Nothing
inst/doc/Specification.R
In Characterization: Implement Descriptive Studies Using the Common Data Model
## -----------------------------------------------------------------------------
targetIds <- c(1)
outcomeIds <- c(2)
## ----echo=FALSE, results='asis'-----------------------------------------------
tteTargetData <- data.frame(
patientId = c(1, 1, 2, 3, 4, 4, 4, 5, 5),
cohortDefinitionId = rep(1, 9),
cohortStartDate = c('2001-01-20', '2001-10-20',
'2005-09-10', '2004-04-02',
'2002-03-03', '2003-02-01',
'2003-08-04', '2005-02-01',
'2007-04-03'),
cohortEndDate = c('2001-01-25', '2001-12-05',
'2005-09-15', '2004-05-17',
'2002-06-12', '2003-02-30',
'2003-08-24', '2005-10-08',
'2007-05-03')
)
knitr::kable(
x = tteTargetData,
caption = 'Example time-to-event data with dates.'
)
## ----echo=FALSE, results='asis'-----------------------------------------------
tteOutcomeData <- data.frame(
patientId = c(1, 1, 3, 4, 4, 5, 5),
cohortDefinitionId = rep(2, 7),
cohortStartDate = c('1999-10-03', '2001-10-30',
'2004-05-16', '2002-06-03',
'2003-02-20', '2006-07-21',
'2008-01-01'),
cohortEndDate = c('1999-10-08', '2001-11-07',
'2004-05-18', '2002-06-14',
'2003-03-01', '2006-08-03',
'2008-01-09')
)
knitr::kable(
x = tteOutcomeData,
caption = 'Example time-to-event data with timing.'
)
## ----echo=FALSE, results='asis'-----------------------------------------------
tteSummaryData <- data.frame(
patientId = c(1, 1, 3, 4, 4, 5, 5),
outcomeDate = c('1999-10-03', '2001-10-30',
'2004-05-16', '2002-06-03',
'2003-02-20', '2006-07-21',
'2008-01-01'),
firstExposureDate = c('2001-01-20', '2001-01-20',
'2004-04-02', '2002-03-03',
'2002-03-03', '2005-02-01',
'2005-02-01'),
timeToEvent = c(-475, 283, 44, 92, 354, 535,
1064),
type = c('Before first exposure',
'During subsequent',
'During first',
'During first',
'During subsequent',
'Between eras',
'After last exposure'),
outcomeType = c('First',
'Subsequent',
'First',
'First',
'Subsequent',
'First',
'Subsequent')
)
knitr::kable(
x = tteSummaryData,
caption = 'Table 3: Time-to-event intermediate summary.'
)
## ----echo=FALSE, results='asis'-----------------------------------------------
tteResultData <- data.frame(
timeType = c(
rep('1-day', 2),
rep('30-day', 7),
rep('365-day', 5)
),
Type = c(
'During first',
'During first',
'Before first exposure',
'During first',
'During first',
'During subsequent',
'During subsequent',
'Between eras',
'After last exposure',
'Before first exposure',
'During first',
'During subsequent' ,
'Between eras',
'After last exposure'
),
outcomeType = c(
'First',
'First',
'First',
'First',
'First',
'Subsequent',
'Subsequent',
'First',
'Subsequent',
'First',
'First',
'Subsequent',
'First',
'Subsequent'
),
timeStart = c(44, 92, -481, 31, 91,
271, 331, 511, 1051, -731,
1, 1, 366, 731),
timeEnd = c(44, 92, -450, 60, 120,
300, 360, 540, 1080, -365,
365, 365, 730, 1095),
count = c(1, 1, 1, 1, 1,
1, 1, 1, 1, 1,
2, 2, 1, 1)
)
knitr::kable(
x = tteResultData,
caption = 'Table 4: Time-to-event output.'
