使用R语言生成CDISC SDTM.AE domain

本文链接：https://blog.csdn.net/Bowen_Wu/article/details/139618873

写在前面

- 使用的是Rstudio

- 其实R已经有生成sdtm相关的package，以下代码仅作为练习R语言的语法，不是高效生成sdtm的方法

- 代码中没有解决的问题包括：EPOCH相关的逻辑没有考虑partial date的情况；在使用arrange() function做-SEQ排序时，关于大小写英文字母的排序机制似乎与SAS语言的sort function有所不同，导致使用相同的排序变量，通过R和SAS排序后，record的顺序会有不同；输出xpt结果是乱码，暂时输出到csv文件中。

- 还没有写生成SUPPAE的代码

- 代码参考了以下材料

Generating .xpt files with SAS, R and Python

https://www.pharmasug.org/proceedings/2021/EP/PharmaSUG-2021-EP-057.pdf

Yotube @mycsg

mycsg TASKS-SDTMGEN

以下是R代码

setwd('C://R_software')
library(haven)
library(dplyr)
library(tidyverse)
library(sas7bdat)
library(SASxport)
library(Hmisc)

# import source data
raw_ae_001 <- read_sas('C://rawdata/ae_001.sas7bdat')
raw_meddrathsaurus <- read_sas('C://rawdata/meddrathesaurus.sas7bdat')
sdtm_dm <- read_sas('C://sdtmdata/SDTM/DM.sas7bdat')
sdtm_se <- read_sas('C://rawdata/SE.sas7bdat')

# Update the variable name to uppercase, because var name is case sensitive in R
names(raw_ae_001) <- toupper(names(raw_ae_001))
names(raw_meddrathsaurus) <- toupper(names(raw_meddrathsaurus))

# Filter ae raw data with AETERM not missing, and keep necessary variables
ae <- raw_ae_001 %>%
select(SUBJECT,RECORDPOSITION,AETERM,AESTDAT_RAW,AESTTIM,AEENDAT_RAW,AEENTIM,
AESEV_STD,AESER_STD,AEACN_STD,AEREL_STD,AEREL_WD_STD,AEPATT_STD,AEOUT_STD,AESCONG_STD,
AESDISAB_STD,AESDTH_STD,AESHOSP_STD,AESLIFE_STD,AESMIE_STD,AEONGO) %>%
filter(AETERM != "")

# Update AETERM value to uppercase in order to merge with source MedDRA coding data
ae$AETERM <- toupper(ae$AETERM)

# Filter MedDRA source data with AE pannel only
meddra <- raw_meddrathsaurus %>%
filter(PANEL=="AE")

# Merge AE and MedDRA data (left join) by AETERM, create AESTDTC/AEENDTC
ae1 <- merge (ae, meddra, by.x = c("AETERM"), by.y = c("VERBATIM"), all.x = T) %>%
# create AESTDTC
mutate(
stdayn = suppressWarnings(as.numeric(word(AESTDAT_RAW,1))), ### as.numeric>>input, word>>scan
stday = if_else(!is.na(stdayn), str_pad(stdayn, width = 2, pad = "0"), "-"), ### is.na>>not missing, !>>not, str_pad>>put xx.
stmonthc = str_to_upper(word(AESTDAT_RAW, 2)), ### str_to_upper>>uppercase
stmonth = case_when(
stmonthc == "JAN" ~ "01",
stmonthc == "FEB" ~ "02",
stmonthc == "MAR" ~ "03",
stmonthc == "APR" ~ "04",
stmonthc == "MAY" ~ "05",
stmonthc == "JUN" ~ "06",
stmonthc == "JUL" ~ "07",
stmonthc == "AUG" ~ "08",
stmonthc == "SEP" ~ "09",
stmonthc == "OCT" ~ "10",
stmonthc == "NOV" ~ "11",
stmonthc == "DEC" ~ "12",
TRUE ~ "-"
),
styear = word(AESTDAT_RAW,3),
styear1 = if_else((styear == "UNK") | (is.na(styear)), "-", styear), ### | >> or
aestdate = str_c(styear1, stmonth, stday, sep = "-"), ### str_c >> catx
AESTDTC = if_else(AESTTIM != "", str_c(aestdate, str_pad(AESTTIM, width = 5, pad = "0"), sep = "T"), aestdate),

