Nothing
R/odk2openVA_2014.R
In CrossVA: Verbal Autopsy Data Transformation for InSilicoVA and InterVA5 Algorithms
#' Map VA records to InterVA5 and InSilico (with option data.type = "WHO2016").
#'
#' \code{odk2openVA_2014} transforms data collected with the 2014 WHO VA instrument
#' (form id: va_who_2014_final10) to serve as the input to the InterVA5 and
#' InSilicoVA alogrithms for coding cause of death.
#'
#' @param odk A dataframe, obtained from reading an ODK Briefcase
#' export of records collected with the WHO questionnaire.
#'
#' @param id_col A character string of the column name (in odk) with the
#' unique ID for each death.
#'
#' @examples
#' \dontrun{
#' record_f_name <- system.file("sample", "who2014_odk_export.csv", package = "CrossVA")
#' records <- read.csv(record_f_name, stringsAsFactors = FALSE)
#' output <- odk2openVA_2014(records)
#' }
#'
#' @importFrom stringi stri_endswith_fixed
#'
#' @export
#'
odk2openVA_2014 <- function (odk, id_col = "meta.instanceID") {
## Input Data
odkNames <- tolower(names(odk))
## Output Variables
whoNames <- c("id3A280", "id3A280", "id1A110", "id1A110", "id1A220",
"id1A220", "id1A220", "id1A220", "id1A220", "id1A220", "id1A220",
"id1A220", "id1A220", "id1A220", "id1A220", "id1A220", "id1A220",
"id1A220", "id1A600", "id3E100", "id3E115", NA, "id3E310", "id3E510",
"id3E320", "id3E340", "id3E400", "id3E112", "id3E520", "id3E104",
"id3E106", "id3E108", "id3E111", "id3E500", "id3E530", "id3E330",
"id3E113", "id3E102", "id3D285", "id3D290", "id3D292", "id3D294",
"id3D296", "id3D298", "id3D299", "id3D300", NA, "id3D310", "id3D320",
"id3D325", "id3D330", "id3A300", "id3A300", "id3A310", "id3A100",
"id3A110", "id3A120", "id3A130", "id3A135", "id3A140", "id3A150",
"id3A160", "id3A170", "id3A180", "id3A190", "id3A200", "id3A210",
"id3A220", "id3A230", "id3A240", "id3A250", "id3A260", "id3A270",
"id3B100", "id3B110", "id3B110", "id3B110", NA, "id3B115", NA, "id3B120",
"id3B130", "id3B140", "id3B140", "id3B150", "id3B155", "id3B160",
"id3B170", "id3B242", "id3B244", "id3B246", "id3B190", "id3B200",
"id3B200", "id3B210", "id3B220", "id3B220", "id3B230", "id3B240",
"id3B250", "id3B260", NA, "id3B270", "id3B272", "id3B274", "id3B280",
"id3B290", "id3B290", "id3B290", "id3B292", "id3B294", "id3B296",
"id3B300", "id3B305", "id3B310", NA, "id3B315", "id3B320", "id3B325",
"id3B330", NA, "id3B340", "id3B350", "id3B350", "id3B355", "id3B355",
"id3B360", "id3B370", "id3B370", "id3B375", "id3B380", "id3B390",
"id3B390", "id3B400", "id3B405", "id3B407", "id3B407", "id3B409",
"id3B410", "id3B420", "id3B430", NA, "id3B440", "id3B445", "id3B450",
"id3B455", "id3B460", "id3B465", "id3B470", "id3B470", "id3B480",
"id3B490", "id3B500", "id3B510", "id3B520", "id3B530", "id3B535",
"id3B537", "id3B542", "id3B544", "id3B546", "id3B560", "id3B570",
"id3B570", "id3B575", "id3B575", "id3B575", "id3B575", "id3B580",
"id3B590", "id3B592", "id3B594", NA, "id3B596", "id3B600", "id3B610",
"id3B620", "id3B630", "id3B640", "id3B650", "id3B652", "id3B656",
"id3B658", "id3B660", "id3B665", "id3B670", "id3B680", "id3B690",
"id3B700", "id3B710", "id3B724", "id3B730", "id3B731", "id3B731",
"id3B731", "id3B731", "id3B731", "id3B731", "id3B731", "id3B732",
"id3B734", "id3B740", "id3B740", "id3B745", "id3B750", "id3B755",
"id3B760", "id3B770", "id3B780", "id3B790", "id3D340", NA, "id3D345",
"id3D350", "id3D360", "id3D370", "id3D380", "id3D390", "id3D400", NA,
"id3D410", "id3D420", "id3D430", NA, "id3D435", "id3D440", "id3D445",
"id3D450", "id3D455", "id3B720", "id3B722", "id3B798", NA, "id3B800",
"id3B810", "id3B820", "id3B830", "id3B840", "id3B850", "id3C105",
"id3C110", "id3C120", "id3C125", "id3C135", "id3C210", "id3C212",
"id3C200", "id3C120", "id3C213", "id3C215", "id3C220", "id3C230",
"id3C230", "id3C240", "id3C260", "id3C270", "id3C280", "id3C290",
"id3C310", "id3C320", "id3C330", "id3C340", "id3C350", "id3C360",
"id3C365", "id3C370", "id3C380", "id3C390", "id3C393", "id3C395",
"id3C400", "id3C400", "id3C400", "id3C430", "id3C440", "id3C450",
"id3C460", "id3C470", "id3C480", "id3D100", "id3D102", "id3D104",
"id3D106", "id3D108a", "id3D155", "id3D155", "id3D155", "id3D165",
"id3D180", "id3D190", "id3D201", "id3D200", "id3D210", "id3D210",
"id3D210", "id3D215", "id3D221", "id3D230", "id3D240", "id3D241",
"id3D242", NA, "id3D251", NA, "id3D253", "id3D254", NA, "id3D258",
"id3D259", "id3D260", "id3D261", "id3D265", "id3D267", "id3D267", NA,
"id3D269", NA, "id3D271", "id3D273", "id3D275", NA, "id3D276", "id3D277",
"id3D278", NA, "id3D280", "id3D600", "id3F100", "id3F110", "id3F120",
"id3F120", "id3F130", "id3G110", "id3G120", "id3G130", "id3G140",
"id3G150", "id3G160", "id3G165", "id3G170", "id3G180", "id3G190",
"id3H100", "id4A100", "id4A110", "id4A120", "id4A130", "id4A140",
"id4A150", "id4A160", "id4A170", "id4A180", "id4A190")
whoNames <- tolower(whoNames)
iv5Names <- c("i004a", "i004b", "i019a", "i019b", "i022a", "i022b", "i022c", "i022d",
"i022e", "i022f", "i022g", "i022h", "i022i", "i022j", "i022k", "i022l",
"i022m", "i022n", "i059o", "i077o", "i079o", "i082o", "i083o", "i084o",
"i085o", "i086o", "i087o", "i089o", "i090o", "i091o", "i092o", "i093o",
"i094o", "i095o", "i096o", "i098o", "i099o", "i100o", "i104o", "i105o",
"i106a", "i107o", "i108a", "i109o", "i110o", "i111o", "i112o", "i113o",
"i114o", "i115o", "i116o", "i120a", "i120b", "i123o", "i125o", "i127o",
"i128o", "i129o", "i130o", "i131o", "i132o", "i133o", "i134o", "i135o",
"i136o", "i137o", "i138o", "i139o", "i140o", "i141o", "i142o", "i143o",
"i144o", "i147o", "i148a", "i148b", "i148c", "i149o", "i150a", "i151a",
"i152o", "i153o", "i154a", "i154b", "i155o", "i156o", "i157o", "i158o",
"i159o", "i161a", "i165a", "i166o", "i167a", "i167b", "i168o", "i169a",
"i169b", "i170o", "i171o", "i172o", "i173a", "i174o", "i175o", "i176a",
"i178a", "i181o", "i182a", "i182b", "i182c", "i183a", "i184a", "i185o",
"i186o", "i187o", "i188o", "i189o", "i190o", "i191o", "i192o", "i193o",
"i194o", "i195o", "i197a", "i197b", "i199a", "i199b", "i200o", "i201a",
"i201b", "i203a", "i204o", "i205a", "i205b", "i207o", "i208o", "i209a",
"i209b", "i210o", "i211a", "i212o", "i213o", "i214o", "i215o", "i216a",
"i217o", "i218o", "i219o", "i220o", "i221a", "i221b", "i222o", "i223o",
"i224o", "i225o", "i226o", "i227o", "i228o", "i229o", "i230o", "i231o",
"i232a", "i233o", "i234a", "i234b", "i235a", "i235b", "i235c", "i235d",
"i236o", "i237o", "i238o", "i239o", "i240o", "i241o", "i242o", "i243o",
"i244o", "i245o", "i246o", "i247o", "i248a", "i249o", "i250a", "i251o",
"i252o", "i253o", "i254o", "i255o", "i256o", "i257o", "i258o", "i259o",
"i260a", "i260b", "i260c", "i260d", "i260e", "i260f", "i260g", "i261o",
"i262a", "i263a", "i263b", "i264o", "i265o", "i266a", "i267o", "i268o",
"i269o", "i270o", "i271o", "i272o", "i273o", "i274a", "i275o", "i276o",
"i277o", "i278o", "i279o", "i281o", "i282o", "i283o", "i284o", "i285a",
"i286o", "i287o", "i288o", "i289o", "i290o", "i294o", "i295o", "i296o",
"i297o", "i298o", "i299o", "i300o", "i301o", "i302o", "i303a", "i304o",
"i305o", "i306o", "i309o", "i310o", "i312o", "i313o", "i314o", "i315o",
"i316o", "i317o", "i318o", "i319a", "i319b", "i320o", "i321o", "i322o",
"i323o", "i324o", "i325o", "i326o", "i327o", "i328o", "i329o", "i330o",
"i331o", "i332a", "i333o", "i334o", "i335o", "i336o", "i337a", "i337b",
"i337c", "i338o", "i340o", "i342o", "i343o", "i344o", "i347o", "i354o",
"i355a", "i356o", "i357o", "i358a", "i360a", "i360b", "i360c", "i361o",
"i362o", "i363o", "i364o", "i365o", "i367a", "i367b", "i367c", "i368o",
"i369o", "i370o", "i371o", "i372o", "i373o", "i376o", "i377o", "i382a",
"i383o", "i384o", "i385a", "i387o", "i388o", "i389o", "i391o", "i393o",
"i394a", "i394b", "i395o", "i396o", "i397o", "i398o", "i399o", "i400o",
"i401o", "i402o", "i403o", "i404o", "i405o", "i406o", "i408o", "i411o",
"i412o", "i413o", "i414a", "i415a", "i418o", "i419o", "i420o", "i421o",
"i422o", "i423o", "i424o", "i425o", "i426o", "i427o", "i428o", "i450o",
"i451o", "i452o", "i453o", "i454o", "i455o", "i456o", "i457o", "i458o",
"i459o")
iv5Out <- matrix(".", nrow=nrow(odk), ncol=353)
# check for missing indicators
tmpMat <- matrix(sapply(whoNames, stri_endswith_fixed, str = odkNames), nrow = length(odkNames))
indexData <- apply(tmpMat, 2, which)
warnZeroMatch <- which(sapply(indexData, length) == 0)
warnZeroMatch <- warnZeroMatch[!is.na(whoNames[warnZeroMatch])] # remove NA's
if (length(warnZeroMatch) > 0) {
cat(
paste("Expecting indicator(s) with name(s): ",
whoNames[unique(warnZeroMatch)],
sep = ""),
sep = "\n"
)
stop("Problem with data: please add above columns to your data frame")
}
numNA <- 0 # used for tracking columns with NAs
indexNA <- NULL
flagNonNumeric <- function(x) {
return(tryCatch(as.numeric(x),
error = function(c) -9999,
warning = function(c) -9999)
)
}
# function for creating simple Y/N indicators
qYesNo <- c(20, 21, 23:25, 28:35, 37:40, 42, 44:46, 48:51, 54:74, 81, 82,
85:89, 92, 95, 98:100, 103, 106, 112:115, 118:120, 122, 127,
131, 134, 135, 138, 140, 143, 145:148, 151:160, 162, 169:172,
174:180, 182, 184:192, 200, 204, 205, 207:211, 213, 215:219,
221:223, 225:232, 234:238, 240:242, 244:247, 249:251, 254:265,
267:270, 274:280, 282, 288:290, 292, 296:301, 303, 305, 306,
308:312, 316, 318:320, 322:324, 326:329, 333:353)
tmpMat <- matrix(
sapply(
whoNames[qYesNo],
stri_endswith_fixed,
str = odkNames
),
nrow = length(odkNames)
)
indexData <- apply(tmpMat, 2, which)
if (is.list(indexData)) {
dups <- lapply(indexData, function(x) length(x) > 1)
tmpNames <- whoNames[qYesNo]
cat(
paste("Duplicate column names containing:",
tmpNames[unlist(dups)],
sep = " "),
sep = "\n"
)
stop("Problem with data: please remove or rename one of the duplicate columns.")