)
## -----------------------------------------------------------------------------
targetIds <- c(1)
outcomeIds <- c(2)
dechallengeStopInterval <- 30
dechallengeEvaluationWindow <- 31
## ----echo=FALSE, results='asis'-----------------------------------------------
dcrcTargetData <- data.frame(
patientId = c(1, 1, 2,2,2, 3, 4, 4, 4, 5, 5),
cohortDefinitionId = rep(1, 11),
cohortStartDate = c('2001-01-20', '2001-10-20',
'2005-09-10', '2006-03-04', '2006-05-03',
'2004-04-02',
'2002-03-03', '2003-02-01', '2003-08-04',
'2005-02-01','2007-04-03'
),
cohortEndDate = c('2001-01-25', '2001-12-05',
'2005-09-15','2006-03-21', '2006-05-05',
'2004-05-17',
'2002-06-12', '2003-02-30',
'2003-08-24', '2005-10-08',
'2007-05-03')
)
knitr::kable(
x = dcrcTargetData,
caption = 'Example dechallenge-rechallenge data with dates.'
)
## ----echo=FALSE, results='asis'-----------------------------------------------
dcrcOutcomeData <- data.frame(
patientId = c(1, 1, 2,2,3, 3,4, 4, 5, 5),
cohortDefinitionId = rep(2, 10),
cohortStartDate = c('1999-10-03', '2001-11-30',
'2005-07-01', '2006-03-10',
'2004-05-16', '2004-06-12',
'2002-06-03',
'2003-02-20', '2006-07-21',
'2008-01-01')
)
knitr::kable(
x = tteOutcomeData,
caption = 'Example time-to-event data with timing.'
)
## ----echo=FALSE, results='asis'-----------------------------------------------
dcrcSummaryData <- data.frame(
patientId = c(1,2,3,4),
outcomeDate = c('2001-11-30', '2006-03-10',
'2004-05-16', '2002-06-03'),
exposureEnd = c('2001-12-05', '2006-03-21',
'2004-05-17', '2002-06-12'),
outcomeAfter = c('-','-', '2004-01-12', '-'),
futureExposure = c('-', '2006-05-03', '-', '2003-01-01'),
futureOutcome = c('-','-','-','2003-02-20'),
dechallengeType = c('Success', 'Seccess', 'Fail', 'Success'),
rechallengeType = c('-','Success', '-', 'Fail')
)
knitr::kable(
x = dcrcSummaryData,
caption = 'Dehcallenge-rechallenge summary table showing each dechallenge. Only some patients with a dechallenge will have a rechallenge.'
)
## ----echo=FALSE, results='asis'-----------------------------------------------
dcrcSummaryData2 <- data.frame(
dechallengeAttempts = 4,
dechallengeSuccess = 3,
dechallengeFailure = 1,
rechallengeAttempts = 2,
rechallengeSuccess = 1,
rechallangeFailure = 1
)
knitr::kable(
x = dcrcSummaryData2,
caption = 'Dehcallenge-rechallenge output.'
)
## -----------------------------------------------------------------------------
minPriorObservation <- 365
covariateSettings <- FeatureExtraction::createCovariateSettings(
useDemographicsAge = T,
useDemographicsGender = T,
useConditionOccurrenceAnyTimePrior = T, includedCovariateConceptIds = c(201820)
)
## ----echo=FALSE, results='asis'-----------------------------------------------
targetData <- data.frame(
patientId = c(1, 1, 1, 2, 2, 2, 3, 3, 3,
4, 4, 4, 5, 5, 5, 1, 1, 1,
2, 2, 2, 3, 3, 3),
cohortId = c(rep(1,15), rep(2, 9)),
feature = rep(c('age', 'sex', 'diabetes'),8),
value = c(50, 'Male', 'Yes',
18, 'Female', 'No',
22, 'Male', 'No',
40, 'Male', 'No',
70, 'Female', 'Yes',
24, 'Female', 'No',
35, 'Female', 'No',
31, 'Female', 'No')
)
knitr::kable(
x = targetData,
caption = 'Example patient level feature data.'
)
## ----echo=FALSE, results='asis'-----------------------------------------------
meanData <- data.frame(
cohortId = c(1, 1, 1, 2, 2, 2),
feature = c('Age', 'Sex: Male', 'Diabetes: Yes',
'Age', 'Sex: Male', 'Diabetes: Yes'),
mean = c(40, 0.60, 0.40, 30, 0, 0)
)
knitr::kable(
x = meanData,
caption = 'Example aggregate features for two example cohorts.'