AESTDTC = if_else(str_sub(AESTDTC, -5) == "-----", "", AESTDTC),
AESTDTC = if_else(str_sub(AESTDTC, -4) == "----", str_sub(AESTDTC,end=-5), AESTDTC),
AESTDTC = if_else(str_sub(AESTDTC, -2) == "--", str_sub(AESTDTC,end=-3), AESTDTC)
) %>%
# create AEENDTC
mutate(
endayn = suppressWarnings(as.numeric(word(AEENDAT_RAW,1))), ### as.numeric>>input, word>>scan
enday = if_else(!is.na(endayn), str_pad(endayn, width = 2, pad = "0"), "-"), ### is.na>>not missing, !>>not, str_pad>>put xx.
enmonthc = str_to_upper(word(AEENDAT_RAW, 2)), ### str_to_upper>>uppercase
enmonth = case_when(
enmonthc == "JAN" ~ "01",
enmonthc == "FEB" ~ "02",
enmonthc == "MAR" ~ "03",
enmonthc == "APR" ~ "04",
enmonthc == "MAY" ~ "05",
enmonthc == "JUN" ~ "06",
enmonthc == "JUL" ~ "07",
enmonthc == "AUG" ~ "08",
enmonthc == "SEP" ~ "09",
enmonthc == "OCT" ~ "10",
enmonthc == "NOV" ~ "11",
enmonthc == "DEC" ~ "12",
TRUE ~ "-"
),
enyear = word(AEENDAT_RAW,3),
enyear1 = if_else((enyear == "UNK") | (is.na(enyear)), "-", enyear), ### | >> or
aeendate = str_c(enyear1, enmonth, enday, sep = "-"), ### str_c >> catx
AEENDTC = if_else(AEENTIM != "", str_c(aeendate, str_pad(AEENTIM, width = 5, pad = "0"), sep = "T"), aeendate),

AEENDTC = if_else(str_sub(AEENDTC, -5) == "-----", "", AEENDTC),
AEENDTC = if_else(str_sub(AEENDTC, -4) == "----", str_sub(AEENDTC,end=-5), AEENDTC),
AEENDTC = if_else(str_sub(AEENDTC, -2) == "--", str_sub(AEENDTC,end=-3), AEENDTC)
)

# Create AE domain vars
ae2 <- ae1 %>%
cbind(
STUDYID=c("PROTOCOLID"),
DOMAIN=c("AE"),
USUBJID=str_c(c("PROTOCOLID-0"),substr(ae1$SUBJECT,4,6),c("-00"),substr(ae1$SUBJECT,7,9)), # str_c() is catx() in SAS
SUBJID=ae1$SUBJECT,
AESPID=str_c(c("AE_001-"),ae1$RECORDPOSITION),
AELLT=ae1$LLT_NAME,
AELLTCD=ae1$LLT_CODE,
AEDECOD=ae1$PT_NAME,
AEPTCD=ae1$PT_CODE,
AEHLT=ae1$HLT_NAME,
AEHLTCD=ae1$HLT_CODE,
AEHLGT=ae1$HGT_NAME,
AEHLGTCD=ae1$HGT_CODE,
AEBODSYS=ae1$SOC_NAME,
AEBDSYCD=ae1$SOC_CODE,
AESOC=ae1$SOC_NAME,
AESOCCD=ae1$SOC_CODE,
AESEV=ae1$AESEV_STD,
AESER=ae1$AESER_STD,
AEACN=ae1$AEACN_STD,
AEREL=ae1$AEREL_STD,
AERELNST=ae1$AEREL_WD_STD,
AEPATT=ae1$AEPATT_STD,
AEOUT=ae1$AEOUT_STD,
AESCONG=ae1$AESCONG_STD,
AESDISAB=ae1$AESDISAB_STD,
AESDTH=ae1$AESDTH_STD,
AESHOSP=ae1$AESHOSP_STD,
AESLIFE=ae1$AESLIFE_STD,
AESMIE=ae1$AESMIE_STD
)