}
iv5Out[ , qYesNo] <- as.matrix(odk[ , indexData])
iv5Out[iv5Out=="yes" | iv5Out=="Yes" | iv5Out=="YES"] <- "y"
iv5Out[iv5Out=="no" | iv5Out=="No" | iv5Out=="NO"] <- "n"
iv5Out[iv5Out=="dk" | iv5Out=="DK" | iv5Out=="Doesn't Know"] <- "."
iv5Out[iv5Out=="Doesn't know" | iv5Out=="doesn't know"] <- "."
iv5Out[iv5Out=="does not know" | iv5Out=="Does Not Know" | iv5Out=="Does not know"] <- "."
iv5Out[iv5Out=="ref" | iv5Out=="Ref" | iv5Out=="REF"] <- "."
iv5Out[iv5Out==""] <- "."
iv5Out[is.na(iv5Out)] <- "."
# Step through iv5 indicators to create new values
#1) Did s(he) die during the wet season? d wet & 2) Did s(he) die during the dry season? d dry
indexData <- which(stri_endswith_fixed(odkNames, whoNames[1]))
## table(odk[ , indexData])
iv5Out[tolower(odk[ , indexData])=="wet" | tolower(odk[ , indexData])=="wet season", 1] <- "y" ## wet season
iv5Out[tolower(odk[ , indexData])=="dry" | tolower(odk[ , indexData])=="dry season", 1] <- "n"
iv5Out[tolower(odk[ , indexData])=="wet" | tolower(odk[ , indexData])=="wet season", 2] <- "n" ## dry season
iv5Out[tolower(odk[ , indexData])=="dry" | tolower(odk[ , indexData])=="dry season", 2] <- "y"
#3) Was he male? male & ##4) Was he female? female
indexData_sex <- which(stri_endswith_fixed(odkNames, whoNames[3]))
iv5Out[tolower(odk[ , indexData_sex])=="male", 3] <- "y"
iv5Out[tolower(odk[ , indexData_sex])=="female", 3] <- "n"
iv5Out[tolower(odk[ , indexData_sex])=="male", 4] <- "n"
iv5Out[tolower(odk[ , indexData_sex])=="female", 4] <- "y"
# age
indexData1y <- which(stri_endswith_fixed(odkNames, "ageinyears"))
nonNumeric <- lapply(odk[ , indexData1y], flagNonNumeric)
nonNumeric <- unlist(nonNumeric)
containsNA <- ifelse(
sum(nonNumeric < 0, na.rm = TRUE) > 0,
1, 0)
numNA <- numNA + containsNA
if (containsNA > 0) indexNA <- c(indexNA, odkNames[indexData1y])
nonNumeric[nonNumeric < 0] <- NA
odk[is.na(nonNumeric), indexData1y] <- NA
odk[, indexData1y] <- as.numeric(odk[, indexData1y])
indexData1m <- which(stri_endswith_fixed(odkNames, "ageinmonths"))
nonNumeric <- lapply(odk[ , indexData1m], flagNonNumeric)
nonNumeric <- unlist(nonNumeric)
containsNA <- ifelse(
sum(nonNumeric < 0, na.rm = TRUE) > 0,
1, 0)
numNA <- numNA + containsNA
if (containsNA > 0) indexNA <- c(indexNA, odkNames[indexData1m])
nonNumeric[nonNumeric < 0] <- NA
odk[is.na(nonNumeric), indexData1m] <- NA
odk[, indexData1m] <- as.numeric(odk[, indexData1m])
indexData1d <- which(stri_endswith_fixed(odkNames, "ageindays"))
nonNumeric <- lapply(odk[ , indexData1d], flagNonNumeric)
nonNumeric <- unlist(nonNumeric)
containsNA <- ifelse(
sum(nonNumeric < 0, na.rm = TRUE) > 0,
1, 0)
numNA <- numNA + containsNA
if (containsNA > 0) indexNA <- c(indexNA, odkNames[indexData1d])
nonNumeric[nonNumeric < 0] <- NA
odk[is.na(nonNumeric), indexData1d] <- NA
odk[, indexData1d] <- as.numeric(odk[, indexData1d])
indexData2 <- which(stri_endswith_fixed(odkNames, "age_group"))
indexData3 <- which(stri_endswith_fixed(odkNames, "age_adult"))
nonNumeric <- lapply(odk[ , indexData3], flagNonNumeric)
nonNumeric <- unlist(nonNumeric)
containsNA <- ifelse(
sum(nonNumeric < 0, na.rm = TRUE) > 0,
1, 0)
numNA <- numNA + containsNA
if (containsNA > 0) indexNA <- c(indexNA, odkNames[indexData3])
nonNumeric[nonNumeric < 0] <- NA
odk[is.na(nonNumeric), indexData3] <- NA
odk[, indexData3] <- as.numeric(odk[, indexData3])
indexData4 <- which(stri_endswith_fixed(odkNames, "age_child_unit"))
indexData4d <- which(stri_endswith_fixed(odkNames, "age_child_days"))
nonNumeric <- lapply(odk[ , indexData4d], flagNonNumeric)
nonNumeric <- unlist(nonNumeric)
containsNA <- ifelse(
sum(nonNumeric < 0, na.rm = TRUE) > 0,
1, 0)
numNA <- numNA + containsNA
if (containsNA > 0) indexNA <- c(indexNA, odkNames[indexData4d])
nonNumeric[nonNumeric < 0] <- NA
odk[is.na(nonNumeric), indexData4d] <- NA
odk[, indexData4d] <- as.numeric(odk[, indexData4d])
indexData4m <- which(stri_endswith_fixed(odkNames, "age_child_months"))
nonNumeric <- lapply(odk[ , indexData4m], flagNonNumeric)
nonNumeric <- unlist(nonNumeric)
containsNA <- ifelse(
sum(nonNumeric < 0, na.rm = TRUE) > 0,
1, 0)
numNA <- numNA + containsNA
if (containsNA > 0) indexNA <- c(indexNA, odkNames[indexData4m])
nonNumeric[nonNumeric < 0] <- NA
odk[is.na(nonNumeric), indexData4m] <- NA
odk[, indexData4m] <- as.numeric(odk[, indexData4m])
indexData4y <- which(stri_endswith_fixed(odkNames, "age_child_years"))
nonNumeric <- lapply(odk[ , indexData4y], flagNonNumeric)
nonNumeric <- unlist(nonNumeric)
containsNA <- ifelse(
sum(nonNumeric < 0, na.rm = TRUE) > 0,
1, 0)
numNA <- numNA + containsNA
if (containsNA > 0) indexNA <- c(indexNA, odkNames[indexData4y])
nonNumeric[nonNumeric < 0] <- NA
odk[is.na(nonNumeric), indexData4y] <- NA
odk[, indexData4y] <- as.numeric(odk[, indexData4y])
indexData5d <- which(stri_endswith_fixed(odkNames, "age_neonate_days"))
nonNumeric <- lapply(odk[ , indexData5d], flagNonNumeric)
nonNumeric <- unlist(nonNumeric)
containsNA <- ifelse(
sum(nonNumeric < 0, na.rm = TRUE) > 0,
1, 0)
numNA <- numNA + containsNA
if (containsNA > 0) indexNA <- c(indexNA, odkNames[indexData5d])
nonNumeric[nonNumeric < 0] <- NA
odk[is.na(nonNumeric), indexData5d] <- NA
odk[, indexData5d] <- as.numeric(odk[, indexData5d])
indexData5h <- which(stri_endswith_fixed(odkNames, "age_neonate_hours"))
nonNumeric <- lapply(odk[ , indexData5h], flagNonNumeric)
nonNumeric <- unlist(nonNumeric)
containsNA <- ifelse(
sum(nonNumeric < 0, na.rm = TRUE) > 0,
1, 0)
numNA <- numNA + containsNA
if (containsNA > 0) indexNA <- c(indexNA, odkNames[indexData5h])
nonNumeric[nonNumeric < 0] <- NA
odk[is.na(nonNumeric), indexData5h] <- NA
odk[, indexData5h] <- as.numeric(odk[, indexData5h])
indexData5m <- which(stri_endswith_fixed(odkNames, "age_neonate_minutes"))
nonNumeric <- lapply(odk[ , indexData5m], flagNonNumeric)
nonNumeric <- unlist(nonNumeric)
containsNA <- ifelse(
sum(nonNumeric < 0, na.rm = TRUE) > 0,
1, 0)
numNA <- numNA + containsNA
if (containsNA > 0) indexNA <- c(indexNA, odkNames[indexData5m])
nonNumeric[nonNumeric < 0] <- NA
odk[is.na(nonNumeric), indexData5m] <- NA
odk[, indexData5m] <- as.numeric(odk[, indexData5m])
indexData_isNeonatal <- which(stri_endswith_fixed(odkNames, "isneonatal"))
indexData_isChild <- which(stri_endswith_fixed(odkNames, "ischild"))
indexData_isAdult <- which(stri_endswith_fixed(odkNames, "isadult"))
#5) Was s(he) aged 65 years or more at death? 65+
iv5Out[odk[ , indexData1y]>=65, 5] <- "y"
iv5Out[is.na(odk[ , indexData1y]) & odk[ , indexData2]=="adult" &
odk[ , indexData3]>=65, 5] <- "y"
#6) Was s(he) aged 50 to 64 years at death? 50 to 64
iv5Out[odk[ , indexData1y]< 65 & odk[ , indexData1y]>=50, 6] <- "y"
iv5Out[is.na(odk[ , indexData1y]) & odk[ ,indexData2]=="adult" &
odk[ ,indexData3]< 65 & odk[ ,indexData3]>=50, 6] <- "y"
#7) Was s(he) aged 15 to 49 years at death? 15-49
iv5Out[odk[ , indexData1y]< 50 & odk[ , indexData1y]>=15, 7] <- "y"
iv5Out[is.na(odk[ , indexData1y]) & odk[ , indexData2]=="adult" &
odk[ , indexData3]< 50 & odk[ , indexData3]>=15, 7] <- "y"
#8) Was s(he) aged 5-14 years at death? 5-14 (adult or child)
iv5Out[odk[ , indexData1y]< 15 & odk[ , indexData1y]>= 5, 8] <- "y"
iv5Out[is.na(odk[ , indexData1y]) & odk[ , indexData2]=="adult" &
odk[ , indexData3]< 15 & odk[ , indexData3]>=5, 8] <- "y"
iv5Out[is.na(odk[ , indexData1y]) & odk[ , indexData2]=="child" &
odk[ , indexData4]=="days" & odk[ , indexData4d]< 15*365.25 &
odk[ , indexData4d]>=5*365.25, 8] <- "y"
iv5Out[is.na(odk[ , indexData1y]) & odk[ , indexData2]=="child" &
odk[ , indexData4]=="months" & odk[ , indexData4m]< 15*12 &
odk[ , indexData4m]>=5*12, 8] <- "y"
iv5Out[is.na(odk[ , indexData1y]) & odk[ , indexData2]=="child" &
odk[ , indexData4]=="years" & odk[ , indexData4y]< 15 &
odk[ , indexData4y]>=5, 8] <- "y"
#9) Was s(he) aged 1 to 4 years at death? 1 to 4 (child)
iv5Out[odk[ , indexData1y]< 5 & odk[ , indexData1y]>=1, 9] <- "y"
iv5Out[is.na(odk[ , indexData1y]) & odk[ , indexData2]=="child" &
odk[ , indexData4]=="days" & odk[ , indexData4d]< 5*365.25 &
odk[ , indexData4d]>=1*365.25, 9] <- "y"
iv5Out[is.na(odk[ , indexData1y]) & odk[ , indexData2]=="child" &
odk[ , indexData4]=="months" & odk[ , indexData4m]< 5*12 &
odk[ , indexData4m]>=1*12, 9] <- "y"
iv5Out[is.na(odk[ , indexData1y]) & odk[ , indexData2]=="child" &
odk[ , indexData4]=="years" & odk[ , indexData4y]< 5 &
odk[ , indexData4y]>=1, 9] <- "y"
#10) Was s(he) aged 1 to 11 months at death? 1-11 months (child or neonate?)
