translateSql(sqlOne, targetDialect = connectionDetails$dbms)$sql
HbA1cBefTx <- querySql(conn, sqlOne)
remove(sqlOne)
sqlOne <- paste("SELECT o.treatment,
count(DISTINCT m.person_id) AS patients,
count(*)
AS records,
AVG(m.VALUE_AS_NUMBER) AS AVG,
STDEV(m.VALUE_AS_NUMBER) AS STD
FROM @cdmDatabaseSchema.MEASUREMENT m
JOIN #ohdsiT2DstudyPop o
ON m.person_id = o.SUBJECTID
WHERE m.measurement_concept_id IN (3004410,
3007263,
3003309,
3005673,
40762352,
40758583,
3034639,
4197971)
AND m.MEASUREMENT_DATE > CAST(o.COHORTSTARTDATE AS DATE)
AND m.VALUE_AS_NUMBER < 20
GROUP BY o.treatment", sep = "")
sqlOne <- SqlRender::renderSql(sqlOne, cdmDatabaseSchema = cdmDatabaseSchema)$sql
sqlOne <- SqlRender::translateSql(sqlOne, targetDialect = connectionDetails$dbms)$sql
HbA1cAfTx <- querySql(conn, sqlOne)
remove(sqlOne)
HbA1cBefTx$TcPatients <- NA
HbA1cBefTx$TcPatients[1] <- nrow(subset(matchedPop, treatment == 0))
HbA1cBefTx$TcPatients[2] <- nrow(subset(matchedPop, treatment == 1))
HbA1cBefTx$Index <- c("Before")
HbA1cAfTx$TcPatients <- NA
HbA1cAfTx$TcPatients[1] <- nrow(subset(matchedPop, treatment == 0))
HbA1cAfTx$TcPatients[2] <- nrow(subset(matchedPop, treatment == 1))
HbA1cAfTx$Index <- c("After")
matchedHbA1cMeanSd <- rbind(HbA1cBefTx, HbA1cAfTx)
matchedHbA1cMeanSd$class <- c("matched")
remove(HbA1cBefTx, HbA1cAfTx)
hbA1cStat <- rbind(unMatchedHbA1cMeanSd, matchedHbA1cMeanSd)
write.csv(hbA1cStat, file = paste(results_path,"bigToDpp4_bigToThia_HbA1c7Good_Stat.csv",sep=""))
remove(unMatchedHbA1cMeanSd, matchedHbA1cMeanSd, hbA1cStat)
remove(psScore, matchedPop, studyPop, balance)
}else
{
print(paste("You don't seems to have results for the bigToDpp4 and bigToThia comparision"))
}
#----------------------------------------------------------------------
#---------------------------------------------------------------------
#For outCome 5 representing HbA1c <= 8%, represented as HbA1c7Good
x <- grep("_o5.rds",resFiles)
resFilesOutCome5 <- resFiles[x]
#Get files sorted for t and c comparisions
#bigToSulf and bigToDpp4 (1,2)
tcOne <- grep("_t1_c2",resFilesOutCome5)
#bigToSulf and bigToThia
tcTwo <- grep("_t1_c3",resFilesOutCome5)
#bigToDpp4 and bigToThia
tcThree <- grep("_t2_c3",resFilesOutCome5)
#---- For tcOne
if(length(tcOne)!=0){
resFilesOutCome5tcOne <- resFilesOutCome5[tcOne]
#load the data
ps <- grep("Ps",resFilesOutCome5tcOne)
psScore <- readRDS(paste(results_path,"deleteMeBeforeSharing/",resFilesOutCome5tcOne[ps],sep=""))
matchPop <- grep("StratPop",resFilesOutCome5tcOne)
matchedPop <- readRDS(paste(results_path,"deleteMeBeforeSharing/",resFilesOutCome5tcOne[matchPop],sep=""))
studPop <- grep("StudyPop", resFilesOutCome5tcOne)
