This function adds an event index to each row of the expanded
endpoints data.table. The event index is created based on variable-value
pairs and singleton conditions that define specific events of interest
within the dataset. This index can be used to identify events in the
user-supplied criteria and/or statistical functions
Arguments
- ep
A
data.tablethat contains expanded endpoint definitions, typically the output fromexpand_over_endpoints. It assumes the inclusion of the columnspop_var,pop_value,period_var,period_value,endpoint_filter,endpoint_group_filter, andcustom_pop_filter, which are used to define the conditions for event indexing.- analysis_data_container
A data.table containing the analysis data.
Value
A data.table similar to the input but with an additional
event_index column, which contains the indices of events as determined by
the specified conditions for each endpoint. The indices refer to the
INDEX_ column in the clinical data. This INDEX_ column is created by
chef when a user supplies a clinical dataset.
Examples
library(data.table)
#>
#> Attaching package: ‘data.table’
#> The following object is masked from ‘package:base’:
#>
#> %notin%
library(pharmaverseadam)
# Prepare clinical data with INDEX_ column
adcm_data <- as.data.table(pharmaverseadam::adcm)
adcm_data[, INDEX_ := .I]
#> STUDYID USUBJID SUBJID SITEID COUNTRY DOMAIN RFSTDTC
#> <char> <char> <char> <char> <char> <char> <char>
#> 1: CDISCPILOT01 01-701-1015 1015 701 USA CM 2014-01-02
#> 2: CDISCPILOT01 01-701-1015 1015 701 USA CM 2014-01-02
#> 3: CDISCPILOT01 01-701-1015 1015 701 USA CM 2014-01-02
#> 4: CDISCPILOT01 01-701-1015 1015 701 USA CM 2014-01-02
#> 5: CDISCPILOT01 01-701-1015 1015 701 USA CM 2014-01-02
#> ---
#> 7506: CDISCPILOT01 01-718-1427 1427 718 USA CM 2012-12-17
#> 7507: CDISCPILOT01 01-718-1427 1427 718 USA CM 2012-12-17
#> 7508: CDISCPILOT01 01-718-1427 1427 718 USA CM 2012-12-17
#> 7509: CDISCPILOT01 01-718-1427 1427 718 USA CM 2012-12-17
#> 7510: CDISCPILOT01 01-718-1427 1427 718 USA CM 2012-12-17
#> RFENDTC RFXSTDTC RFXENDTC RFPENDTC SCRFDT FRVDT
#> <char> <char> <char> <char> <Date> <Date>
#> 1: 2014-07-02 2014-01-02 2014-07-02 2014-07-02T11:45 <NA> <NA>
#> 2: 2014-07-02 2014-01-02 2014-07-02 2014-07-02T11:45 <NA> <NA>
#> 3: 2014-07-02 2014-01-02 2014-07-02 2014-07-02T11:45 <NA> <NA>
#> 4: 2014-07-02 2014-01-02 2014-07-02 2014-07-02T11:45 <NA> <NA>
#> 5: 2014-07-02 2014-01-02 2014-07-02 2014-07-02T11:45 <NA> <NA>
#> ---
#> 7506: 2013-02-18 2012-12-17 2013-02-11 2013-06-03 <NA> 2013-06-03
#> 7507: 2013-02-18 2012-12-17 2013-02-11 2013-06-03 <NA> 2013-06-03
#> 7508: 2013-02-18 2012-12-17 2013-02-11 2013-06-03 <NA> 2013-06-03