iv5Out[odk[ , indexData1d]< 365.25 & odk[ , indexData1d]>=28, 10] <- "y"
iv5Out[is.na(odk[ , indexData1d]) & odk[ , indexData2]=="child" &
odk[ , indexData4]=="days" & odk[ , indexData4d]< 365.25 &
odk[ , indexData4d]>=28, 10] <- "y"
iv5Out[is.na(odk[ , indexData1m]) & odk[ , indexData2]=="child" &
odk[ , indexData4]=="months" & odk[ , indexData4m]< 12 &
odk[ , indexData4m]>=1, 10] <- "y"
#11) Was s(he) aged < 1 month (28 days) at death? 0 - 27 days (neonate)
iv5Out[odk[ , indexData1d]< 28, 11] <- "y"
iv5Out[is.na(odk[ , indexData1d]) & odk[ , indexData2]=="neonate", 11] <- "y"
#12) Was s(he) a live baby who died within 24 hours of birth? day0 iv5Names[12]
iv5Out[odk[ , indexData1d]< 1, 12] <- "y"
ageDays <- odk[ , indexData5d]
ageHours <- odk[ , indexData5h]/24
ageHours[is.na(ageHours)] <- 0
ageMinutes <- odk[ , indexData5m]/(24*12)
ageMinutes[is.na(ageMinutes)] <- 0
ageNeonate <- ageDays + ageHours + ageMinutes
iv5Out[odk[ , indexData2]=="neonate" & !is.na(odk[ , indexData5d]) &
ageNeonate< 1, 12] <- "y"
#13) Was s(he) a baby who died between 24 and 48 hours of birth? day1 iv5Names[13]
iv5Out[odk[ , indexData2]=="neonate" & !is.na(odk[ , indexData5d]) &
ageNeonate< 2 & ageNeonate>=1, 13] <- "y"
#14) Was s(he) a baby who died more than 48 hours from birth, but within the first week? day2-6 iv5Names[14]
iv5Out[odk[ , indexData2]=="neonate" & !is.na(odk[ , indexData5d]) &
ageNeonate< 7 & ageNeonate>=2, 14] <- "y"
#15) Was s(he) a baby who died after the first week, but within the first month? wk2-4 iv5Names[15]
iv5Out[odk[ , indexData2]=="neonate" & !is.na(odk[ , indexData5d]) &
ageNeonate< 28 & ageNeonate>=7, 15] <- "y"
# Finish coding age (5-15) -- if only one age has "y", recode all others to "n"
## e.g., if age 65 == "y", then age 50-64 == "n" and age 15-49 == "n" etc.
indexData6 <- iv5Out[ , 5:15] != "y" ## identify elements in age columns that do not equal "y"
##indexData7 <- rowSums(iv5Out[ , 5:15] == "y") ## identify with rows/records only have 1 "y" for all age columns
indexData7 <- rowSums(iv5Out[ , 5:15] == "y", na.rm = TRUE) ## identify which rows/records only have 1 "y" for all age columns
## Now recode all "n"
iv5Out[indexData7 == 1, 5:15][ indexData6[indexData7 == 1, ] ] <- "n"
## extra steps for less than a month #11 & first few weeks #12 - #15
y11_12 <- iv5Out[, 11] == "y" & iv5Out[, 12] == "y"
y11_13 <- iv5Out[, 11] == "y" & iv5Out[, 13] == "y"
y11_14 <- iv5Out[, 11] == "y" & iv5Out[, 14] == "y"
y11_15 <- iv5Out[, 11] == "y" & iv5Out[, 15] == "y"
iv5Out[indexData7 == 2 & y11_12, 5:15][ indexData6[indexData7 == 2 & y11_12, ] ] <- "n"
iv5Out[indexData7 == 2 & y11_13, 5:15][ indexData6[indexData7 == 2 & y11_13, ] ] <- "n"
iv5Out[indexData7 == 2 & y11_14, 5:15][ indexData6[indexData7 == 2 & y11_14, ] ] <- "n"
iv5Out[indexData7 == 2 & y11_15, 5:15][ indexData6[indexData7 == 2 & y11_15, ] ] <- "n"
#16) Was she a woman aged 12-19 years at death? f-19
iv5Out[ , 16] <- ifelse(odk[ , indexData_sex]=="female" &
odk[ , indexData1y]< 20 &
odk[ , indexData1y]>= 12, "y", ".")
iv5Out[odk[ , indexData_sex]=="female" & odk[ , indexData1y]< 12, 16] <- "n"
iv5Out[odk[ , indexData_sex]=="female" & odk[ , indexData1y]> 19, 16] <- "n"
iv5Out[odk[ , indexData_sex]=="female" & is.na(odk[ , indexData1y]) &
odk[ , indexData2]=="adult" &
odk[ , indexData3]< 20 & odk[ , indexData3]>=12, 16] <- "y"
iv5Out[odk[ , indexData_sex]=="female" & is.na(odk[ , indexData1y]) &
odk[ , indexData2]=="adult" & odk[ , indexData3]< 12, 16] <- "n"
iv5Out[odk[ , indexData_sex]=="female" & is.na(odk[ , indexData1y]) &
odk[ , indexData2]=="adult" & odk[ , indexData3]> 19, 16] <- "n"
iv5Out[odk[ , indexData2]=="neonate", 16] <- "n"
iv5Out[odk[ , indexData_isNeonatal] == 1, 16] <- "n"
iv5Out[odk[ , indexData_isChild] == 1 & odk[ , indexData1y] < 12, 16] <- "n"
iv5Out[odk[ , indexData_isChild] == 1 & odk[ , indexData4y] < 12, 16] <- "n"
iv5Out[odk[ , indexData_isChild] == 1 &
odk[ , indexData4m] < 12*12, 16] <- "n"
iv5Out[odk[ , indexData_isChild] == 1 &
odk[ , indexData4d] < 12*365.25, 16] <- "n"
iv5Out[odk[ , indexData2] == "child" & odk[ , indexData1y] < 12, 16] <- "n"
iv5Out[odk[ , indexData2] == "child" & odk[ , indexData4y] < 12, 16] <- "n"
iv5Out[odk[ , indexData2] == "child" &
odk[ , indexData4m] < 12*12, 16] <- "n"
iv5Out[odk[ , indexData2] == "child" &
odk[ , indexData4d] < 12*365.25, 16] <- "n"
iv5Out[odk[ , indexData_sex]=="male", 16] <- "n"
#17) Was she a woman aged 20-34 years at death? f20-34
iv5Out[ , 17] <- ifelse(odk[ , indexData_sex]=="female" &
odk[ , indexData1y]< 35 &
odk[ , indexData1y]>= 20, "y", ".")
iv5Out[odk[ , indexData_sex]=="female" & odk[ , indexData1y]< 20, 17] <- "n"
iv5Out[odk[ , indexData_sex]=="female" & odk[ , indexData1y]> 34, 17] <- "n"
iv5Out[odk[ , indexData_sex]=="female" & is.na(odk[ , indexData1y]) &
odk[ , indexData2]=="adult" & odk[ , indexData3]< 35 &
odk[ , indexData3]>=20, 17] <- "y"
iv5Out[odk[ , indexData_sex]=="female" & is.na(odk[ , indexData1y]) &
odk[ , indexData2]=="adult" & odk[ , indexData3]< 20, 17] <- "n"
iv5Out[odk[ , indexData_sex]=="female" & is.na(odk[ , indexData1y]) &
odk[ , indexData2]=="adult" & odk[ , indexData3]> 34, 17] <- "n"
iv5Out[odk[ , indexData2]=="neonate", 17] <- "n"
iv5Out[odk[ , indexData2]=="child", 17] <- "n"
iv5Out[odk[ , indexData_isNeonatal] == 1, 17] <- "n"
iv5Out[odk[ , indexData_isChild] == 1, 17] <- "n"
iv5Out[odk[ , indexData_sex]=="male", 17] <- "n"
#18) Was she a woman aged 35 to 49 years at death? f35-49
iv5Out[ , 18] <- ifelse(odk[ , indexData_sex]=="female" &
odk[ , indexData1y]< 50 &
odk[ , indexData1y]>= 35, "y", ".")