studyPop <- readRDS(paste(results_path,"deleteMeBeforeSharing/",resFilesOutCome5tcOne[studPop],sep=""))
bl <- grep("Bal",resFilesOutCome5tcOne)
balance <- readRDS(paste(results_path,"deleteMeBeforeSharing/",resFilesOutCome5tcOne[bl],sep=""))
remove(ps,matchPop,studPop,bl)
conn <- DatabaseConnector::connect(connectionDetails)
insertTable(conn,
"ohdsiT2DstudyPop",
studyPop,
dropTableIfExists = TRUE,
createTable = TRUE,
tempTable = TRUE,
oracleTempSchema = NULL)
sqlOne <- paste("SELECT o.treatment,
count(DISTINCT m.person_id) AS patients,
count(*)
AS records,
AVG(m.VALUE_AS_NUMBER) AS AVG,
STDEV(m.VALUE_AS_NUMBER) AS STD
FROM @cdmDatabaseSchema.MEASUREMENT m
JOIN #ohdsiT2DstudyPop o
ON m.person_id = o.SUBJECTID
WHERE m.measurement_concept_id IN (3004410,
3007263,
3003309,
3005673,
40762352,
40758583,
3034639,
4197971)
AND m.MEASUREMENT_DATE < CAST(o.COHORTSTARTDATE AS DATE)
AND m.VALUE_AS_NUMBER < 20
GROUP BY o.treatment", sep = "")
sqlOne <- SqlRender::renderSql(sqlOne, cdmDatabaseSchema = cdmDatabaseSchema)$sql
sqlOne <- SqlRender::translateSql(sqlOne, targetDialect = connectionDetails$dbms)$sql
HbA1cBefTx <- querySql(conn, sqlOne)
remove(sqlOne)
sqlOne <- paste("SELECT o.treatment,
count(DISTINCT m.person_id) AS patients,
count(*)
AS records,
AVG(m.VALUE_AS_NUMBER) AS AVG,
STDEV(m.VALUE_AS_NUMBER) AS STD
FROM @cdmDatabaseSchema.MEASUREMENT m
JOIN #ohdsiT2DstudyPop o
ON m.person_id = o.SUBJECTID
WHERE m.measurement_concept_id IN (3004410,
3007263,
3003309,
3005673,
40762352,
40758583,
3034639,
4197971)
AND m.MEASUREMENT_DATE > CAST(o.COHORTSTARTDATE AS DATE)
AND m.VALUE_AS_NUMBER < 20
GROUP BY o.treatment", sep = "")
sqlOne <- SqlRender::renderSql(sqlOne, cdmDatabaseSchema = cdmDatabaseSchema)$sql
sqlOne <- SqlRender::translateSql(sqlOne, targetDialect = connectionDetails$dbms)$sql
HbA1cAfTx <- querySql(conn, sqlOne)
remove(sqlOne)
HbA1cBefTx$TcPatients <- NA
HbA1cBefTx$TcPatients[1] <- nrow(subset(studyPop, treatment == 0))
HbA1cBefTx$TcPatients[2] <- nrow(subset(studyPop, treatment == 1))
HbA1cBefTx$Index <- c("Before")
HbA1cAfTx$TcPatients <- NA
HbA1cAfTx$TcPatients[1] <- nrow(subset(studyPop, treatment == 0))
HbA1cAfTx$TcPatients[2] <- nrow(subset(studyPop, treatment == 1))
HbA1cAfTx$Index <- c("After")
unMatchedHbA1cMeanSd <- rbind(HbA1cBefTx, HbA1cAfTx)
unMatchedHbA1cMeanSd$class <- c("unMatched")
remove(HbA1cBefTx, HbA1cAfTx)
# Matched Cohort
insertTable(conn,
"ohdsiT2DstudyPop",
matchedPop,
dropTableIfExists = TRUE,
createTable = TRUE,
tempTable = TRUE,
oracleTempSchema = NULL)
sqlOne <- paste("SELECT o.treatment,
count(DISTINCT m.person_id) AS patients,
count(*)
AS records,