#> 7509: 2013-02-18 2012-12-17 2013-02-11 2013-06-03 <NA> 2013-06-03
#> 7510: 2013-02-18 2012-12-17 2013-02-11 2013-06-03 <NA> 2013-06-03
#> DTHDTC DTHADY DTHFL LDDTHELD LDDTHGR1 DTH30FL DTHA30FL DTHDOM DTHB30FL
#> <char> <num> <char> <num> <char> <char> <char> <char> <char>
#> 1: <NA> NA <NA> NA <NA> <NA> <NA> <NA> <NA>
#> 2: <NA> NA <NA> NA <NA> <NA> <NA> <NA> <NA>
#> 3: <NA> NA <NA> NA <NA> <NA> <NA> <NA> <NA>
#> 4: <NA> NA <NA> NA <NA> <NA> <NA> <NA> <NA>
#> 5: <NA> NA <NA> NA <NA> <NA> <NA> <NA> <NA>
#> ---
#> 7506: <NA> NA <NA> NA <NA> <NA> <NA> <NA> <NA>
#> 7507: <NA> NA <NA> NA <NA> <NA> <NA> <NA> <NA>
#> 7508: <NA> NA <NA> NA <NA> <NA> <NA> <NA> <NA>
#> 7509: <NA> NA <NA> NA <NA> <NA> <NA> <NA> <NA>
#> 7510: <NA> NA <NA> NA <NA> <NA> <NA> <NA> <NA>
#> REGION1 DMDTC DMDY AGE AGEU AGEGR1 SEX
#> <char> <char> <num> <num> <char> <char> <char>
#> 1: NA 2013-12-26 -7 63 YEARS 18-64 F
#> 2: NA 2013-12-26 -7 63 YEARS 18-64 F
#> 3: NA 2013-12-26 -7 63 YEARS 18-64 F
#> 4: NA 2013-12-26 -7 63 YEARS 18-64 F
#> 5: NA 2013-12-26 -7 63 YEARS 18-64 F
#> ---
#> 7506: NA 2012-12-13 -4 74 YEARS >64 F
#> 7507: NA 2012-12-13 -4 74 YEARS >64 F
#> 7508: NA 2012-12-13 -4 74 YEARS >64 F
#> 7509: NA 2012-12-13 -4 74 YEARS >64 F
#> 7510: NA 2012-12-13 -4 74 YEARS >64 F
#> RACE RACEGR1 ETHNIC SAFFL
#> <char> <char> <char> <char>
#> 1: WHITE White HISPANIC OR LATINO Y
#> 2: WHITE White HISPANIC OR LATINO Y
#> 3: WHITE White HISPANIC OR LATINO Y
#> 4: WHITE White HISPANIC OR LATINO Y
#> 5: WHITE White HISPANIC OR LATINO Y
#> ---
#> 7506: BLACK OR AFRICAN AMERICAN Non-white NOT HISPANIC OR LATINO Y
#> 7507: BLACK OR AFRICAN AMERICAN Non-white NOT HISPANIC OR LATINO Y
#> 7508: BLACK OR AFRICAN AMERICAN Non-white NOT HISPANIC OR LATINO Y
#> 7509: BLACK OR AFRICAN AMERICAN Non-white NOT HISPANIC OR LATINO Y
#> 7510: BLACK OR AFRICAN AMERICAN Non-white NOT HISPANIC OR LATINO Y
#> ARM ARMCD ACTARM ACTARMCD
#> <char> <char> <char> <char>
#> 1: Placebo Pbo Placebo Pbo
#> 2: Placebo Pbo Placebo Pbo
#> 3: Placebo Pbo Placebo Pbo
#> 4: Placebo Pbo Placebo Pbo
#> 5: Placebo Pbo Placebo Pbo
#> ---
#> 7506: Xanomeline High Dose Xan_Hi Xanomeline High Dose Xan_Hi
#> 7507: Xanomeline High Dose Xan_Hi Xanomeline High Dose Xan_Hi
#> 7508: Xanomeline High Dose Xan_Hi Xanomeline High Dose Xan_Hi
#> 7509: Xanomeline High Dose Xan_Hi Xanomeline High Dose Xan_Hi
#> 7510: Xanomeline High Dose Xan_Hi Xanomeline High Dose Xan_Hi
#> TRTP TRTA TRT01P
#> <char> <char> <char>
#> 1: Placebo Placebo Placebo
#> 2: Placebo Placebo Placebo
#> 3: Placebo Placebo Placebo
#> 4: Placebo Placebo Placebo
#> 5: Placebo Placebo Placebo
#> ---