iv5Out[odk[ , indexData_sex]=="female" & odk[ , indexData1y]< 35, 18] <- "n"
iv5Out[odk[ , indexData_sex]=="female" & odk[ , indexData1y]> 49, 18] <- "n"
iv5Out[odk[ , indexData_sex]=="female" & is.na(odk[ , indexData1y]) &
odk[ , indexData2]=="adult" & odk[ , indexData3]< 50 &
odk[ , indexData3]>=35, 18] <- "y"
iv5Out[odk[ , indexData_sex]=="female" & is.na(odk[ , indexData1y]) &
odk[ , indexData2]=="adult" & odk[ , indexData3]< 35, 18] <- "n"
iv5Out[odk[ , indexData_sex]=="female" & is.na(odk[ , indexData1y]) &
odk[ , indexData2]=="adult" & odk[ , indexData3]> 49, 18] <- "n"
iv5Out[odk[ , indexData2]=="neonate", 18] <- "n"
iv5Out[odk[ , indexData2]=="child", 18] <- "n"
iv5Out[odk[ , indexData_isNeonatal] == 1, 18] <- "n"
iv5Out[odk[ , indexData_isChild] == 1, 18] <- "n"
iv5Out[odk[ , indexData_sex]=="male", 18] <- "n"
#19) Was she married at the time of death? married
indexData <- which(stri_endswith_fixed(odkNames, whoNames[19]))
## table(odk[ , indexData])
iv5Out[odk[ , indexData_sex]=="female" & tolower(odk[ , indexData])=="married", 19] <- "y"
iv5Out[odk[ , indexData_sex]=="female" & tolower(odk[ , indexData])=="single", 19] <- "n"
iv5Out[odk[ , indexData_sex]=="female" & tolower(odk[ , indexData])=="partner", 19] <- "n"
iv5Out[odk[ , indexData_sex]=="female" & tolower(odk[ , indexData])=="divorced", 19] <- "n"
iv5Out[odk[ , indexData_sex]=="female" & tolower(odk[ , indexData])=="widowed", 19] <- "n"
iv5Out[odk[ , indexData_sex]=="female" & tolower(odk[ , indexData])=="too_young_to_be_married", 19] <- "n"
iv5Out[odk[ , indexData_sex]=="female" & tolower(odk[ , indexData])=="child", 19] <- "n"
iv5Out[odk[ , indexData_sex]=="male", 19] <- "n"
#22) Was (s)he injured in a non-road transport accident? inj nrta (NOT INCLUDED)
#26) Was (s)he injured by the bite or sting of a venomous animal? inj venom
indexData1 <- which(stri_endswith_fixed(odkNames, whoNames[26]))
indexData2 <- which(stri_endswith_fixed(odkNames, "id3e400"))
iv5Out[odk[ , indexData1] == "y" & odk[ , indexData2] == "snake", 26] <- "y"
iv5Out[odk[ , indexData1] == "y" & odk[ , indexData2] == "insect_or_scorpion", 26] <- "y"
#27) Was (s)he injured by an animal or insect (non-venomous) inj anim
iv5Out[odk[ , indexData2] == "dog", 27] <- "y"
#36) Was the injury accidental? inj accid
indexData1 <- which(stri_endswith_fixed(odkNames, whoNames[36]))
indexData2 <- which(stri_endswith_fixed(odkNames, "id3e335"))
iv5Out[odk[ , indexData1] == "y" | odk[ , indexData2] == "y", 36] <- "y"
#41) Was it more than 5 minutes after birth before the baby first cried? cry 5+m
indexData <- which(stri_endswith_fixed(odkNames, whoNames[41]))
iv5Out[odk[ , indexData]> 5, 41] <- "y"
iv5Out[odk[ , indexData]<=5, 41] <- "n"
#43) Did the baby stop crying more than a day before (s)he died? cry st 1+d
indexData <- which(stri_endswith_fixed(odkNames, whoNames[43]))
iv5Out[odk[ , indexData]> 24, 43] <- "y"
iv5Out[odk[ , indexData]<=24, 43] <- "n"
#47) Did the baby have a breathing problem? brth prob (NOT INCLUDED)
#52) Did the final illness last less than 3 weeks? ill <3w.
indexData <- which(stri_endswith_fixed(odkNames, whoNames[52]))
iv5Out[odk[ , indexData]< 21, 52] <- "y"
iv5Out[odk[ , indexData]>=21, 52] <- "n"
#53) Did the final illness last at least 3 weeks? ill 3+w
iv5Out[odk[ , indexData]>=21, 53] <- "y"
iv5Out[odk[ , indexData]< 21, 53] <- "n"
#75) Did the fever last less than a week before death? fev <1w
indexData <- which(stri_endswith_fixed(odkNames, whoNames[75]))
iv5Out[odk[ , indexData]< 7, 75] <- "y"
iv5Out[odk[ , indexData]>=7, 75] <- "n"
#76) Did the fever last at least one week, but less than 2 weeks before death? fev 1-2w
iv5Out[odk[ , indexData]>= 7 & odk[ , indexData]< 14, 76] <- "y"
iv5Out[odk[ , indexData]< 7, 76] <- "n"
#77) Did the fever last at least 2 weeks before death? fev 2+w
iv5Out[odk[ , indexData]>= 14, 77] <- "y"
iv5Out[odk[ , indexData]< 14, 77] <- "n"
#78) Did the fever continue until death? fev death (NOT INCLUDED)
#79) Was the fever severe? fev sev
indexData <- which(stri_endswith_fixed(odkNames, whoNames[79]))
iv5Out[tolower(odk[ , indexData])=="severe", 79] <- "y"
iv5Out[tolower(odk[ , indexData])=="mild", 79] <- "n"
iv5Out[tolower(odk[ , indexData])=="moderate", 79] <- "n"
#80) Was the fever continuous? fev cont (NOT INCLUDED)
#83) Did the cough last less than 3 weeks before death? cou <3w
indexData <- which(stri_endswith_fixed(odkNames, whoNames[83]))
iv5Out[odk[ , indexData[1]]< 21, 83] <- "y"
iv5Out[odk[ , indexData[1]]>=21, 83] <- "n"
#84) Did the cough last at least 3 weeks before death? cou 3+w
iv5Out[odk[ , indexData[1]]>=21, 84] <- "y"
iv5Out[odk[ , indexData[1]]< 21, 84] <- "n"
#90) Did the difficult breathing last for at least 3 days before death? dif br 3d
indexDatad <- which(stri_endswith_fixed(odkNames, whoNames[90]))
iv5Out[odk[ , indexDatad]>=3, 90] <- "y"
iv5Out[odk[ , indexDatad]< 3, 90] <- "n"
#91) Was the difficult breathing continuous during this period? dif br con
indexData <- which(stri_endswith_fixed(odkNames, whoNames[91]))
iv5Out[tolower(odk[ , indexData])=="continuous", 91] <- "y"
iv5Out[tolower(odk[ , indexData])=="on_and_off", 91] <- "n"
#93) Did the fast breathing last for less than two weeks before death? br fs <2w
indexData <- which(stri_endswith_fixed(odkNames, whoNames[93]))
iv5Out[odk[ , indexData]< 14, 93] <- "y"
iv5Out[odk[ , indexData]>=14, 93] <- "n"
#94) Did the fast breathing last for at least 2 weeks before death? br fs 2+w
iv5Out[odk[ , indexData]>=14, 94] <- "y"
iv5Out[odk[ , indexData]< 14, 94] <- "n"
#96) Did the breathlessness last for less than 2 weeks before death? brl <2w
indexData <- which(stri_endswith_fixed(odkNames, whoNames[96]))
iv5Out[odk[ , indexData]< 2, 96] <- "y"
iv5Out[odk[ , indexData]>=2, 96] <- "n"
#97) Did the breathlessness last for at least 2 weeks before death? brl 2+w
iv5Out[odk[ , indexData]>=2, 97] <- "y"
iv5Out[odk[ , indexData]< 2, 97] <- "n"
#101) Did his/her breathing sound like wheezing or grunting? whz grun
indexData <- which(stri_endswith_fixed(odkNames, whoNames[101]))
iv5Out[stri_endswith_fixed(tolower(odk[ , indexData]), "grunting"), 101] <- "y"
iv5Out[stri_endswith_fixed(tolower(odk[ , indexData]), "stridor"), 101] <- "y"
iv5Out[stri_endswith_fixed(tolower(odk[ , indexData]), "wheezing"), 101] <- "y"
iv5Out[stri_endswith_fixed(tolower(odk[ , indexData]), "no"), 101] <- "n"
#102) During the illness that led to death, did (s)he have chest pain? ch pain (NOT INCLUDED)
#104) Did (s)he experience chest pain at least 3 days before death? chp 3d
indexData <- which(stri_endswith_fixed(odkNames, whoNames[104]))
iv5Out[odk[ , indexData]>=3, 104] <- "y"
iv5Out[odk[ , indexData]< 3, 104] <- "n"
#105) Did the chest pain last for at least 30 minutes? chp 30m
indexDatam <- which(stri_endswith_fixed(odkNames, whoNames[105]))
iv5Out[odk[ , indexDatam]>=30, 105] <- "y"
iv5Out[odk[ , indexDatam]< 30, 105] <- "n"
#107) Did (s)he have diarrhoea for less than 2 weeks before death? drr <2w
indexData <- which(stri_endswith_fixed(odkNames, whoNames[107]))
iv5Out[odk[ , indexData]< 14, 107] <- "y"
iv5Out[odk[ , indexData]>=14, 107] <- "n"
#108) Did (s)he have diarrhoea for at least 2 weeks but less than 4 weeks before death? drr 2-4w
iv5Out[odk[ , indexData]< 28 & odk[ , indexData]>=14, 108] <- "y"
iv5Out[odk[ , indexData]< 14, 108] <- "n"
iv5Out[odk[ , indexData]>=28, 108] <- "n"
#109) Did (s)he have diarrhoea for at least 4 weeks before death? drr 4+w
iv5Out[odk[ , indexData]>=28, 109] <- "y"
iv5Out[odk[ , indexData]< 28, 109] <- "n"
#110) Did the baby or child have at least 4 stools on the day that loose liquid stools were most frequent? 4+ stls
indexData <- which(stri_endswith_fixed(odkNames, whoNames[110]))
iv5Out[odk[ , indexData]>= 4 & odk[ , indexData]< 999, 110] <- "y"
iv5Out[odk[ , indexData]< 4, 110] <- "n"
#111) Did the frequent loose or liquid stools start at least 3 days before death? drr 3d
indexData <- which(stri_endswith_fixed(odkNames, whoNames[111]))
iv5Out[odk[ , indexData]>= 3 & odk[ , indexData]< 999, 111] <- "y"
iv5Out[odk[ , indexData]< 3, 111] <- "n"
#116)Did (s)he vomit in the week preceding the death? vom bd (NOT INCLUDED)
#117) Did (s)he vomit for at least 3 days before death? vom 3d
indexData <- which(stri_endswith_fixed(odkNames, whoNames[117]))
iv5Out[odk[ , indexData]>= 3 & odk[ , indexData]< 999, 117] <- "y"
iv5Out[odk[ , indexData]< 3, 117] <- "n"
#121) Did (s)he have abdominal pain? abd pain (NOT INCLUDED)
#123) Did (s)he have severe abdominal pain for less than 2 weeks before death? abd p <2w
indexData <- which(stri_endswith_fixed(odkNames, whoNames[123]))
iv5Out[odk[ , indexData]< 14, 123] <- "y"
iv5Out[odk[ , indexData]>=14, 123] <- "n"
#124) Did (s)he have severe abdominal pain for at least 2 weeks before death? abd p 2+w
iv5Out[odk[ , indexData]>=14, 124] <- "y"
iv5Out[odk[ , indexData]< 14, 124] <- "n"
#125) Was the pain in the upper abdomen? abd p up
indexData <- which(stri_endswith_fixed(odkNames, whoNames[125]))
iv5Out[tolower(odk[ , indexData])=="upper_abdomen", 125] <- "y"
iv5Out[tolower(odk[ , indexData])=="lower_abdomen", 125] <- "n"
#126) Was the pain in the lower abdomen? abd p lo
iv5Out[tolower(odk[ , indexData])=="upper_abdomen", 126] <- "n"
iv5Out[tolower(odk[ , indexData])=="lower_abdomen", 126] <- "y"
#128) Did (s)he have a more than usually protruding abdomen for less than 2 weeks before death? abd pr <2w
indexData <- which(stri_endswith_fixed(odkNames, whoNames[128]))