)
## -----------------------------------------------------------------------------
targetId <- 1
outcomeId <- 2
minPriorObservation <- 365
outcomeWashoutDays <- 365
riskWindowStart <- 1
startAnchor <- 'cohort start'
riskWindowEnd <- 180
endAnchor <- 'cohort start'
covariateSettings <- FeatureExtraction::createCovariateSettings(
useDemographicsAge = T,
useDemographicsGender = T,
useConditionOccurrenceAnyTimePrior = T, includedCovariateConceptIds = c(201820)
)
## ----echo=FALSE, results='asis'-----------------------------------------------
data <- data.frame(
patientId = c(1, 1, 2, 3, 4, 4, 4, 5, 5),
targetCohortId = rep(1,9),
cohortStartDate = c('2001-01-20', '2001-10-20',
'2005-09-10', '2004-04-02',
'2002-03-03', '2003-02-01',
'2003-08-04', '2005-02-01',
'2007-04-03'),
cohortEndDate = c('2001-01-25', '2001-12-05',
'2005-09-15', '2004-05-17',
'2002-06-12', '2003-02-30',
'2003-08-24', '2005-10-08',
'2007-05-03'),
observationStart = c('2000-02-01', '2000-02-01',
'2001-02-01', '2001-02-01',
'2001-02-01', '2001-02-01',
'2001-02-01', '2001-02-01',
'2001-02-01')
)
knitr::kable(
x = data,
caption = 'Example target cohort.'
)
## ----echo=FALSE, results='asis'-----------------------------------------------
data <- data.frame(
patientId = c(1, 1, 3, 4, 4, 5, 5 ),
targetCohortId = rep(2,7),
cohortStartDate = c('1999-10-03', '2001-10-30',
'2004-05-16', '2002-06-03',
'2003-02-20', '2006-07-21',
'2008-01-01'
),
cohortEndDate = c('1999-10-08', '2001-11-07',
'2004-05-18', '2002-06-14',
'2003-03-01', '2006-08-03',
'2008-01-09')
)
knitr::kable(
x = data,
caption = 'Example outcome cohort.'
)
## ----echo=FALSE, results='asis'-----------------------------------------------
data <- data.frame(
patientId = c(2, 3, 4, 5),
targetCohortId = rep(1,4),
cohortStartDate = c('2005-09-10', '2004-04-02',
'2002-03-03', '2005-02-01'),
cohortEndDate = c('2005-09-15', '2004-05-17',
'2002-06-12','2005-10-08')
)
knitr::kable(
x = data,
caption = 'Example target cohort meeting risk factor inclusion criteria.'
)
## ----echo=FALSE, results='asis'-----------------------------------------------
data <- data.frame(
patientId = c(2, 3, 4, 5),
targetCohortId = rep(1,4),
cohortStartDate = c('2005-09-10', '2004-04-02',
'2002-03-03', '2005-02-01'),
cohortEndDate = c('2005-09-15', '2004-05-17',
'2002-06-12','2005-10-08'),
labels = c('Non-outcome', 'Outcome', 'Outcome',
'Non-outcome')
)
knitr::kable(
x = data,
caption = 'Example target cohort meeting risk factor inclusion criteria.'
)
## ----echo=FALSE, results='asis'-----------------------------------------------
targetData <- data.frame(
patientId = c(2,2,2,3,3,3,4,4,4,5,5,5),
cohortId = c(rep('Non-outcome',3), rep('Outcome',3), rep('Outcome',3), rep('Non-outcome',3)),
feature = rep(c('age', 'sex', 'diabetes'),4),
value = c(50, 'Male', 'Yes',
18, 'Female', 'No',
22, 'Male', 'No',
40, 'Male', 'No'
)
)
knitr::kable(
x = targetData,
caption = 'Example patient level feature data.'
)
## ----echo=FALSE, results='asis'-----------------------------------------------
meanData <- data.frame(
cohortId = c(rep('Outcome', 3), rep('Non-outcome',3)),
feature = c('Age', 'Sex: Male', 'Diabetes: Yes',
'Age', 'Sex: Male', 'Diabetes: Yes'),
mean = c(20, 0.50, 0, 45, 1, 0.5)
)
knitr::kable(
x = meanData,
caption = 'Example aggregate features for risk factor analysis.'