#> 7506: Xanomeline High Dose Xanomeline High Dose Xanomeline High Dose
#> 7507: Xanomeline High Dose Xanomeline High Dose Xanomeline High Dose
#> 7508: Xanomeline High Dose Xanomeline High Dose Xanomeline High Dose
#> 7509: Xanomeline High Dose Xanomeline High Dose Xanomeline High Dose
#> 7510: Xanomeline High Dose Xanomeline High Dose Xanomeline High Dose
#> TRT01A TRTSDT TRTSDTM TRTSTMF TRTEDT
#> <char> <Date> <POSc> <char> <Date>
#> 1: Placebo 2014-01-02 2014-01-02 H 2014-07-02
#> 2: Placebo 2014-01-02 2014-01-02 H 2014-07-02
#> 3: Placebo 2014-01-02 2014-01-02 H 2014-07-02
#> 4: Placebo 2014-01-02 2014-01-02 H 2014-07-02
#> 5: Placebo 2014-01-02 2014-01-02 H 2014-07-02
#> ---
#> 7506: Xanomeline High Dose 2012-12-17 2012-12-17 H 2013-02-11
#> 7507: Xanomeline High Dose 2012-12-17 2012-12-17 H 2013-02-11
#> 7508: Xanomeline High Dose 2012-12-17 2012-12-17 H 2013-02-11
#> 7509: Xanomeline High Dose 2012-12-17 2012-12-17 H 2013-02-11
#> 7510: Xanomeline High Dose 2012-12-17 2012-12-17 H 2013-02-11
#> TRTEDTM TRTETMF APHASE APHASEN EOSSTT EOSDT
#> <POSc> <char> <char> <num> <char> <Date>
#> 1: 2014-07-02 23:59:59 H On-Treatment 2 COMPLETED 2014-07-02
#> 2: 2014-07-02 23:59:59 H On-Treatment 2 COMPLETED 2014-07-02
#> 3: 2014-07-02 23:59:59 H On-Treatment 2 COMPLETED 2014-07-02
#> 4: 2014-07-02 23:59:59 H On-Treatment 2 COMPLETED 2014-07-02
#> 5: 2014-07-02 23:59:59 H On-Treatment 2 COMPLETED 2014-07-02
#> ---
#> 7506: 2013-02-11 23:59:59 H Pre-Treatment 1 DISCONTINUED 2013-02-18
#> 7507: 2013-02-11 23:59:59 H Pre-Treatment 1 DISCONTINUED 2013-02-18
#> 7508: 2013-02-11 23:59:59 H Pre-Treatment 1 DISCONTINUED 2013-02-18
#> 7509: 2013-02-11 23:59:59 H Pre-Treatment 1 DISCONTINUED 2013-02-18
#> 7510: 2013-02-11 23:59:59 H Pre-Treatment 1 DISCONTINUED 2013-02-18
#> RFICDTC RANDDT LSTALVDT TRTDURD DTHDT DTHDTF DTHCAUS DTHCGR1 CMSEQ
#> <char> <Date> <Date> <num> <Date> <char> <char> <char> <num>
#> 1: <NA> 2014-01-02 2014-07-02 182 <NA> <NA> <NA> <NA> 48
#> 2: <NA> 2014-01-02 2014-07-02 182 <NA> <NA> <NA> <NA> 54
#> 3: <NA> 2014-01-02 2014-07-02 182 <NA> <NA> <NA> <NA> 60
#> 4: <NA> 2014-01-02 2014-07-02 182 <NA> <NA> <NA> <NA> 66
#> 5: <NA> 2014-01-02 2014-07-02 182 <NA> <NA> <NA> <NA> 17
#> ---
#> 7506: <NA> 2012-12-17 2013-02-25 57 <NA> <NA> <NA> <NA> 6
#> 7507: <NA> 2012-12-17 2013-02-25 57 <NA> <NA> <NA> <NA> 8
#> 7508: <NA> 2012-12-17 2013-02-25 57 <NA> <NA> <NA> <NA> 9
#> 7509: <NA> 2012-12-17 2013-02-25 57 <NA> <NA> <NA> <NA> 12
#> 7510: <NA> 2012-12-17 2013-02-25 57 <NA> <NA> <NA> <NA> 13
#> CMDECOD CMTRT CMCLAS
#> <char> <char> <char>
#> 1: HYDROCORTISONE HYDROCORTISONE SYSTEMIC HORMONAL PREPARATIONS, EXCL.