iv5Out[odk[ , indexData]< 14, 128] <- "y"
iv5Out[odk[ , indexData]>=14, 128] <- "n"
#129) Did (s)he have a more than usually protruding abdomen for at least 2 weeks before death? abd pr 2+w
iv5Out[odk[ , indexData]>=14, 129] <- "y"
iv5Out[odk[ , indexData]< 14, 129] <- "n"
#130) Did (s)he develop the protruding abdomen rapidly? abd pr rap
indexData <- which(stri_endswith_fixed(odkNames, whoNames[130]))
iv5Out[tolower(odk[ , indexData])=="rapidly", 130] <- "y"
iv5Out[tolower(odk[ , indexData])=="slowly", 130] <- "n"
#132) Did (s)he have a mass in the abdomen for less than 2 weeks before death? ab ms <2w
indexData <- which(stri_endswith_fixed(odkNames, whoNames[132]))
iv5Out[odk[ , indexData]< 14, 132] <- "y"
iv5Out[odk[ , indexData]>=14, 132] <- "n"
#133) Did (s)he have a mass in the abdomen for at least 2 weeks before death? ab ms 2+w
iv5Out[odk[ , indexData]< 14, 133] <- "n"
iv5Out[odk[ , indexData]>=14, 133] <- "y"
#136) Did (s)he have a stiff neck for less than one week before death? st n <1w
indexData <- which(stri_endswith_fixed(odkNames, whoNames[136]))
iv5Out[odk[ , indexData]< 7, 136] <- "y"
iv5Out[odk[ , indexData]>=7, 136] <- "n"
#137) Did (s)he have a stiff neck for at least one week before death? st n 1+w
iv5Out[odk[ , indexData]>=7, 137] <- "y"
iv5Out[odk[ , indexData]< 7, 137] <- "n"
#139) Did (s)he have a painful neck for at least one week before death? pa n 1+w
indexData <- which(stri_endswith_fixed(odkNames, whoNames[139]))
iv5Out[odk[ , indexData]>=7, 139] <- "y"
iv5Out[odk[ , indexData]< 7, 139] <- "n"
#141) Did (s)he have mental confusion for at least 3 months before death? menc 3+m
indexData <- which(stri_endswith_fixed(odkNames, whoNames[141]))
iv5Out[odk[ , indexData]>=3, 141] <- "y"
iv5Out[odk[ , indexData]< 3, 141] <- "n"
#142) Did (s)he have mental confusion for at least 3 months before death? menc 3+m (NOT INCLUDED)
#144) Was (s)he unsconscious for at least 6 hours before death? unc 6+h
indexData <- which(stri_endswith_fixed(odkNames, whoNames[144]))
iv5Out[odk[ , indexData]>=6, 144] <- "y"
iv5Out[odk[ , indexData]< 6, 144] <- "n"
#149) Did the convulsions last for less than 10 minutes? conv <10m
indexData <- which(stri_endswith_fixed(odkNames, whoNames[149]))
iv5Out[odk[ , indexData]< 10, 149] <- "y"
iv5Out[odk[ , indexData]>=10, 149] <- "n"
#150) Did the convulsions last for at least 10 minutes? conv 10+m
iv5Out[odk[ , indexData]< 10, 150] <- "n"
iv5Out[odk[ , indexData]>=10, 150] <- "y"
#161) Did the ulcer ooze pus for at least 2 weeks? sk ul 2+w
indexData <- which(stri_endswith_fixed(odkNames, whoNames[161]))
iv5Out[odk[ , indexData]>=14, 161] <- "y"
iv5Out[odk[ , indexData]< 14, 161] <- "n"
#163) Did (s)he have the skin rash for less than one week? sk ra <1w
indexData <- which(stri_endswith_fixed(odkNames, whoNames[163]))
iv5Out[odk[ , indexData]< 7, 163] <- "y"
iv5Out[odk[ , indexData]>=7, 163] <- "n"
#164) Did (s)he have the skin rash for at least one week? sk ra 1+w
iv5Out[odk[ , indexData]>=7, 164] <- "y"
iv5Out[odk[ , indexData]< 7, 164] <- "n"
#165) Did (s)he have a rash on the face? sk ra face
indexData <- which(stri_endswith_fixed(odkNames, whoNames[165]))
iv5Out[stri_endswith_fixed(tolower(odk[ , indexData]), "face"), 165] <- "y"
iv5Out[stri_endswith_fixed(tolower(odk[ , indexData]), negate = TRUE, "face"), 165] <- "n"
iv5Out[tolower(odk[ , indexData])=="", 165] <- "."
#166) Did (s)he have a rash on the trunk or abdomen? sk ra abd
indexData <- which(stri_endswith_fixed(odkNames, whoNames[166]))
iv5Out[stri_endswith_fixed(tolower(odk[ , indexData]), "abdomen|trunk"), 166] <- "y"
iv5Out[stri_endswith_fixed(tolower(odk[ , indexData]), negate = TRUE, "abdomen|trunk"), 166] <- "n"
iv5Out[tolower(odk[ , indexData])=="", 166] <- "."
#167) Did (s)he have a rash on the extremities? sk ra ext
indexData <- which(stri_endswith_fixed(odkNames, whoNames[167]))
iv5Out[stri_endswith_fixed(tolower(odk[ , indexData]), "extremities"), 167] <- "y"
iv5Out[stri_endswith_fixed(tolower(odk[ , indexData]), negate = TRUE, "extremities"), 167] <- "n"
iv5Out[tolower(odk[ , indexData])=="", 167] <- "."
#168) Did (s)he have a rash everywhere? sk ra all
indexData <- which(stri_endswith_fixed(odkNames, whoNames[168]))
iv5Out[stri_endswith_fixed(tolower(odk[ , indexData]), "everywhere"), 168] <- "y"
iv5Out[stri_endswith_fixed(tolower(odk[ , indexData]), negate = TRUE, "everywhere"), 168] <- "n"
iv5Out[tolower(odk[ , indexData])=="", 168] <- "."
#173) During the illness that led to death, did he/she have areas of the skin with redness and swelling? sk red
# (NOT INCLUDED)
#181) Did (s)he have puffiness of the face for at least one week before death? sw p f 1+w
indexData <- which(stri_endswith_fixed(odkNames, whoNames[181]))
iv5Out[odk[ , indexData]>=7, 181] <- "y"
iv5Out[odk[ , indexData]< 7, 181] <- "n"
#183) Did the swelling last for at least 3 days before death? sw lf 3+d
indexData <- which(stri_endswith_fixed(odkNames, whoNames[183]))
iv5Out[odk[ , indexData]>=3, 183] <- "y"
iv5Out[odk[ , indexData]< 3, 183] <- "n"
#193) Was only the right side of the body paralysed? par rs
indexData <- which(stri_endswith_fixed(odkNames, whoNames[193]))
iv5Out[tolower(odk[ , indexData])=="right_side", 193] <- "y"
iv5Out[tolower(odk[ , indexData])!="right_side", 193] <- "n"
iv5Out[tolower(odk[ , indexData])=="", 193] <- "."
#194) Was only the left side of the body paralysed? par ls
iv5Out[tolower(odk[ , indexData])=="left_side", 194] <- "y"
iv5Out[tolower(odk[ , indexData])!="left_side", 194] <- "n"
iv5Out[tolower(odk[ , indexData])=="", 194] <- "."
#195) Was only the lower part of the body paralysed? par lo
iv5Out[tolower(odk[ , indexData])=="lower_part_of_body", 195] <- "y"
iv5Out[tolower(odk[ , indexData])!="lower_part_of_body", 195] <- "n"
iv5Out[tolower(odk[ , indexData])=="", 195] <- "."
#196) Was only the upper part of the body paralysed? par up
iv5Out[tolower(odk[ , indexData])=="upper_part_of_body", 196] <- "y"
iv5Out[tolower(odk[ , indexData])!="upper_part_of_body", 196] <- "n"
iv5Out[tolower(odk[ , indexData])=="", 196] <- "."
#197) Was only one leg paralysed? par leg
iv5Out[tolower(odk[ , indexData])=="one_leg_only", 197] <- "y"
iv5Out[tolower(odk[ , indexData])!="one_leg_only", 197] <- "n"
iv5Out[tolower(odk[ , indexData])=="", 197] <- "."
#198) Was only one arm paralysed? par arm
iv5Out[tolower(odk[ , indexData])=="one_arm_only", 198] <- "y"
iv5Out[tolower(odk[ , indexData])!="one_arm_only", 198] <- "n"
iv5Out[tolower(odk[ , indexData])=="", 198] <- "."
#199) Was the entire body paralysed? par all
iv5Out[tolower(odk[ , indexData])=="whole_body", 199] <- "y"
iv5Out[tolower(odk[ , indexData])!="whole_body", 199] <- "n"
iv5Out[tolower(odk[ , indexData])=="", 199] <- "."
#201) Did (s)he have difficulty swallowing for at least one week before death? swa 1+w
indexData <- which(stri_endswith_fixed(odkNames, whoNames[201]))
iv5Out[odk[ , indexData]>=7, 201] <- "y"
iv5Out[odk[ , indexData]< 7, 201] <- "n"
#202) Did (s)he have difficulty with swallowing solids? swa sol
indexData <- which(stri_endswith_fixed(odkNames, whoNames[202]))
iv5Out[tolower(odk[ , indexData])=="solids", 202] <- "y"
iv5Out[tolower(odk[ , indexData])=="both", 202] <- "y"
iv5Out[tolower(odk[ , indexData])=="liquids", 202] <- "n"
#203) Did (s)he have difficulty with swallowing liquids? swa liq
iv5Out[tolower(odk[ , indexData])=="solids", 203] <- "n"
iv5Out[tolower(odk[ , indexData])=="both", 203] <- "y"
iv5Out[tolower(odk[ , indexData])=="liquids", 203] <- "y"
#206) Did (s)he have the yellow discolouration for at least 3 weeks before death? yell 3+w
indexData <- which(stri_endswith_fixed(odkNames, whoNames[206]))
iv5Out[odk[ , indexData]>=21, 206] <- "y"
iv5Out[odk[ , indexData]< 21, 206] <- "n"
#212) Did the baby ever suckle in a normal way? suck ev (NOT INCLUDED)
#214) Did the baby stop suckling on the 2nd day of life or later? suck st d1
indexData <- which(stri_endswith_fixed(odkNames, whoNames[214]))
iv5Out[odk[ , indexData[1]]>=2, 214] <- "y"
iv5Out[odk[ , indexData[1]]< 2, 214] <- "n"
#220) During the illness that led to death, did the baby become unresponsive or unconscious? unresp
# (NOT INCLUDED)
#224) Was the baby more than 3 days old when it started feeling cold to touch? cold 3+d
indexData <- which(stri_endswith_fixed(odkNames, whoNames[224]))
iv5Out[odk[ , indexData]> 3, 224] <- "y"
iv5Out[odk[ , indexData]<=3, 224] <- "n"
#224) Was the baby more than 3 days old when it started feeling cold to touch? cold 3+d (NOT INCLUDED)
#233) During the illness that led to death, did she have excessive vaginal bleeding in between menstrual periods? men betw
# (NOT INCLUDED)
#239) Had her period been overdue for at least 4 weeks? men l 4+w
indexData <- which(stri_endswith_fixed(odkNames, whoNames[239]))
iv5Out[odk[ , indexData]>=4, 239] <- "y"
iv5Out[odk[ , indexData]< 4, 239] <- "n"
#243) Was she, or had she been, pregnant for less than 6 months when she died? d <6m pr
indexData <- which(stri_endswith_fixed(odkNames, whoNames[243]))
iv5Out[odk[ , indexData]< 6, 243] <- "y"
iv5Out[odk[ , indexData]>=6, 243] <- "n"
#248) Did she die within 6 weeks of childbirth? d <6w chb
indexData_a <- which(stri_endswith_fixed(odkNames, whoNames[248]))
indexData_b <- which(stri_endswith_fixed(odkNames, "id3c212"))
iv5Out[odk[ , indexData_a] == "y" & odk[ , indexData_b] == "y", 248] <- "y"
iv5Out[odk[ , indexData_a] == "n" | odk[ , indexData_b] == "n", 248] <- "n"
#252) Did she die during or after her first pregnancy? 1st pr.