AVG(m.VALUE_AS_NUMBER) AS AVG,
STDEV(m.VALUE_AS_NUMBER) AS STD
FROM @cdmDatabaseSchema.MEASUREMENT m
JOIN #ohdsiT2DstudyPop o
ON m.person_id = o.SUBJECTID
WHERE m.measurement_concept_id IN (3004410,
3007263,
3003309,
3005673,
40762352,
40758583,
3034639,
4197971)
AND m.MEASUREMENT_DATE < CAST(o.COHORTSTARTDATE AS DATE)
AND m.measurement_date >= dateadd(day,
-365,
CAST(o.COHORTSTARTDATE AS DATE)) AND m.measurement_date <= CAST(o.COHORTSTARTDATE AS DATE)
AND m.VALUE_AS_NUMBER < 20
GROUP BY o.treatment", sep = "")
sqlOne <- SqlRender::renderSql(sqlOne, cdmDatabaseSchema = cdmDatabaseSchema)$sql
sqlOne <- SqlRender::translateSql(sqlOne, targetDialect = connectionDetails$dbms)$sql
HbA1cBefTx <- querySql(conn, sqlOne)
remove(sqlOne)
sqlOne <- paste("SELECT o.treatment,
count(DISTINCT m.person_id) AS patients,
count(*)
AS records,
AVG(m.VALUE_AS_NUMBER) AS AVG,
STDEV(m.VALUE_AS_NUMBER) AS STD
FROM @cdmDatabaseSchema.MEASUREMENT m
JOIN #ohdsiT2DstudyPop o
ON m.person_id = o.SUBJECTID
WHERE m.measurement_concept_id IN (3004410,
3007263,
3003309,
3005673,
40762352,
40758583,
3034639,
4197971)
AND m.MEASUREMENT_DATE > CAST(o.COHORTSTARTDATE AS DATE)
AND m.VALUE_AS_NUMBER < 20
GROUP BY o.treatment", sep = "")
sqlOne <- SqlRender::renderSql(sqlOne, cdmDatabaseSchema = cdmDatabaseSchema)$sql
sqlOne <- SqlRender::translateSql(sqlOne, targetDialect = connectionDetails$dbms)$sql
HbA1cAfTx <- querySql(conn, sqlOne)
remove(sqlOne)
HbA1cBefTx$TcPatients <- NA
HbA1cBefTx$TcPatients[1] <- nrow(subset(matchedPop, treatment == 0))
HbA1cBefTx$TcPatients[2] <- nrow(subset(matchedPop, treatment == 1))
HbA1cBefTx$Index <- c("Before")
HbA1cAfTx$TcPatients <- NA
HbA1cAfTx$TcPatients[1] <- nrow(subset(matchedPop, treatment == 0))
HbA1cAfTx$TcPatients[2] <- nrow(subset(matchedPop, treatment == 1))
HbA1cAfTx$Index <- c("After")
matchedHbA1cMeanSd <- rbind(HbA1cBefTx, HbA1cAfTx)
matchedHbA1cMeanSd$class <- c("matched")
remove(HbA1cBefTx, HbA1cAfTx)
hbA1cStat <- rbind(unMatchedHbA1cMeanSd, matchedHbA1cMeanSd)
write.csv(hbA1cStat, file = paste(results_path,"bigToSulf_bigToDpp4_HbA1c8Moderate_Stat.csv",sep=""))
remove(unMatchedHbA1cMeanSd, matchedHbA1cMeanSd, hbA1cStat)
remove(psScore, matchedPop, studyPop, balance)
}else
{
print(paste("You don't seems to have results for the bigToSulf and bigToDpp4 comparision"))
}
#---- For tcTwo
if(length(tcTwo)!=0){
resFilesOutCome5tcTwo <- resFilesOutCome5[tcTwo]
#load the data
ps <- grep("Ps",resFilesOutCome5tcTwo)
psScore <- readRDS(paste(results_path,"deleteMeBeforeSharing/",resFilesOutCome5tcTwo[ps],sep=""))
matchPop <- grep("StratPop",resFilesOutCome5tcTwo)