# Merge AE and SDTM.DM by USUBJID, create AESTDY/AEENDY
sdtm_dm <- select(sdtm_dm,USUBJID,RFSTDTC,RFENDTC)

ae3 <- merge (ae2, sdtm_dm, by = c("USUBJID"), all.x = T) %>%
mutate(
aestdt=as.Date(AESTDTC),
rfstdt=as.Date(RFSTDTC),
rfstdate=str_sub(RFSTDTC,1,10),
rfst_year=str_sub(RFSTDTC,1,4),
rfst_month=str_sub(RFSTDTC,6,7),
rfst_day=str_sub(RFSTDTC,9,10),
AESTDY=ifelse(!is.na(aestdt) & !is.na(rfstdt),
ifelse((aestdt>=rfstdt),aestdt-rfstdt+1,aestdt-rfstdt), ""
)
) %>%
mutate(
aeendt=as.Date(AEENDTC),
rfstdt=as.Date(RFSTDTC),
AEENDY=ifelse(!is.na(aeendt) & !is.na(rfstdt),
ifelse((aeendt>=rfstdt),aeendt-rfstdt+1,aeendt-rfstdt), ""
)
) %>%
# create AEENRTPT, AEENTPT
mutate(
AEENRTPT=ifelse(AEONGO==1,"ONGOING",""),
AEENTPT=ifelse(AEONGO==1,
ifelse(is.na(rfstdt)==T,"SCREENING","END OF STUDY"),""
)
)

# prepare SE dataset for creating EPOCH
sdtm_se <- select(sdtm_se,USUBJID,ETCD,SESTDTC,SEENDTC)

sest <- sdtm_se %>%
select(USUBJID,ETCD,SESTDTC) %>%
pivot_wider(names_from=ETCD, values_from=SESTDTC)

colnames(sest) <- c("USUBJID","st1","st2","st3")

seen <- sdtm_se %>%
select(USUBJID,ETCD,SEENDTC) %>%
pivot_wider(names_from=ETCD, values_from=SEENDTC)

colnames(seen) <- c("USUBJID","en1","en2","en3")

sesten <- merge (sest, seen, by = c("USUBJID"))

ae4 <- merge (ae3, sesten, by = c("USUBJID"), all.x = T)

ae5 <- ae4 %>%
mutate(EPOCH=NA) %>%
mutate(
EPOCH=ifelse((st1<=aestdt & aestdt<en1) | (aestdt<=en1 & is.na(st2)==T), "SCREENING",ifelse(st2<=aestdt & aestdt<=en2, "TREATMENT", "FOLLOW-UP"))
) %>%
#mutate(
# EPOCH=ifelse(!is.na(EPOCH)==T & !is.na(stday)==T, EPOCH, ifelse())
#) %>%
arrange(STUDYID,USUBJID,AEDECOD,AESTDTC,AEENDTC,AESPID) %>%
group_by(USUBJID) %>%
mutate(AESEQ=row_number())

# select target vars in AE
sdtm_ae <- select(ae5,STUDYID,DOMAIN,USUBJID,SUBJID,AESEQ,AESPID,
AETERM,AELLT,AELLTCD,AEDECOD,AEPTCD,AEHLT,AEHLTCD,AEHLGT,AEHLGTCD,AEBODSYS,AEBDSYCD,AESOC,AESOCCD,
AESEV,AESER,AEACN,AEREL,AERELNST,AEPATT,AEOUT,AESCONG,AESDISAB,AESDTH,AESHOSP,AESLIFE,AESMIE,
EPOCH,AESTDTC,AEENDTC,AESTDY,AEENDY,AEENRTPT,AEENTPT)