# WHO question is "How many births, including stillbirths, did she/the mother have before this baby?"
indexData <- which(stri_endswith_fixed(odkNames, whoNames[252]))
iv5Out[odk[ , indexData]==0, 252] <- "y"
iv5Out[odk[ , indexData]> 0, 252] <- "n"
#253) Did she have four or more pregnancies before this one? 4+ pr
iv5Out[odk[ , indexData]>=4, 253] <- "y"
iv5Out[odk[ , indexData]< 4, 253] <- "n"
#266) Did her labour last longer than 24 hours? lab 24+h
indexData <- which(stri_endswith_fixed(odkNames, whoNames[266]))
iv5Out[odk[ , indexData]> 24, 266] <- "y"
iv5Out[odk[ , indexData]<=24, 266] <- "n"
#271) Did the mother deliver at a health facility or clinic? del hfac
indexData <- which(stri_endswith_fixed(odkNames, whoNames[271]))
iv5Out[tolower(odk[ , indexData])=="hospital", 271] <- "y"
iv5Out[tolower(odk[ , indexData])=="other_health_facility", 271] <- "y"
iv5Out[tolower(odk[ , indexData])=="home", 271] <- "n"
iv5Out[tolower(odk[ , indexData])=="on_route_to_hospital_or_facility", 271] <- "n"
iv5Out[tolower(odk[ , indexData])=="other", 271] <- "n"
#272) Did the mother deliver at home? del home
iv5Out[tolower(odk[ , indexData])=="hospital", 272] <- "n"
iv5Out[tolower(odk[ , indexData])=="other_health_facility", 272] <- "n"
iv5Out[tolower(odk[ , indexData])=="home", 272] <- "y"
iv5Out[tolower(odk[ , indexData])=="on_route_to_hospital_or_facility", 272] <- "n"
iv5Out[tolower(odk[ , indexData])=="other", 272] <- "n"
#273) Did the mother deliver elsewhere (not at a health facility nor at home)? del else
iv5Out[tolower(odk[ , indexData])=="hospital", 273] <- "n"
iv5Out[tolower(odk[ , indexData])=="other_health_facility", 273] <- "n"
iv5Out[tolower(odk[ , indexData])=="home", 273] <- "n"
iv5Out[tolower(odk[ , indexData])=="on_route_to_hospital_or_facility", 273] <- "y"
iv5Out[tolower(odk[ , indexData])=="other", 273] <- "y"
#281) If the child was part of a multiple birth, was it born first? mult fir
indexData <- which(stri_endswith_fixed(odkNames, whoNames[281]))
iv5Out[tolower(odk[ , indexData])=="first", 281] <- "y"
iv5Out[tolower(odk[ , indexData])=="second_or_later", 281] <- "n"
#283) Did the child's mother die during or shortly after the delivery? moth d del
indexData <- which(stri_endswith_fixed(odkNames, whoNames[283]))
iv5Out[tolower(odk[ , indexData])=="after_delivery", 283] <- "y"
iv5Out[tolower(odk[ , indexData])=="during_delivery" , 283] <- "y"
#284) Did the child's mother die in the baby's first year of life? moth d y1
indexDatam <- which(stri_endswith_fixed(odkNames, whoNames[284]))
indexDatad <- which(stri_endswith_fixed(odkNames, "id3d108b"))
nMonths <- odk[ , indexDatam]
nDays <- odk[ , indexDatad]
nMonths[is.na(nMonths) & !is.na(nDays)] <- 0
nDays[is.na(nDays) & !is.na(nMonths)] <- 0
iv5Out[nMonths + nDays/30.4 <=12, 284] <- "y"
iv5Out[nMonths + nDays/30.4 > 12, 284] <- "n"
#285) Was the baby born in a health facility or clinic? born fac
indexData <- which(stri_endswith_fixed(odkNames, whoNames[285]))
iv5Out[tolower(odk[ , indexData])=="hospital", 285] <- "y"
iv5Out[tolower(odk[ , indexData])=="other_health_facility", 285] <- "y"
iv5Out[tolower(odk[ , indexData])=="home", 285] <- "n"
iv5Out[tolower(odk[ , indexData])=="other", 285] <- "n"
iv5Out[tolower(odk[ , indexData])=="on_route_to_hospital_or_facility", 285] <- "n"
#286) Was the baby born at home? born home
iv5Out[tolower(odk[ , indexData])=="hospital", 286] <- "n"
iv5Out[tolower(odk[ , indexData])=="other_health_facility", 286] <- "n"
iv5Out[tolower(odk[ , indexData])=="home", 286] <- "y"
iv5Out[tolower(odk[ , indexData])=="other", 286] <- "n"
iv5Out[tolower(odk[ , indexData])=="on_route_to_hospital_or_facility", 286] <- "n"
#287) Was the baby born somewhere else (e.g. on the way to a clinic)? born on way
iv5Out[tolower(odk[ , indexData])=="hospital", 287] <- "n"
iv5Out[tolower(odk[ , indexData])=="other_health_facility", 287] <- "n"
iv5Out[tolower(odk[ , indexData])=="home", 287] <- "n"
iv5Out[tolower(odk[ , indexData])=="other", 287] <- "y"
iv5Out[tolower(odk[ , indexData])=="on_route_to_hospital_or_facility", 287] <- "y"
#291) At birth, was the baby very much smaller than usual, (weighing under 1 kg)? bwt vsmall
indexData <- which(stri_endswith_fixed(odkNames, whoNames[291]))
iv5Out[odk[ , indexData]< 1000, 291] <- "y"
iv5Out[odk[ , indexData]>=1000, 291] <- "n"
#293) Was the baby born during the ninth month (at least 37 weeks) of pregnancy? gest 9m
indexData <- which(stri_endswith_fixed(odkNames, whoNames[293]))
iv5Out[odk[ , indexData]>=9, 293] <- "y"
iv5Out[odk[ , indexData]< 9, 293] <- "n"
#294) Was the baby born during the eighth month (34 to 37 weeks) of pregnancy? gest 8m
iv5Out[odk[ , indexData]> 8, 294] <- "n"
iv5Out[odk[ , indexData]==8, 294] <- "y"
iv5Out[odk[ , indexData]< 8, 294] <- "n"
#295) Was the baby born before the eighth month (less than 34 weeks) of pregnancy? gest 7m
iv5Out[odk[ , indexData]>=8, 295] <- "n"
iv5Out[odk[ , indexData]< 8, 295] <- "y"
#302) Was the baby moving in the last few days before the birth? bab mov (NOT INCLUDED)
#304) Did labour and delivery take more than 24 hours? lab 24+h (NOT INCLUDED)
#307) Was the liquor a green or brown colour when the waters broke? liq gr-br (NOT INCLUDED)
#313) Was this baby born from the mother's first pregnancy? born 1st pr
indexData <- which(stri_endswith_fixed(odkNames, whoNames[313]))
iv5Out[odk[ , indexData]==0, 313] <- "y"
iv5Out[odk[ , indexData]> 0, 313] <- "n"
#314) Did the baby's mother have four or more births before this one? born 4+ pr
iv5Out[odk[ , indexData]>=4, 314] <- "y"
iv5Out[odk[ , indexData]< 4, 314] <- "n"
#315) During labour, did the baby's mother suffer from fever? moth fev (NOT INCLUDED)
#317) Did the baby's mother have diabetes mellitus? moth diab (NOT INCLUDED)
#321) Did the baby's mother have severe anaemia? moth anaem (NOT INCLUDED)
#325) Was the umbilical cord delivered first? cord first (NOT INCLUDED)
#330) Did (s)he smoke tobacco? tobac ns
indexData <- which(stri_endswith_fixed(odkNames, whoNames[330]))
iv5Out[tolower(odk[ , indexData])=="chewing_tobacco", 330] <- "n"
iv5Out[tolower(odk[ , indexData])=="cigarettes", 330] <- "y"
iv5Out[tolower(odk[ , indexData])=="pipe", 330] <- "y"
#331) Did (s)he use non-smoking tobacco? tobac ns
indexData <- which(stri_endswith_fixed(odkNames, whoNames[331]))
iv5Out[tolower(odk[ , indexData])=="chewing_tobacco", 331] <- "y"
iv5Out[tolower(odk[ , indexData])=="cigarettes", 331] <- "n"
iv5Out[tolower(odk[ , indexData])=="pipe", 331] <- "n"
iv5Out[tolower(odk[ , indexData])=="local_form_of_tobacco", 331] <- "n"
iv5Out[tolower(odk[ , indexData])=="other", 331] <- "n"
#332) Did (s)he smoke at least 10 cigarettes daily? cigs >10
indexData <- which(stri_endswith_fixed(odkNames, whoNames[332]))
iv5Out[odk[ , indexData]>=10, 332] <- "y"
iv5Out[odk[ , indexData]< 10, 332] <- "n"
# check for NAs
if (numNA > 0) {
warning("Found unexpected input values (coded as missing)", call. = FALSE)
cat("Unexpected values found in: ", sep = "\n")
cat(paste(indexNA), sep = ", ")
cat("\n")
}
numNA <- colSums(is.na(iv5Out))
indexNA <- which(numNA > 0)
if (length(indexNA) > 0) {
warning("NA's included in output", call. = FALSE)
cat(
paste("odk2openVA produced NA's in the following columns",
" (this may cause errors with openVA)",
sep = ""),
sep = "\n"
)
cat(
paste(iv5Names[indexNA], ## subtract 1 since ID is omitted
" Probably associated with WHO column containing: ",
whoNames[indexNA], ## subtract 1 since ID is omitted
sep = ""),
sep = "\n"
)
}
# Add ID as first column
indexID <- which(stri_endswith_fixed(odkNames, tolower(id_col)))
if (length(indexID)) {
iv5Out <- cbind(as.character(odk[, indexID]), iv5Out)
} else {
message("Did not find id_col, so assigning row numbers for IDs.",
call. = FALSE)
iv5Out <- cbind(as.character(1:nrow(iv5Out)), iv5Out)
}
# Attach column names
colnames(iv5Out) <- c("ID", iv5Names)
# That's all folks!
return(as.data.frame(iv5Out, stringsAsFactors = FALSE))
}
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#' Map VA records to InterVA5 and InSilico (with option data.type = "WHO2016").
#'
#' \code{odk2openVA_2014} transforms data collected with the 2014 WHO VA instrument
#' (form id: va_who_2014_final10) to serve as the input to the InterVA5 and
#' InSilicoVA alogrithms for coding cause of death.
#'
#' @param odk A dataframe, obtained from reading an ODK Briefcase
#' export of records collected with the WHO questionnaire.
#'
#' @param id_col A character string of the column name (in odk) with the
#' unique ID for each death.