matchedPop <- readRDS(paste(results_path,"deleteMeBeforeSharing/",resFilesOutCome5tcTwo[matchPop],sep=""))
studPop <- grep("StudyPop", resFilesOutCome5tcTwo)
studyPop <- readRDS(paste(results_path,"deleteMeBeforeSharing/",resFilesOutCome5tcTwo[studPop],sep=""))
bl <- grep("Bal",resFilesOutCome5tcTwo)
balance <- readRDS(paste(results_path,"deleteMeBeforeSharing/",resFilesOutCome5tcTwo[bl],sep=""))
remove(ps,matchPop,studPop,bl)
conn <- DatabaseConnector::connect(connectionDetails)
insertTable(conn,
"ohdsiT2DstudyPop",
studyPop,
dropTableIfExists = TRUE,
createTable = TRUE,
tempTable = TRUE,
oracleTempSchema = NULL)
sqlOne <- paste("SELECT o.treatment,
count(DISTINCT m.person_id) AS patients,
count(*)
AS records,
AVG(m.VALUE_AS_NUMBER) AS AVG,
STDEV(m.VALUE_AS_NUMBER) AS STD
FROM @cdmDatabaseSchema.MEASUREMENT m
JOIN #ohdsiT2DstudyPop o
ON m.person_id = o.SUBJECTID
WHERE m.measurement_concept_id IN (3004410,
3007263,
3003309,
3005673,
40762352,
40758583,
3034639,
4197971)
AND m.MEASUREMENT_DATE < CAST(o.COHORTSTARTDATE AS DATE)
AND m.VALUE_AS_NUMBER < 20
GROUP BY o.treatment", sep = "")
sqlOne <- SqlRender::renderSql(sqlOne, cdmDatabaseSchema = cdmDatabaseSchema)$sql
sqlOne <- SqlRender::translateSql(sqlOne, targetDialect = connectionDetails$dbms)$sql
HbA1cBefTx <- querySql(conn, sqlOne)
remove(sqlOne)
sqlOne <- paste("SELECT o.treatment,
count(DISTINCT m.person_id) AS patients,
count(*)
AS records,
AVG(m.VALUE_AS_NUMBER) AS AVG,
STDEV(m.VALUE_AS_NUMBER) AS STD
FROM @cdmDatabaseSchema.MEASUREMENT m
JOIN #ohdsiT2DstudyPop o
ON m.person_id = o.SUBJECTID
WHERE m.measurement_concept_id IN (3004410,
3007263,
3003309,
3005673,
40762352,
40758583,
3034639,
4197971)
AND m.MEASUREMENT_DATE > CAST(o.COHORTSTARTDATE AS DATE)
AND m.VALUE_AS_NUMBER < 20
GROUP BY o.treatment", sep = "")
sqlOne <- SqlRender::renderSql(sqlOne, cdmDatabaseSchema = cdmDatabaseSchema)$sql
sqlOne <- SqlRender::translateSql(sqlOne, targetDialect = connectionDetails$dbms)$sql
HbA1cAfTx <- querySql(conn, sqlOne)
remove(sqlOne)
HbA1cBefTx$TcPatients <- NA
HbA1cBefTx$TcPatients[1] <- nrow(subset(studyPop, treatment == 0))
HbA1cBefTx$TcPatients[2] <- nrow(subset(studyPop, treatment == 1))
HbA1cBefTx$Index <- c("Before")
HbA1cAfTx$TcPatients <- NA
HbA1cAfTx$TcPatients[1] <- nrow(subset(studyPop, treatment == 0))
HbA1cAfTx$TcPatients[2] <- nrow(subset(studyPop, treatment == 1))
HbA1cAfTx$Index <- c("After")
unMatchedHbA1cMeanSd <- rbind(HbA1cBefTx, HbA1cAfTx)
unMatchedHbA1cMeanSd$class <- c("unMatched")
remove(HbA1cBefTx, HbA1cAfTx)
# Matched Cohort
insertTable(conn,
"ohdsiT2DstudyPop",
matchedPop,
dropTableIfExists = TRUE,
createTable = TRUE,
tempTable = TRUE,
oracleTempSchema = NULL)