#> 2: HYDROCORTISONE HYDROCORTISONE SYSTEMIC HORMONAL PREPARATIONS, EXCL.
#> 3: HYDROCORTISONE HYDROCORTISONE SYSTEMIC HORMONAL PREPARATIONS, EXCL.
#> 4: HYDROCORTISONE HYDROCORTISONE SYSTEMIC HORMONAL PREPARATIONS, EXCL.
#> 5: UNCODED NEOSPORIN /USA/ UNCODED
#> ---
#> 7506: UNCODED MULTIVITAMINS UNCODED
#> 7507: UNCODED MULTIVITAMINS UNCODED
#> 7508: UNCODED MULTIVITAMINS UNCODED
#> 7509: UNCODED MULTIVITAMINS UNCODED
#> 7510: UNCODED MULTIVITAMINS UNCODED
#> CMSTDTC ASTDT ASTDTM ASTDTF ASTTMF CMENDTC AENDT AENDTM
#> <char> <Date> <POSc> <char> <char> <char> <Date> <POSc>
#> 1: 2014-03-27 2014-03-27 2014-03-27 <NA> H <NA> <NA> <NA>
#> 2: 2014-03-27 2014-03-27 2014-03-27 <NA> H <NA> <NA> <NA>
#> 3: 2014-03-27 2014-03-27 2014-03-27 <NA> H <NA> <NA> <NA>
#> 4: 2014-03-27 2014-03-27 2014-03-27 <NA> H <NA> <NA> <NA>
#> 5: 2014-01-03 2014-01-03 2014-01-03 <NA> H <NA> <NA> <NA>
#> ---
#> 7506: 2002-08 2002-08-01 2002-08-01 D H <NA> <NA> <NA>
#> 7507: 2002-08 2002-08-01 2002-08-01 D H <NA> <NA> <NA>
#> 7508: 2002-08 2002-08-01 2002-08-01 D H <NA> <NA> <NA>
#> 7509: 2002-08 2002-08-01 2002-08-01 D H <NA> <NA> <NA>
#> 7510: 2002-08 2002-08-01 2002-08-01 D H <NA> <NA> <NA>
#> AENDTF AENTMF ASTDY CMSTDY AENDY CMENDY ADURN ADURU ANL01FL ONTRTFL
#> <char> <char> <num> <num> <num> <num> <num> <char> <char> <char>
#> 1: <NA> <NA> 85 85 NA NA NA <NA> Y Y
#> 2: <NA> <NA> 85 85 NA NA NA <NA> Y Y
#> 3: <NA> <NA> 85 85 NA NA NA <NA> Y Y
#> 4: <NA> <NA> 85 85 NA NA NA <NA> Y Y
#> 5: <NA> <NA> 2 2 NA NA NA <NA> Y Y
#> ---
#> 7506: <NA> <NA> -3791 NA NA NA NA <NA> <NA> <NA>
#> 7507: <NA> <NA> -3791 NA NA NA NA <NA> <NA> <NA>
#> 7508: <NA> <NA> -3791 NA NA NA NA <NA> <NA> <NA>
#> 7509: <NA> <NA> -3791 NA NA NA NA <NA> <NA> <NA>
#> 7510: <NA> <NA> -3791 NA NA NA NA <NA> <NA> <NA>
#> PREFL FUPFL AOCCPFL CMINDC CMDOSE CMDOSU
#> <char> <char> <char> <char> <num> <char>
#> 1: <NA> <NA> Y <NA> 1 VIAL
#> 2: <NA> <NA> <NA> <NA> 1 VIAL
#> 3: <NA> <NA> <NA> <NA> 1 VIAL
#> 4: <NA> <NA> <NA> <NA> 1 VIAL
#> 5: <NA> <NA> Y <NA> 1 VIAL