)
## -----------------------------------------------------------------------------
targetId <- 1
outcomeId <- 2
minPriorObservation <- 365
outcomeWashoutDays <- 365
preTargetIndexDays <- 365
postOutcomeIndexDays <- 365
riskWindowStart <- 1
startAnchor <- 'cohort start'
riskWindowEnd <- 180
endAnchor <- 'cohort start'
covariateSettings <- FeatureExtraction::createCovariateSettings(
useConditionOccurrenceAnyTimePrior = T, includedCovariateConceptIds = c(201820)
)
## ----echo=FALSE, results='asis'-----------------------------------------------
data <- data.frame(
patientId = c(1, 1, 2, 3, 4, 4, 4, 5, 5),
targetCohortId = rep(1,9),
cohortStartDate = c('2001-01-20', '2001-10-20',
'2005-09-10', '2004-04-02',
'2002-03-03', '2003-02-01',
'2003-08-04', '2005-02-01',
'2007-04-03'),
cohortEndDate = c('2001-01-25', '2001-12-05',
'2005-09-15', '2004-05-17',
'2002-06-12', '2003-02-30',
'2003-08-24', '2005-10-08',
'2007-05-03'),
observationStart = c('2000-02-01', '2000-02-01',
'2001-02-01', '2001-02-01',
'2001-02-01', '2001-02-01',
'2001-02-01', '2001-02-01',
'2001-02-01')
)
knitr::kable(
x = data,
caption = 'Example target cohort.'
)
## ----echo=FALSE, results='asis'-----------------------------------------------
data <- data.frame(
patientId = c(1, 1, 3, 4, 4, 5, 5 ),
targetCohortId = rep(2,7),
cohortStartDate = c('1999-10-03', '2001-10-30',
'2004-05-16', '2002-06-03',
'2003-02-20', '2006-07-21',
'2008-01-01'
),
cohortEndDate = c('1999-10-08', '2001-11-07',
'2004-05-18', '2002-06-14',
'2003-03-01', '2006-08-03',
'2008-01-09')
)
knitr::kable(
x = data,
caption = 'Example outcome cohort.'
)
## ----echo=FALSE, results='asis'-----------------------------------------------
data <- data.frame(
patientId = c(2, 3, 4, 5),
targetCohortId = rep(1,4),
cohortStartDate = c('2005-09-10', '2004-04-02',
'2002-03-03', '2005-02-01'),
cohortEndDate = c('2005-09-15', '2004-05-17',
'2002-06-12','2005-10-08')
)
knitr::kable(
x = data,
caption = 'Example target cohort meeting risk factor inclusion criteria.'
)
## ----echo=FALSE, results='asis'-----------------------------------------------
data <- data.frame(
patientId = c(3, 4),
targetCohortId = rep(1,2),
cohortStartDate = c('2004-04-02',
'2002-03-03'),
cohortEndDate = c('2004-05-17',
'2002-06-12'),
labels = c('Outcome', 'Outcome')
)
knitr::kable(
x = data,
caption = 'Example target cohort meeting case inclusion criteria.'
)
## ----echo=FALSE, results='asis'-----------------------------------------------
data <- data.frame(
patientId = c(3, 4),
targetCohortId = rep(1,2),
targetStartDate = c('2004-04-02',
'2002-03-03'),
outcomeStartDate = c('2004-05-16',
'2002-06-03'),
beforeStartDate = c("2003-04-03", "2001-03-03"),
beforeEndDate = c('2004-04-02','2002-03-03'),
duringStartDate = c('2004-04-03','2002-03-04'),
duringEndDate = c('2004-05-16','2002-06-03'),
afterStartDate = c('2004-05-17','2002-06-04'),
afterEndDate = c("2005-05-16", "2003-06-03")
)
knitr::kable(
x = data,
caption = 'Example cases with before/during/after dates.'
)
## ----echo=FALSE, results='asis'-----------------------------------------------
targetData <- data.frame(
patientId = c(3,3,3,4,4,4),
feature = rep(c('diabetes'),6),
timePeriod = rep(c('before','during', 'after'),2),
value = c('No', 'No', 'Yes',
'Yes', 'Yes', 'Yes'
)
)
knitr::kable(
x = targetData,
caption = 'Example patient level case feature data.'
)
## ----echo=FALSE, results='asis'-----------------------------------------------
targetData <- data.frame(
feature = rep(c('diabetes: Yes'),3),
timePeriod = c('before', 'during', 'after'),
value = c(0.5,0.5,1)
)
knitr::kable(
x = targetData,
caption = 'Example patient level case feature data.'