#'
#' @examples
#' \dontrun{
#' record_f_name <- system.file("sample", "who2014_odk_export.csv", package = "CrossVA")
#' records <- read.csv(record_f_name, stringsAsFactors = FALSE)
#' output <- odk2openVA_2014(records)
#' }
#'
#' @importFrom stringi stri_endswith_fixed
#'
#' @export
#'
odk2openVA_2014 <- function (odk, id_col = "meta.instanceID") {
## Input Data
odkNames <- tolower(names(odk))
## Output Variables
whoNames <- c("id3A280", "id3A280", "id1A110", "id1A110", "id1A220",
"id1A220", "id1A220", "id1A220", "id1A220", "id1A220", "id1A220",
"id1A220", "id1A220", "id1A220", "id1A220", "id1A220", "id1A220",
"id1A220", "id1A600", "id3E100", "id3E115", NA, "id3E310", "id3E510",
"id3E320", "id3E340", "id3E400", "id3E112", "id3E520", "id3E104",
"id3E106", "id3E108", "id3E111", "id3E500", "id3E530", "id3E330",
"id3E113", "id3E102", "id3D285", "id3D290", "id3D292", "id3D294",
"id3D296", "id3D298", "id3D299", "id3D300", NA, "id3D310", "id3D320",
"id3D325", "id3D330", "id3A300", "id3A300", "id3A310", "id3A100",
"id3A110", "id3A120", "id3A130", "id3A135", "id3A140", "id3A150",
"id3A160", "id3A170", "id3A180", "id3A190", "id3A200", "id3A210",
"id3A220", "id3A230", "id3A240", "id3A250", "id3A260", "id3A270",
"id3B100", "id3B110", "id3B110", "id3B110", NA, "id3B115", NA, "id3B120",
"id3B130", "id3B140", "id3B140", "id3B150", "id3B155", "id3B160",
"id3B170", "id3B242", "id3B244", "id3B246", "id3B190", "id3B200",
"id3B200", "id3B210", "id3B220", "id3B220", "id3B230", "id3B240",
"id3B250", "id3B260", NA, "id3B270", "id3B272", "id3B274", "id3B280",
"id3B290", "id3B290", "id3B290", "id3B292", "id3B294", "id3B296",
"id3B300", "id3B305", "id3B310", NA, "id3B315", "id3B320", "id3B325",
"id3B330", NA, "id3B340", "id3B350", "id3B350", "id3B355", "id3B355",
"id3B360", "id3B370", "id3B370", "id3B375", "id3B380", "id3B390",
"id3B390", "id3B400", "id3B405", "id3B407", "id3B407", "id3B409",
"id3B410", "id3B420", "id3B430", NA, "id3B440", "id3B445", "id3B450",
"id3B455", "id3B460", "id3B465", "id3B470", "id3B470", "id3B480",
"id3B490", "id3B500", "id3B510", "id3B520", "id3B530", "id3B535",
"id3B537", "id3B542", "id3B544", "id3B546", "id3B560", "id3B570",
"id3B570", "id3B575", "id3B575", "id3B575", "id3B575", "id3B580",
"id3B590", "id3B592", "id3B594", NA, "id3B596", "id3B600", "id3B610",
"id3B620", "id3B630", "id3B640", "id3B650", "id3B652", "id3B656",
"id3B658", "id3B660", "id3B665", "id3B670", "id3B680", "id3B690",
"id3B700", "id3B710", "id3B724", "id3B730", "id3B731", "id3B731",
"id3B731", "id3B731", "id3B731", "id3B731", "id3B731", "id3B732",
"id3B734", "id3B740", "id3B740", "id3B745", "id3B750", "id3B755",
"id3B760", "id3B770", "id3B780", "id3B790", "id3D340", NA, "id3D345",
"id3D350", "id3D360", "id3D370", "id3D380", "id3D390", "id3D400", NA,
"id3D410", "id3D420", "id3D430", NA, "id3D435", "id3D440", "id3D445",
"id3D450", "id3D455", "id3B720", "id3B722", "id3B798", NA, "id3B800",
"id3B810", "id3B820", "id3B830", "id3B840", "id3B850", "id3C105",
"id3C110", "id3C120", "id3C125", "id3C135", "id3C210", "id3C212",
"id3C200", "id3C120", "id3C213", "id3C215", "id3C220", "id3C230",
"id3C230", "id3C240", "id3C260", "id3C270", "id3C280", "id3C290",
"id3C310", "id3C320", "id3C330", "id3C340", "id3C350", "id3C360",
"id3C365", "id3C370", "id3C380", "id3C390", "id3C393", "id3C395",
"id3C400", "id3C400", "id3C400", "id3C430", "id3C440", "id3C450",
"id3C460", "id3C470", "id3C480", "id3D100", "id3D102", "id3D104",
"id3D106", "id3D108a", "id3D155", "id3D155", "id3D155", "id3D165",
"id3D180", "id3D190", "id3D201", "id3D200", "id3D210", "id3D210",
"id3D210", "id3D215", "id3D221", "id3D230", "id3D240", "id3D241",
"id3D242", NA, "id3D251", NA, "id3D253", "id3D254", NA, "id3D258",
"id3D259", "id3D260", "id3D261", "id3D265", "id3D267", "id3D267", NA,
"id3D269", NA, "id3D271", "id3D273", "id3D275", NA, "id3D276", "id3D277",
"id3D278", NA, "id3D280", "id3D600", "id3F100", "id3F110", "id3F120",
"id3F120", "id3F130", "id3G110", "id3G120", "id3G130", "id3G140",
"id3G150", "id3G160", "id3G165", "id3G170", "id3G180", "id3G190",
"id3H100", "id4A100", "id4A110", "id4A120", "id4A130", "id4A140",
"id4A150", "id4A160", "id4A170", "id4A180", "id4A190")
whoNames <- tolower(whoNames)
iv5Names <- c("i004a", "i004b", "i019a", "i019b", "i022a", "i022b", "i022c", "i022d",
"i022e", "i022f", "i022g", "i022h", "i022i", "i022j", "i022k", "i022l",
"i022m", "i022n", "i059o", "i077o", "i079o", "i082o", "i083o", "i084o",
"i085o", "i086o", "i087o", "i089o", "i090o", "i091o", "i092o", "i093o",
"i094o", "i095o", "i096o", "i098o", "i099o", "i100o", "i104o", "i105o",
"i106a", "i107o", "i108a", "i109o", "i110o", "i111o", "i112o", "i113o",
"i114o", "i115o", "i116o", "i120a", "i120b", "i123o", "i125o", "i127o",
"i128o", "i129o", "i130o", "i131o", "i132o", "i133o", "i134o", "i135o",
"i136o", "i137o", "i138o", "i139o", "i140o", "i141o", "i142o", "i143o",
"i144o", "i147o", "i148a", "i148b", "i148c", "i149o", "i150a", "i151a",
"i152o", "i153o", "i154a", "i154b", "i155o", "i156o", "i157o", "i158o",
"i159o", "i161a", "i165a", "i166o", "i167a", "i167b", "i168o", "i169a",
"i169b", "i170o", "i171o", "i172o", "i173a", "i174o", "i175o", "i176a",
"i178a", "i181o", "i182a", "i182b", "i182c", "i183a", "i184a", "i185o",
"i186o", "i187o", "i188o", "i189o", "i190o", "i191o", "i192o", "i193o",
"i194o", "i195o", "i197a", "i197b", "i199a", "i199b", "i200o", "i201a",
"i201b", "i203a", "i204o", "i205a", "i205b", "i207o", "i208o", "i209a",
"i209b", "i210o", "i211a", "i212o", "i213o", "i214o", "i215o", "i216a",
"i217o", "i218o", "i219o", "i220o", "i221a", "i221b", "i222o", "i223o",
"i224o", "i225o", "i226o", "i227o", "i228o", "i229o", "i230o", "i231o",
"i232a", "i233o", "i234a", "i234b", "i235a", "i235b", "i235c", "i235d",
"i236o", "i237o", "i238o", "i239o", "i240o", "i241o", "i242o", "i243o",
"i244o", "i245o", "i246o", "i247o", "i248a", "i249o", "i250a", "i251o",
"i252o", "i253o", "i254o", "i255o", "i256o", "i257o", "i258o", "i259o",
"i260a", "i260b", "i260c", "i260d", "i260e", "i260f", "i260g", "i261o",
"i262a", "i263a", "i263b", "i264o", "i265o", "i266a", "i267o", "i268o",
"i269o", "i270o", "i271o", "i272o", "i273o", "i274a", "i275o", "i276o",
"i277o", "i278o", "i279o", "i281o", "i282o", "i283o", "i284o", "i285a",
"i286o", "i287o", "i288o", "i289o", "i290o", "i294o", "i295o", "i296o",
"i297o", "i298o", "i299o", "i300o", "i301o", "i302o", "i303a", "i304o",
"i305o", "i306o", "i309o", "i310o", "i312o", "i313o", "i314o", "i315o",
"i316o", "i317o", "i318o", "i319a", "i319b", "i320o", "i321o", "i322o",
"i323o", "i324o", "i325o", "i326o", "i327o", "i328o", "i329o", "i330o",
"i331o", "i332a", "i333o", "i334o", "i335o", "i336o", "i337a", "i337b",
"i337c", "i338o", "i340o", "i342o", "i343o", "i344o", "i347o", "i354o",
"i355a", "i356o", "i357o", "i358a", "i360a", "i360b", "i360c", "i361o",
"i362o", "i363o", "i364o", "i365o", "i367a", "i367b", "i367c", "i368o",
"i369o", "i370o", "i371o", "i372o", "i373o", "i376o", "i377o", "i382a",
"i383o", "i384o", "i385a", "i387o", "i388o", "i389o", "i391o", "i393o",
"i394a", "i394b", "i395o", "i396o", "i397o", "i398o", "i399o", "i400o",
"i401o", "i402o", "i403o", "i404o", "i405o", "i406o", "i408o", "i411o",
"i412o", "i413o", "i414a", "i415a", "i418o", "i419o", "i420o", "i421o",
"i422o", "i423o", "i424o", "i425o", "i426o", "i427o", "i428o", "i450o",
"i451o", "i452o", "i453o", "i454o", "i455o", "i456o", "i457o", "i458o",
"i459o")
iv5Out <- matrix(".", nrow=nrow(odk), ncol=353)
# check for missing indicators
tmpMat <- matrix(sapply(whoNames, stri_endswith_fixed, str = odkNames), nrow = length(odkNames))
indexData <- apply(tmpMat, 2, which)
warnZeroMatch <- which(sapply(indexData, length) == 0)
warnZeroMatch <- warnZeroMatch[!is.na(whoNames[warnZeroMatch])] # remove NA's
if (length(warnZeroMatch) > 0) {
cat(
paste("Expecting indicator(s) with name(s): ",
whoNames[unique(warnZeroMatch)],
sep = ""),
sep = "\n"
)
stop("Problem with data: please add above columns to your data frame")
}
numNA <- 0 # used for tracking columns with NAs
indexNA <- NULL
flagNonNumeric <- function(x) {
return(tryCatch(as.numeric(x),
error = function(c) -9999,
warning = function(c) -9999)
)
}
# function for creating simple Y/N indicators
qYesNo <- c(20, 21, 23:25, 28:35, 37:40, 42, 44:46, 48:51, 54:74, 81, 82,
85:89, 92, 95, 98:100, 103, 106, 112:115, 118:120, 122, 127,
131, 134, 135, 138, 140, 143, 145:148, 151:160, 162, 169:172,
174:180, 182, 184:192, 200, 204, 205, 207:211, 213, 215:219,
221:223, 225:232, 234:238, 240:242, 244:247, 249:251, 254:265,
267:270, 274:280, 282, 288:290, 292, 296:301, 303, 305, 306,
308:312, 316, 318:320, 322:324, 326:329, 333:353)
tmpMat <- matrix(
sapply(
whoNames[qYesNo],
stri_endswith_fixed,
str = odkNames
),
nrow = length(odkNames)
)
indexData <- apply(tmpMat, 2, which)
if (is.list(indexData)) {
dups <- lapply(indexData, function(x) length(x) > 1)
tmpNames <- whoNames[qYesNo]
cat(
paste("Duplicate column names containing:",
tmpNames[unlist(dups)],
sep = " "),
sep = "\n"
)
stop("Problem with data: please remove or rename one of the duplicate columns.")