sqlOne <- paste("SELECT o.treatment,
count(DISTINCT m.person_id) AS patients,
count(*)
AS records,
AVG(m.VALUE_AS_NUMBER) AS AVG,
STDEV(m.VALUE_AS_NUMBER) AS STD
FROM @cdmDatabaseSchema.MEASUREMENT m
JOIN #ohdsiT2DstudyPop o
ON m.person_id = o.SUBJECTID
WHERE m.measurement_concept_id IN (3004410,
3007263,
3003309,
3005673,
40762352,
40758583,
3034639,
4197971)
AND m.MEASUREMENT_DATE < CAST(o.COHORTSTARTDATE AS DATE)
AND m.measurement_date >= dateadd(day,
-365,
CAST(o.COHORTSTARTDATE AS DATE)) AND m.measurement_date <= CAST(o.COHORTSTARTDATE AS DATE)
AND m.VALUE_AS_NUMBER < 20
GROUP BY o.treatment", sep = "")
sqlOne <- SqlRender::renderSql(sqlOne, cdmDatabaseSchema = cdmDatabaseSchema)$sql
sqlOne <- SqlRender::translateSql(sqlOne, targetDialect = connectionDetails$dbms)$sql
HbA1cBefTx <- querySql(conn, sqlOne)
remove(sqlOne)
sqlOne <- paste("SELECT o.treatment,
count(DISTINCT m.person_id) AS patients,
count(*)
AS records,
AVG(m.VALUE_AS_NUMBER) AS AVG,
STDEV(m.VALUE_AS_NUMBER) AS STD
FROM @cdmDatabaseSchema.MEASUREMENT m
JOIN #ohdsiT2DstudyPop o
ON m.person_id = o.SUBJECTID
WHERE m.measurement_concept_id IN (3004410,
3007263,
3003309,
3005673,
40762352,
40758583,
3034639,
4197971)
AND m.MEASUREMENT_DATE > CAST(o.COHORTSTARTDATE AS DATE)
AND m.VALUE_AS_NUMBER < 20
GROUP BY o.treatment", sep = "")
sqlOne <- SqlRender::renderSql(sqlOne, cdmDatabaseSchema = cdmDatabaseSchema)$sql
sqlOne <- SqlRender::translateSql(sqlOne, targetDialect = connectionDetails$dbms)$sql
HbA1cAfTx <- querySql(conn, sqlOne)
remove(sqlOne)
HbA1cBefTx$TcPatients <- NA
HbA1cBefTx$TcPatients[1] <- nrow(subset(matchedPop, treatment == 0))
HbA1cBefTx$TcPatients[2] <- nrow(subset(matchedPop, treatment == 1))
HbA1cBefTx$Index <- c("Before")
HbA1cAfTx$TcPatients <- NA
HbA1cAfTx$TcPatients[1] <- nrow(subset(matchedPop, treatment == 0))
HbA1cAfTx$TcPatients[2] <- nrow(subset(matchedPop, treatment == 1))
HbA1cAfTx$Index <- c("After")
matchedHbA1cMeanSd <- rbind(HbA1cBefTx, HbA1cAfTx)
matchedHbA1cMeanSd$class <- c("matched")
remove(HbA1cBefTx, HbA1cAfTx)
hbA1cStat <- rbind(unMatchedHbA1cMeanSd, matchedHbA1cMeanSd)
write.csv(hbA1cStat, file = paste(results_path,"bigToSulf_bigToThia_HbA1c8Moderate_Stat.csv",sep=""))
remove(unMatchedHbA1cMeanSd, matchedHbA1cMeanSd, hbA1cStat)
remove(psScore, matchedPop, studyPop, balance)
}else
{
print(paste("You don't seems to have results for the bigToSulf and bigToThia comparision"))
}
#---- For tcThree
if(length(tcThree)!=0){
resFilesOutCome5tcThree <- resFilesOutCome5[tcThree]
#load the data
ps <- grep("Ps",resFilesOutCome5tcThree)
psScore <- readRDS(paste(results_path,"deleteMeBeforeSharing/",resFilesOutCome5tcThree[ps],sep=""))