)
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## -----------------------------------------------------------------------------
targetIds <- c(1)
outcomeIds <- c(2)
## ----echo=FALSE, results='asis'-----------------------------------------------
tteTargetData <- data.frame(
patientId = c(1, 1, 2, 3, 4, 4, 4, 5, 5),
cohortDefinitionId = rep(1, 9),
cohortStartDate = c('2001-01-20', '2001-10-20',
'2005-09-10', '2004-04-02',
'2002-03-03', '2003-02-01',
'2003-08-04', '2005-02-01',
'2007-04-03'),
cohortEndDate = c('2001-01-25', '2001-12-05',
'2005-09-15', '2004-05-17',
'2002-06-12', '2003-02-30',
'2003-08-24', '2005-10-08',
'2007-05-03')
)
knitr::kable(
x = tteTargetData,
caption = 'Example time-to-event data with dates.'
)
## ----echo=FALSE, results='asis'-----------------------------------------------
tteOutcomeData <- data.frame(
patientId = c(1, 1, 3, 4, 4, 5, 5),
cohortDefinitionId = rep(2, 7),
cohortStartDate = c('1999-10-03', '2001-10-30',
'2004-05-16', '2002-06-03',
'2003-02-20', '2006-07-21',
'2008-01-01'),
cohortEndDate = c('1999-10-08', '2001-11-07',
'2004-05-18', '2002-06-14',
'2003-03-01', '2006-08-03',
'2008-01-09')
)
knitr::kable(
x = tteOutcomeData,
caption = 'Example time-to-event data with timing.'
)
## ----echo=FALSE, results='asis'-----------------------------------------------
tteSummaryData <- data.frame(
patientId = c(1, 1, 3, 4, 4, 5, 5),
outcomeDate = c('1999-10-03', '2001-10-30',
'2004-05-16', '2002-06-03',
'2003-02-20', '2006-07-21',
'2008-01-01'),
firstExposureDate = c('2001-01-20', '2001-01-20',
'2004-04-02', '2002-03-03',
'2002-03-03', '2005-02-01',
'2005-02-01'),
timeToEvent = c(-475, 283, 44, 92, 354, 535,
1064),
type = c('Before first exposure',
'During subsequent',
'During first',
'During first',
'During subsequent',
'Between eras',
'After last exposure'),
outcomeType = c('First',
'Subsequent',
'First',
'First',
'Subsequent',
'First',
'Subsequent')
)
knitr::kable(
x = tteSummaryData,
caption = 'Table 3: Time-to-event intermediate summary.'
)
## ----echo=FALSE, results='asis'-----------------------------------------------
tteResultData <- data.frame(
timeType = c(
rep('1-day', 2),
rep('30-day', 7),
rep('365-day', 5)
),
Type = c(
'During first',
'During first',
'Before first exposure',
'During first',
'During first',
'During subsequent',
'During subsequent',
'Between eras',
'After last exposure',
'Before first exposure',
'During first',
'During subsequent' ,
'Between eras',
'After last exposure'
),
outcomeType = c(
'First',
'First',
'First',
'First',
'First',
'Subsequent',
'Subsequent',
'First',
'Subsequent',
'First',
'First',
'Subsequent',
'First',
'Subsequent'
),
timeStart = c(44, 92, -481, 31, 91,
271, 331, 511, 1051, -731,
1, 1, 366, 731),
timeEnd = c(44, 92, -450, 60, 120,
300, 360, 540, 1080, -365,
365, 365, 730, 1095),
count = c(1, 1, 1, 1, 1,
1, 1, 1, 1, 1,
2, 2, 1, 1)
)
knitr::kable(
x = tteResultData,
caption = 'Table 4: Time-to-event output.'
)
## -----------------------------------------------------------------------------
targetIds <- c(1)
outcomeIds <- c(2)
dechallengeStopInterval <- 30
dechallengeEvaluationWindow <- 31
## ----echo=FALSE, results='asis'-----------------------------------------------
dcrcTargetData <- data.frame(
patientId = c(1, 1, 2,2,2, 3, 4, 4, 4, 5, 5),
cohortDefinitionId = rep(1, 11),
cohortStartDate = c('2001-01-20', '2001-10-20',
'2005-09-10', '2006-03-04', '2006-05-03',
'2004-04-02',
'2002-03-03', '2003-02-01', '2003-08-04',
'2005-02-01','2007-04-03'
),
cohortEndDate = c('2001-01-25', '2001-12-05',
'2005-09-15','2006-03-21', '2006-05-05',
'2004-05-17',
'2002-06-12', '2003-02-30',
'2003-08-24', '2005-10-08',
'2007-05-03')
)
knitr::kable(
x = dcrcTargetData,
caption = 'Example dechallenge-rechallenge data with dates.'