# convert following vars to numeric per CDSIC definition
sdtm_ae$AELLTCD <- as.numeric(sdtm_ae$AELLTCD)
sdtm_ae$AEPTCD <- as.numeric(sdtm_ae$AEPTCD)
sdtm_ae$AEHLTCD <- as.numeric(sdtm_ae$AEHLTCD)
sdtm_ae$AEHLGTCD <- as.numeric(sdtm_ae$AEHLGTCD)
sdtm_ae$AEBDSYCD <- as.numeric(sdtm_ae$AEBDSYCD)
sdtm_ae$AESOCCD <- as.numeric(sdtm_ae$AESOCCD)
sdtm_ae$AESTDY <- as.numeric(sdtm_ae$AESTDY)
sdtm_ae$AEENDY <- as.numeric(sdtm_ae$AEENDY)

# convert NA to null
sdtm_ae$AESTDY[is.na(sdtm_ae$AESTDY)] <- ""
sdtm_ae$AEENDY[is.na(sdtm_ae$AEENDY)] <- ""

# add label
label(sdtm_ae) <- "Adverse Events"
label(sdtm_ae$STUDYID) <- "Study Identifier"
label(sdtm_ae$DOMAIN) <- "Domain Abbreviation"
label(sdtm_ae$USUBJID) <- "Unique Subject Identifier"
label(sdtm_ae$SUBJID) <- "Subject Identifier for the Study"
label(sdtm_ae$AESEQ) <- "Sequence Number"
label(sdtm_ae$AESPID) <- "Sponsor-Defined Identifier"
label(sdtm_ae$AETERM) <- "Reported Term for the Adverse Event"
label(sdtm_ae$AELLT) <- "Lowest Level Term"
label(sdtm_ae$AELLTCD) <- "Lowest Level Term Code"
label(sdtm_ae$AEDECOD) <- "Dictionary-Derived Term"
label(sdtm_ae$AEPTCD) <- "Preferred Term Code"
label(sdtm_ae$AEHLT) <- "High Level Term"
label(sdtm_ae$AEHLTCD) <- "High Level Term Code"
label(sdtm_ae$AEHLGT) <- "High Level Group Term"
label(sdtm_ae$AEHLGTCD) <- "High Level Group Term Code"
label(sdtm_ae$AEBODSYS) <- "Body System or Organ Class"
label(sdtm_ae$AEBDSYCD) <- "Body System or Organ Class Code"
label(sdtm_ae$AESOC) <- "Primary System Organ Class"
label(sdtm_ae$AESOCCD) <- "Primary System Organ Class Code"
label(sdtm_ae$AESEV) <- "Severity/Intensity"
label(sdtm_ae$AESER) <- "Serious Event"
label(sdtm_ae$AEACN) <- "Action Taken with Study Treatment"
label(sdtm_ae$AEREL) <- "Causality"
label(sdtm_ae$AERELNST) <- "Relationship to Non-Study Treatment"
label(sdtm_ae$AEPATT) <- "Pattern of Adverse Event"
label(sdtm_ae$AEOUT) <- "Outcome of Adverse Event"
label(sdtm_ae$AESCONG) <- "Congenital Anomaly or Birth Defect"
label(sdtm_ae$AESDISAB) <- "Persist or Signif Disability/Incapacity"
label(sdtm_ae$AESDTH) <- "Results in Death"
label(sdtm_ae$AESHOSP) <- "Requires or Prolongs Hospitalization"
label(sdtm_ae$AESLIFE) <- "Is Life Threatening"
label(sdtm_ae$AESMIE) <- "Other Medically Important Serious Event"
label(sdtm_ae$EPOCH) <- "Epoch"
label(sdtm_ae$AESTDTC) <- "Start Date/Time of Adverse Event"
label(sdtm_ae$AEENDTC) <- "End Date/Time of Adverse Event"
label(sdtm_ae$AESTDY) <- "Study Day of Start of Adverse Event"
label(sdtm_ae$AEENDY) <- "Study Day of End of Adverse Event"
label(sdtm_ae$AEENRTPT) <- "End Relative to Reference Time Point"
label(sdtm_ae$AEENTPT) <- "End Reference Time Point"