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performanceCheck.R
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performanceCheck.R
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library(dxpr)
library(tictoc)
library(dplyr)
load("DeliveryCCSDataLong.rda")
#devtools::install_github("DHLab-TSENG/dxpr")
#devtools::install_github("jabiru/tictoc")
DeliveryCCSDataLong<-
dplyr::rename(DeliveryCCSDataLong,Date=DateServiceStarted,ID=FinalID)
nRuns<-100
AllTimeLog<-NULL
######################################################
# run time start
######################################################
tic.clearlog()
tagName<-"AHRQ grouping"
for (i in 1:nRuns){
tic(tagName)
AHRQData<-icdDxToComorbid(DeliveryCCSDataLong,
idColName = ID,
icdColName = ICD,
dateColName = Date,
icd10usingDate = "2015-10-1",
comorbidMethod = ahrq
)
toc(log = TRUE, quiet = TRUE)
}
log.lst <- tic.log(format = FALSE)
timings <- unlist(lapply(log.lst, function(x) x$toc - x$tic))
TimeLog<-data.frame(tagName,timings,stringsAsFactors = F)
AllTimeLog<-bind_rows(AllTimeLog,TimeLog)
tic.clearlog()
tagName<-"Analysis ready data generation"
for (i in 1:nRuns){
tic(tagName)
groupedData_Wide <- groupedDataLongToWide(dxDataFile = AHRQData$groupedDT,
idColName = ID,
categoryColName = Comorbidity,
dateColName = Date,
reDup = TRUE,
numericOrBinary = B,
count = 2)
toc(log = TRUE, quiet = TRUE)
}
log.lst <- tic.log(format = FALSE)
timings <- unlist(lapply(log.lst, function(x) x$toc - x$tic))
TimeLog<-data.frame(tagName,timings,stringsAsFactors = F)
AllTimeLog<-bind_rows(AllTimeLog,TimeLog)
rm(AHRQData)
rm(groupedData_Wide)
tic.clearlog()
tagName<-"Case selection"
for (i in 1:nRuns){
tic(tagName)
case <- selectCases(dxDataFile = DeliveryCCSDataLong,
idColName = ID,
icdColName = ICD,
dateColName = Date,
icd10usingDate = "2015-10-1",
groupDataType = ccslvl2,
caseCondition = "Diseases of the urinary system",
caseCount = 1,
caseName = "US")
toc(log = TRUE, quiet = TRUE)
}
log.lst <- tic.log(format = FALSE)
timings <- unlist(lapply(log.lst, function(x) x$toc - x$tic))
TimeLog<-data.frame(tagName,timings,stringsAsFactors = F)
AllTimeLog<-bind_rows(AllTimeLog,TimeLog)
rm(case)
tic.clearlog()
tagName<-"Eligible period identification"
for (i in 1:nRuns){
tic(tagName)
eligible <- getEligiblePeriod(dxDataFile = DeliveryCCSDataLong,
idColName = ID,
dateColName = Date)
toc(log = TRUE, quiet = TRUE)
}
log.lst <- tic.log(format = FALSE)
timings <- unlist(lapply(log.lst, function(x) x$toc - x$tic))
TimeLog<-data.frame(tagName,timings,stringsAsFactors = F)
AllTimeLog<-bind_rows(AllTimeLog,TimeLog)
tic.clearlog()
library(dplyr)
indexDateTable <- eligible %>%
select(ID,endRecordDate) %>%
rename(indexDate=endRecordDate)
rm(eligible)
tagName<-"Data split"
for (i in 1:nRuns){
tic(tagName)
split<-splitDataByDate(dxDataFile = DeliveryCCSDataLong,
idColName = ID,
icdColName = ICD,
dateColName = Date,
indexDateFile = indexDateTable,
gap = 30)
toc(log = TRUE, quiet = TRUE)
}
log.lst <- tic.log(format = FALSE)
timings <- unlist(lapply(log.lst, function(x) x$toc - x$tic))
TimeLog<-data.frame(tagName,timings,stringsAsFactors = F)
AllTimeLog<-bind_rows(AllTimeLog,TimeLog)
######################################################
# wait for debug
######################################################
tic.clearlog()
tagName<-"Condition era generation"
for (i in 1:nRuns){
tic(tagName)
Era <- getConditionEra(dxDataFile = DeliveryCCSDataLong,
idColName = ID,
icdColName = ICD,
dateColName = Date,
icd10usingDate = "2015/10/01",
groupDataType = CCS,
isDescription = FALSE,
gapDate = 30)
toc(log = TRUE, quiet = TRUE)
}
log.lst <- tic.log(format = FALSE)
timings <- unlist(lapply(log.lst, function(x) x$toc - x$tic))
TimeLog<-data.frame(tagName,timings,stringsAsFactors = F)
AllTimeLog<-bind_rows(AllTimeLog,TimeLog)
tic.clearlog()
######################################################
# analysis
# done 20201112
######################################################
AllTimeLog
saveRDS(AllTimeLog,paste0("AllTimeLog",Sys.Date(),"ConditionEra.rds"))
AllTimeLog %>% group_by(tagName) %>%
summarise(count=n(),meanT=mean(timings),sdT=sd(timings))
AllTimeLog<-
readRDS("AllTimeLog2020-12-01.rds")
AllTimeLog %>% group_by(tagName) %>%
summarise(count=n(),meanT=mean(timings),sdT=sd(timings))