)
## ----echo=FALSE, results='asis'-----------------------------------------------
dcrcOutcomeData <- data.frame(
patientId = c(1, 1, 2,2,3, 3,4, 4, 5, 5),
cohortDefinitionId = rep(2, 10),
cohortStartDate = c('1999-10-03', '2001-11-30',
'2005-07-01', '2006-03-10',
'2004-05-16', '2004-06-12',
'2002-06-03',
'2003-02-20', '2006-07-21',
'2008-01-01')
)
knitr::kable(
x = tteOutcomeData,
caption = 'Example time-to-event data with timing.'
)
## ----echo=FALSE, results='asis'-----------------------------------------------
dcrcSummaryData <- data.frame(
patientId = c(1,2,3,4),
outcomeDate = c('2001-11-30', '2006-03-10',
'2004-05-16', '2002-06-03'),
exposureEnd = c('2001-12-05', '2006-03-21',
'2004-05-17', '2002-06-12'),
outcomeAfter = c('-','-', '2004-01-12', '-'),
futureExposure = c('-', '2006-05-03', '-', '2003-01-01'),
futureOutcome = c('-','-','-','2003-02-20'),
dechallengeType = c('Success', 'Seccess', 'Fail', 'Success'),
rechallengeType = c('-','Success', '-', 'Fail')
)
knitr::kable(
x = dcrcSummaryData,
caption = 'Dehcallenge-rechallenge summary table showing each dechallenge. Only some patients with a dechallenge will have a rechallenge.'
)
## ----echo=FALSE, results='asis'-----------------------------------------------
dcrcSummaryData2 <- data.frame(
dechallengeAttempts = 4,
dechallengeSuccess = 3,
dechallengeFailure = 1,
rechallengeAttempts = 2,
rechallengeSuccess = 1,
rechallangeFailure = 1
)
knitr::kable(
x = dcrcSummaryData2,
caption = 'Dehcallenge-rechallenge output.'
)
## -----------------------------------------------------------------------------
minPriorObservation <- 365
covariateSettings <- FeatureExtraction::createCovariateSettings(
useDemographicsAge = T,
useDemographicsGender = T,
useConditionOccurrenceAnyTimePrior = T, includedCovariateConceptIds = c(201820)
)
## ----echo=FALSE, results='asis'-----------------------------------------------
targetData <- data.frame(
patientId = c(1, 1, 1, 2, 2, 2, 3, 3, 3,
4, 4, 4, 5, 5, 5, 1, 1, 1,
2, 2, 2, 3, 3, 3),
cohortId = c(rep(1,15), rep(2, 9)),
feature = rep(c('age', 'sex', 'diabetes'),8),
value = c(50, 'Male', 'Yes',
18, 'Female', 'No',
22, 'Male', 'No',
40, 'Male', 'No',
70, 'Female', 'Yes',
24, 'Female', 'No',
35, 'Female', 'No',
31, 'Female', 'No')
)
knitr::kable(
x = targetData,
caption = 'Example patient level feature data.'
)
## ----echo=FALSE, results='asis'-----------------------------------------------
meanData <- data.frame(
cohortId = c(1, 1, 1, 2, 2, 2),
feature = c('Age', 'Sex: Male', 'Diabetes: Yes',
'Age', 'Sex: Male', 'Diabetes: Yes'),
mean = c(40, 0.60, 0.40, 30, 0, 0)
)
knitr::kable(
x = meanData,
caption = 'Example aggregate features for two example cohorts.'