matchPop <- grep("StratPop",resFilesOutCome5tcThree)
matchedPop <- readRDS(paste(results_path,"deleteMeBeforeSharing/",resFilesOutCome5tcThree[matchPop],sep=""))
studPop <- grep("StudyPop", resFilesOutCome5tcThree)
studyPop <- readRDS(paste(results_path,"deleteMeBeforeSharing/",resFilesOutCome5tcThree[studPop],sep=""))
bl <- grep("Bal",resFilesOutCome5tcThree)
balance <- readRDS(paste(results_path,"deleteMeBeforeSharing/",resFilesOutCome5tcThree[bl],sep=""))
remove(ps,matchPop,studPop,bl)
conn <- DatabaseConnector::connect(connectionDetails)
insertTable(conn,
"ohdsiT2DstudyPop",
studyPop,
dropTableIfExists = TRUE,
createTable = TRUE,
tempTable = TRUE,
oracleTempSchema = NULL)
sqlOne <- paste("SELECT o.treatment,
count(DISTINCT m.person_id) AS patients,
count(*)
AS records,
AVG(m.VALUE_AS_NUMBER) AS AVG,
STDEV(m.VALUE_AS_NUMBER) AS STD
FROM @cdmDatabaseSchema.MEASUREMENT m
JOIN #ohdsiT2DstudyPop o
ON m.person_id = o.SUBJECTID
WHERE m.measurement_concept_id IN (3004410,
3007263,
3003309,
3005673,
40762352,
40758583,
3034639,
4197971)
AND m.MEASUREMENT_DATE < CAST(o.COHORTSTARTDATE AS DATE)
AND m.VALUE_AS_NUMBER < 20
GROUP BY o.treatment", sep = "")
sqlOne <- SqlRender::renderSql(sqlOne, cdmDatabaseSchema = cdmDatabaseSchema)$sql
sqlOne <- SqlRender::translateSql(sqlOne, targetDialect = connectionDetails$dbms)$sql
HbA1cBefTx <- querySql(conn, sqlOne)
remove(sqlOne)
sqlOne <- paste("SELECT o.treatment,
count(DISTINCT m.person_id) AS patients,
count(*)
AS records,
AVG(m.VALUE_AS_NUMBER) AS AVG,
STDEV(m.VALUE_AS_NUMBER) AS STD
FROM @cdmDatabaseSchema.MEASUREMENT m
JOIN #ohdsiT2DstudyPop o
ON m.person_id = o.SUBJECTID
WHERE m.measurement_concept_id IN (3004410,
3007263,
3003309,
3005673,
40762352,
40758583,
3034639,
4197971)
AND m.MEASUREMENT_DATE > CAST(o.COHORTSTARTDATE AS DATE)
AND m.VALUE_AS_NUMBER < 20
GROUP BY o.treatment", sep = "")
sqlOne <- SqlRender::renderSql(sqlOne, cdmDatabaseSchema = cdmDatabaseSchema)$sql
sqlOne <- SqlRender::translateSql(sqlOne, targetDialect = connectionDetails$dbms)$sql
HbA1cAfTx <- querySql(conn, sqlOne)
remove(sqlOne)
HbA1cBefTx$TcPatients <- NA
HbA1cBefTx$TcPatients[1] <- nrow(subset(studyPop, treatment == 0))
HbA1cBefTx$TcPatients[2] <- nrow(subset(studyPop, treatment == 1))
HbA1cBefTx$Index <- c("Before")
HbA1cAfTx$TcPatients <- NA
HbA1cAfTx$TcPatients[1] <- nrow(subset(studyPop, treatment == 0))
HbA1cAfTx$TcPatients[2] <- nrow(subset(studyPop, treatment == 1))
HbA1cAfTx$Index <- c("After")
unMatchedHbA1cMeanSd <- rbind(HbA1cBefTx, HbA1cAfTx)
unMatchedHbA1cMeanSd$class <- c("unMatched")
remove(HbA1cBefTx, HbA1cAfTx)
# Matched Cohort
insertTable(conn,
"ohdsiT2DstudyPop",