#> ---
#> 7506: Y <NA> <NA> PROPHYLAXIS OR NON-THERAPEUTIC USE 1 TABLET
#> 7507: Y <NA> <NA> PROPHYLAXIS OR NON-THERAPEUTIC USE 1 TABLET
#> 7508: Y <NA> <NA> PROPHYLAXIS OR NON-THERAPEUTIC USE 1 TABLET
#> 7509: Y <NA> <NA> PROPHYLAXIS OR NON-THERAPEUTIC USE 1 TABLET
#> 7510: Y <NA> <NA> PROPHYLAXIS OR NON-THERAPEUTIC USE 1 TABLET
#> CMDOSFRQ CMROUTE CMSPID CMENRTPT VISITNUM VISIT VISITDY
#> <char> <char> <char> <char> <num> <char> <num>
#> 1: PRN TOPICAL 6 ONGOING 10 WEEK 16 112
#> 2: PRN TOPICAL 6 ONGOING 11 WEEK 20 140
#> 3: PRN TOPICAL 6 ONGOING 12 WEEK 24 168
#> 4: PRN TOPICAL 6 ONGOING 13 WEEK 26 182
#> 5: PRN TOPICAL 5 ONGOING 4 WEEK 2 14
#> ---
#> 7506: QD ORAL 1 ONGOING 5 WEEK 4 28
#> 7507: QD ORAL 1 ONGOING 6 AMBUL ECG REMOVAL 30
#> 7508: QD ORAL 1 ONGOING 7 WEEK 6 42
#> 7509: QD ORAL 1 ONGOING 8 WEEK 8 56
#> 7510: QD ORAL 1 ONGOING 201 RETRIEVAL 168
#> CMDTC INDEX_
#> <char> <int>
#> 1: 2014-05-07 1
#> 2: 2014-05-21 2
#> 3: 2014-06-18 3
#> 4: 2014-07-02 4
#> 5: 2014-01-16 5
#> ---
#> 7506: 2013-01-17 7506
#> 7507: 2013-01-19 7507
#> 7508: 2013-01-28 7508
#> 7509: 2013-02-18 7509
#> 7510: 2013-06-03 7510
analysis_data_container <- data.table(
dat = list(adcm_data),
key_analysis_data = "a"
)
setkey(analysis_data_container, key_analysis_data)
# Create endpoint with specific filters
ep <- data.table(
endpoint_id = 1L,
pop_var = "SAFFL",
pop_value = "Y",
period_var = NA_character_,
period_value = NA_character_,
endpoint_filter = NA_character_,
endpoint_group_filter = NA_character_,
custom_pop_filter = NA_character_,
key_analysis_data = "a"
)
setkey(ep, key_analysis_data)
# Add event index: identifies which rows match endpoint criteria
ep_with_index <- add_event_index(ep, analysis_data_container)
# event_index contains row numbers from adcm_data matching the criteria
str(ep_with_index$event_index) # integer vector of INDEX_ values
#> List of 1
#> $ : int [1:7510] 1 2 3 4 5 6 7 8 9 10 ...
length(ep_with_index$event_index[[1]]) # e.g., 47 events match SAFFL="Y"
#> [1] 7510