)
## -----------------------------------------------------------------------------
targetId <- 1
outcomeId <- 2
minPriorObservation <- 365
outcomeWashoutDays <- 365
riskWindowStart <- 1
startAnchor <- 'cohort start'
riskWindowEnd <- 180
endAnchor <- 'cohort start'
covariateSettings <- FeatureExtraction::createCovariateSettings(
useDemographicsAge = T,
useDemographicsGender = T,
useConditionOccurrenceAnyTimePrior = T, includedCovariateConceptIds = c(201820)
)
## ----echo=FALSE, results='asis'-----------------------------------------------
data <- data.frame(
patientId = c(1, 1, 2, 3, 4, 4, 4, 5, 5),
targetCohortId = rep(1,9),
cohortStartDate = c('2001-01-20', '2001-10-20',
'2005-09-10', '2004-04-02',
'2002-03-03', '2003-02-01',
'2003-08-04', '2005-02-01',
'2007-04-03'),
cohortEndDate = c('2001-01-25', '2001-12-05',
'2005-09-15', '2004-05-17',
'2002-06-12', '2003-02-30',
'2003-08-24', '2005-10-08',
'2007-05-03'),
observationStart = c('2000-02-01', '2000-02-01',
'2001-02-01', '2001-02-01',
'2001-02-01', '2001-02-01',
'2001-02-01', '2001-02-01',
'2001-02-01')
)
knitr::kable(
x = data,
caption = 'Example target cohort.'
)
## ----echo=FALSE, results='asis'-----------------------------------------------
data <- data.frame(
patientId = c(1, 1, 3, 4, 4, 5, 5 ),
targetCohortId = rep(2,7),
cohortStartDate = c('1999-10-03', '2001-10-30',
'2004-05-16', '2002-06-03',
'2003-02-20', '2006-07-21',
'2008-01-01'
),
cohortEndDate = c('1999-10-08', '2001-11-07',
'2004-05-18', '2002-06-14',
'2003-03-01', '2006-08-03',
'2008-01-09')
)
knitr::kable(
x = data,
caption = 'Example outcome cohort.'
)
## ----echo=FALSE, results='asis'-----------------------------------------------
data <- data.frame(
patientId = c(2, 3, 4, 5),
targetCohortId = rep(1,4),
cohortStartDate = c('2005-09-10', '2004-04-02',
'2002-03-03', '2005-02-01'),
cohortEndDate = c('2005-09-15', '2004-05-17',
'2002-06-12','2005-10-08')
)
knitr::kable(
x = data,
caption = 'Example target cohort meeting risk factor inclusion criteria.'
)
## ----echo=FALSE, results='asis'-----------------------------------------------
data <- data.frame(
patientId = c(2, 3, 4, 5),
targetCohortId = rep(1,4),
cohortStartDate = c('2005-09-10', '2004-04-02',
'2002-03-03', '2005-02-01'),
cohortEndDate = c('2005-09-15', '2004-05-17',
'2002-06-12','2005-10-08'),
labels = c('Non-outcome', 'Outcome', 'Outcome',
'Non-outcome')
)
knitr::kable(
x = data,
caption = 'Example target cohort meeting risk factor inclusion criteria.'
)
## ----echo=FALSE, results='asis'-----------------------------------------------
targetData <- data.frame(
patientId = c(2,2,2,3,3,3,4,4,4,5,5,5),
cohortId = c(rep('Non-outcome',3), rep('Outcome',3), rep('Outcome',3), rep('Non-outcome',3)),
feature = rep(c('age', 'sex', 'diabetes'),4),
value = c(50, 'Male', 'Yes',
18, 'Female', 'No',
22, 'Male', 'No',
40, 'Male', 'No'
)
)
knitr::kable(
x = targetData,
caption = 'Example patient level feature data.'
)
## ----echo=FALSE, results='asis'-----------------------------------------------
meanData <- data.frame(
cohortId = c(rep('Outcome', 3), rep('Non-outcome',3)),
feature = c('Age', 'Sex: Male', 'Diabetes: Yes',
'Age', 'Sex: Male', 'Diabetes: Yes'),
mean = c(20, 0.50, 0, 45, 1, 0.5)
)
knitr::kable(
x = meanData,
caption = 'Example aggregate features for risk factor analysis.'