matchedPop,
dropTableIfExists = TRUE,
createTable = TRUE,
tempTable = TRUE,
oracleTempSchema = NULL)
sqlOne <- paste("SELECT o.treatment,
count(DISTINCT m.person_id) AS patients,
count(*)
AS records,
AVG(m.VALUE_AS_NUMBER) AS AVG,
STDEV(m.VALUE_AS_NUMBER) AS STD
FROM @cdmDatabaseSchema.MEASUREMENT m
JOIN #ohdsiT2DstudyPop o
ON m.person_id = o.SUBJECTID
WHERE m.measurement_concept_id IN (3004410,
3007263,
3003309,
3005673,
40762352,
40758583,
3034639,
4197971)
AND m.MEASUREMENT_DATE < CAST(o.COHORTSTARTDATE AS DATE)
AND m.measurement_date >= dateadd(day,
-365,
CAST(o.COHORTSTARTDATE AS DATE)) AND m.measurement_date <= CAST(o.COHORTSTARTDATE AS DATE)
AND m.VALUE_AS_NUMBER < 20
GROUP BY o.treatment", sep = "")
sqlOne <- SqlRender::renderSql(sqlOne, cdmDatabaseSchema = cdmDatabaseSchema)$sql
sqlOne <- SqlRender::translateSql(sqlOne, targetDialect = connectionDetails$dbms)$sql
HbA1cBefTx <- querySql(conn, sqlOne)
remove(sqlOne)
sqlOne <- paste("SELECT o.treatment,
count(DISTINCT m.person_id) AS patients,
count(*)
AS records,
AVG(m.VALUE_AS_NUMBER) AS AVG,
STDEV(m.VALUE_AS_NUMBER) AS STD
FROM @cdmDatabaseSchema.MEASUREMENT m
JOIN #ohdsiT2DstudyPop o
ON m.person_id = o.SUBJECTID
WHERE m.measurement_concept_id IN (3004410,
3007263,
3003309,
3005673,
40762352,
40758583,
3034639,
4197971)
AND m.MEASUREMENT_DATE > CAST(o.COHORTSTARTDATE AS DATE)
AND m.VALUE_AS_NUMBER < 20
GROUP BY o.treatment", sep = "")
sqlOne <- SqlRender::renderSql(sqlOne, cdmDatabaseSchema = cdmDatabaseSchema)$sql
sqlOne <- SqlRender::translateSql(sqlOne, targetDialect = connectionDetails$dbms)$sql
HbA1cAfTx <- querySql(conn, sqlOne)
remove(sqlOne)
HbA1cBefTx$TcPatients <- NA
HbA1cBefTx$TcPatients[1] <- nrow(subset(matchedPop, treatment == 0))
HbA1cBefTx$TcPatients[2] <- nrow(subset(matchedPop, treatment == 1))
HbA1cBefTx$Index <- c("Before")
HbA1cAfTx$TcPatients <- NA
HbA1cAfTx$TcPatients[1] <- nrow(subset(matchedPop, treatment == 0))
HbA1cAfTx$TcPatients[2] <- nrow(subset(matchedPop, treatment == 1))
HbA1cAfTx$Index <- c("After")
matchedHbA1cMeanSd <- rbind(HbA1cBefTx, HbA1cAfTx)
matchedHbA1cMeanSd$class <- c("matched")
remove(HbA1cBefTx, HbA1cAfTx)
hbA1cStat <- rbind(unMatchedHbA1cMeanSd, matchedHbA1cMeanSd)
write.csv(hbA1cStat, file = paste(results_path,"bigToDpp4_bigToThia_HbA1c8Moderate_Stat.csv",sep=""))
remove(unMatchedHbA1cMeanSd, matchedHbA1cMeanSd, hbA1cStat)
remove(psScore, matchedPop, studyPop, balance)
}else
{
print(paste("You don't seems to have results for the bigToDpp4 and bigToThia comparision"))
}
#----------------------------------------------------------------------
}
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