)
## -----------------------------------------------------------------------------
targetId <- 1
outcomeId <- 2
minPriorObservation <- 365
outcomeWashoutDays <- 365
preTargetIndexDays <- 365
postOutcomeIndexDays <- 365
riskWindowStart <- 1
startAnchor <- 'cohort start'
riskWindowEnd <- 180
endAnchor <- 'cohort start'
covariateSettings <- FeatureExtraction::createCovariateSettings(
useConditionOccurrenceAnyTimePrior = T, includedCovariateConceptIds = c(201820)
)
## ----echo=FALSE, results='asis'-----------------------------------------------
data <- data.frame(
patientId = c(1, 1, 2, 3, 4, 4, 4, 5, 5),
targetCohortId = rep(1,9),
cohortStartDate = c('2001-01-20', '2001-10-20',
'2005-09-10', '2004-04-02',
'2002-03-03', '2003-02-01',
'2003-08-04', '2005-02-01',
'2007-04-03'),
cohortEndDate = c('2001-01-25', '2001-12-05',
'2005-09-15', '2004-05-17',
'2002-06-12', '2003-02-30',
'2003-08-24', '2005-10-08',
'2007-05-03'),
observationStart = c('2000-02-01', '2000-02-01',
'2001-02-01', '2001-02-01',
'2001-02-01', '2001-02-01',
'2001-02-01', '2001-02-01',
'2001-02-01')
)
knitr::kable(
x = data,
caption = 'Example target cohort.'
)
## ----echo=FALSE, results='asis'-----------------------------------------------
data <- data.frame(
patientId = c(1, 1, 3, 4, 4, 5, 5 ),
targetCohortId = rep(2,7),
cohortStartDate = c('1999-10-03', '2001-10-30',
'2004-05-16', '2002-06-03',
'2003-02-20', '2006-07-21',
'2008-01-01'
),
cohortEndDate = c('1999-10-08', '2001-11-07',
'2004-05-18', '2002-06-14',
'2003-03-01', '2006-08-03',
'2008-01-09')
)
knitr::kable(
x = data,
caption = 'Example outcome cohort.'
)
## ----echo=FALSE, results='asis'-----------------------------------------------
data <- data.frame(
patientId = c(2, 3, 4, 5),
targetCohortId = rep(1,4),
cohortStartDate = c('2005-09-10', '2004-04-02',
'2002-03-03', '2005-02-01'),
cohortEndDate = c('2005-09-15', '2004-05-17',
'2002-06-12','2005-10-08')
)
knitr::kable(
x = data,
caption = 'Example target cohort meeting risk factor inclusion criteria.'
)
## ----echo=FALSE, results='asis'-----------------------------------------------
data <- data.frame(
patientId = c(3, 4),
targetCohortId = rep(1,2),
cohortStartDate = c('2004-04-02',
'2002-03-03'),
cohortEndDate = c('2004-05-17',
'2002-06-12'),
labels = c('Outcome', 'Outcome')
)
knitr::kable(
x = data,
caption = 'Example target cohort meeting case inclusion criteria.'
)
## ----echo=FALSE, results='asis'-----------------------------------------------
data <- data.frame(
patientId = c(3, 4),
targetCohortId = rep(1,2),
targetStartDate = c('2004-04-02',
'2002-03-03'),
outcomeStartDate = c('2004-05-16',
'2002-06-03'),
beforeStartDate = c("2003-04-03", "2001-03-03"),
beforeEndDate = c('2004-04-02','2002-03-03'),
duringStartDate = c('2004-04-03','2002-03-04'),
duringEndDate = c('2004-05-16','2002-06-03'),
afterStartDate = c('2004-05-17','2002-06-04'),
afterEndDate = c("2005-05-16", "2003-06-03")
)
knitr::kable(
x = data,
caption = 'Example cases with before/during/after dates.'
)
## ----echo=FALSE, results='asis'-----------------------------------------------
targetData <- data.frame(
patientId = c(3,3,3,4,4,4),
feature = rep(c('diabetes'),6),
timePeriod = rep(c('before','during', 'after'),2),
value = c('No', 'No', 'Yes',
'Yes', 'Yes', 'Yes'
)
)
knitr::kable(
x = targetData,
caption = 'Example patient level case feature data.'
)
## ----echo=FALSE, results='asis'-----------------------------------------------
targetData <- data.frame(
feature = rep(c('diabetes: Yes'),3),
timePeriod = c('before', 'during', 'after'),
value = c(0.5,0.5,1)
)
knitr::kable(
x = targetData,
caption = 'Example patient level case feature data.'
)
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