}
iv5Out[ , qYesNo] <- as.matrix(odk[ , indexData])
iv5Out[iv5Out=="yes" | iv5Out=="Yes" | iv5Out=="YES"] <- "y"
iv5Out[iv5Out=="no" | iv5Out=="No" | iv5Out=="NO"] <- "n"
iv5Out[iv5Out=="dk" | iv5Out=="DK" | iv5Out=="Doesn't Know"] <- "."
iv5Out[iv5Out=="Doesn't know" | iv5Out=="doesn't know"] <- "."
iv5Out[iv5Out=="does not know" | iv5Out=="Does Not Know" | iv5Out=="Does not know"] <- "."
iv5Out[iv5Out=="ref" | iv5Out=="Ref" | iv5Out=="REF"] <- "."
iv5Out[iv5Out==""] <- "."
iv5Out[is.na(iv5Out)] <- "."
# Step through iv5 indicators to create new values
#1) Did s(he) die during the wet season? d wet & 2) Did s(he) die during the dry season? d dry
indexData <- which(stri_endswith_fixed(odkNames, whoNames[1]))
## table(odk[ , indexData])
iv5Out[tolower(odk[ , indexData])=="wet" | tolower(odk[ , indexData])=="wet season", 1] <- "y" ## wet season
iv5Out[tolower(odk[ , indexData])=="dry" | tolower(odk[ , indexData])=="dry season", 1] <- "n"
iv5Out[tolower(odk[ , indexData])=="wet" | tolower(odk[ , indexData])=="wet season", 2] <- "n" ## dry season
iv5Out[tolower(odk[ , indexData])=="dry" | tolower(odk[ , indexData])=="dry season", 2] <- "y"
#3) Was he male? male & ##4) Was he female? female
indexData_sex <- which(stri_endswith_fixed(odkNames, whoNames[3]))
iv5Out[tolower(odk[ , indexData_sex])=="male", 3] <- "y"
iv5Out[tolower(odk[ , indexData_sex])=="female", 3] <- "n"
iv5Out[tolower(odk[ , indexData_sex])=="male", 4] <- "n"
iv5Out[tolower(odk[ , indexData_sex])=="female", 4] <- "y"
# age
indexData1y <- which(stri_endswith_fixed(odkNames, "ageinyears"))
nonNumeric <- lapply(odk[ , indexData1y], flagNonNumeric)
nonNumeric <- unlist(nonNumeric)
containsNA <- ifelse(
sum(nonNumeric < 0, na.rm = TRUE) > 0,
1, 0)
numNA <- numNA + containsNA
if (containsNA > 0) indexNA <- c(indexNA, odkNames[indexData1y])
nonNumeric[nonNumeric < 0] <- NA
odk[is.na(nonNumeric), indexData1y] <- NA
odk[, indexData1y] <- as.numeric(odk[, indexData1y])
indexData1m <- which(stri_endswith_fixed(odkNames, "ageinmonths"))
nonNumeric <- lapply(odk[ , indexData1m], flagNonNumeric)
nonNumeric <- unlist(nonNumeric)
containsNA <- ifelse(
sum(nonNumeric < 0, na.rm = TRUE) > 0,
1, 0)
numNA <- numNA + containsNA
if (containsNA > 0) indexNA <- c(indexNA, odkNames[indexData1m])
nonNumeric[nonNumeric < 0] <- NA
odk[is.na(nonNumeric), indexData1m] <- NA
odk[, indexData1m] <- as.numeric(odk[, indexData1m])
indexData1d <- which(stri_endswith_fixed(odkNames, "ageindays"))
nonNumeric <- lapply(odk[ , indexData1d], flagNonNumeric)
nonNumeric <- unlist(nonNumeric)
containsNA <- ifelse(
sum(nonNumeric < 0, na.rm = TRUE) > 0,
1, 0)
numNA <- numNA + containsNA
if (containsNA > 0) indexNA <- c(indexNA, odkNames[indexData1d])
nonNumeric[nonNumeric < 0] <- NA
odk[is.na(nonNumeric), indexData1d] <- NA
odk[, indexData1d] <- as.numeric(odk[, indexData1d])
indexData2 <- which(stri_endswith_fixed(odkNames, "age_group"))
indexData3 <- which(stri_endswith_fixed(odkNames, "age_adult"))
nonNumeric <- lapply(odk[ , indexData3], flagNonNumeric)
nonNumeric <- unlist(nonNumeric)
containsNA <- ifelse(
sum(nonNumeric < 0, na.rm = TRUE) > 0,
1, 0)
numNA <- numNA + containsNA
if (containsNA > 0) indexNA <- c(indexNA, odkNames[indexData3])
nonNumeric[nonNumeric < 0] <- NA
odk[is.na(nonNumeric), indexData3] <- NA
odk[, indexData3] <- as.numeric(odk[, indexData3])
indexData4 <- which(stri_endswith_fixed(odkNames, "age_child_unit"))
indexData4d <- which(stri_endswith_fixed(odkNames, "age_child_days"))
nonNumeric <- lapply(odk[ , indexData4d], flagNonNumeric)
nonNumeric <- unlist(nonNumeric)
containsNA <- ifelse(
sum(nonNumeric < 0, na.rm = TRUE) > 0,
1, 0)
numNA <- numNA + containsNA
if (containsNA > 0) indexNA <- c(indexNA, odkNames[indexData4d])
nonNumeric[nonNumeric < 0] <- NA
odk[is.na(nonNumeric), indexData4d] <- NA
odk[, indexData4d] <- as.numeric(odk[, indexData4d])
indexData4m <- which(stri_endswith_fixed(odkNames, "age_child_months"))
nonNumeric <- lapply(odk[ , indexData4m], flagNonNumeric)
nonNumeric <- unlist(nonNumeric)
containsNA <- ifelse(
sum(nonNumeric < 0, na.rm = TRUE) > 0,
1, 0)
numNA <- numNA + containsNA
if (containsNA > 0) indexNA <- c(indexNA, odkNames[indexData4m])
nonNumeric[nonNumeric < 0] <- NA
odk[is.na(nonNumeric), indexData4m] <- NA
odk[, indexData4m] <- as.numeric(odk[, indexData4m])
indexData4y <- which(stri_endswith_fixed(odkNames, "age_child_years"))
nonNumeric <- lapply(odk[ , indexData4y], flagNonNumeric)
nonNumeric <- unlist(nonNumeric)
containsNA <- ifelse(
sum(nonNumeric < 0, na.rm = TRUE) > 0,
1, 0)
numNA <- numNA + containsNA
if (containsNA > 0) indexNA <- c(indexNA, odkNames[indexData4y])
nonNumeric[nonNumeric < 0] <- NA
odk[is.na(nonNumeric), indexData4y] <- NA
odk[, indexData4y] <- as.numeric(odk[, indexData4y])
indexData5d <- which(stri_endswith_fixed(odkNames, "age_neonate_days"))
nonNumeric <- lapply(odk[ , indexData5d], flagNonNumeric)
nonNumeric <- unlist(nonNumeric)
containsNA <- ifelse(
sum(nonNumeric < 0, na.rm = TRUE) > 0,
1, 0)
numNA <- numNA + containsNA
if (containsNA > 0) indexNA <- c(indexNA, odkNames[indexData5d])
nonNumeric[nonNumeric < 0] <- NA
odk[is.na(nonNumeric), indexData5d] <- NA
odk[, indexData5d] <- as.numeric(odk[, indexData5d])
indexData5h <- which(stri_endswith_fixed(odkNames, "age_neonate_hours"))
nonNumeric <- lapply(odk[ , indexData5h], flagNonNumeric)
nonNumeric <- unlist(nonNumeric)
containsNA <- ifelse(
sum(nonNumeric < 0, na.rm = TRUE) > 0,
1, 0)
numNA <- numNA + containsNA
if (containsNA > 0) indexNA <- c(indexNA, odkNames[indexData5h])
nonNumeric[nonNumeric < 0] <- NA
odk[is.na(nonNumeric), indexData5h] <- NA
odk[, indexData5h] <- as.numeric(odk[, indexData5h])
indexData5m <- which(stri_endswith_fixed(odkNames, "age_neonate_minutes"))
nonNumeric <- lapply(odk[ , indexData5m], flagNonNumeric)
nonNumeric <- unlist(nonNumeric)
containsNA <- ifelse(
sum(nonNumeric < 0, na.rm = TRUE) > 0,
1, 0)
numNA <- numNA + containsNA
if (containsNA > 0) indexNA <- c(indexNA, odkNames[indexData5m])
nonNumeric[nonNumeric < 0] <- NA
odk[is.na(nonNumeric), indexData5m] <- NA
odk[, indexData5m] <- as.numeric(odk[, indexData5m])
indexData_isNeonatal <- which(stri_endswith_fixed(odkNames, "isneonatal"))
indexData_isChild <- which(stri_endswith_fixed(odkNames, "ischild"))
indexData_isAdult <- which(stri_endswith_fixed(odkNames, "isadult"))
#5) Was s(he) aged 65 years or more at death? 65+
iv5Out[odk[ , indexData1y]>=65, 5] <- "y"
iv5Out[is.na(odk[ , indexData1y]) & odk[ , indexData2]=="adult" &
odk[ , indexData3]>=65, 5] <- "y"
#6) Was s(he) aged 50 to 64 years at death? 50 to 64
iv5Out[odk[ , indexData1y]< 65 & odk[ , indexData1y]>=50, 6] <- "y"
iv5Out[is.na(odk[ , indexData1y]) & odk[ ,indexData2]=="adult" &
odk[ ,indexData3]< 65 & odk[ ,indexData3]>=50, 6] <- "y"
#7) Was s(he) aged 15 to 49 years at death? 15-49
iv5Out[odk[ , indexData1y]< 50 & odk[ , indexData1y]>=15, 7] <- "y"
iv5Out[is.na(odk[ , indexData1y]) & odk[ , indexData2]=="adult" &
odk[ , indexData3]< 50 & odk[ , indexData3]>=15, 7] <- "y"
#8) Was s(he) aged 5-14 years at death? 5-14 (adult or child)
iv5Out[odk[ , indexData1y]< 15 & odk[ , indexData1y]>= 5, 8] <- "y"
iv5Out[is.na(odk[ , indexData1y]) & odk[ , indexData2]=="adult" &
odk[ , indexData3]< 15 & odk[ , indexData3]>=5, 8] <- "y"
iv5Out[is.na(odk[ , indexData1y]) & odk[ , indexData2]=="child" &
odk[ , indexData4]=="days" & odk[ , indexData4d]< 15*365.25 &
odk[ , indexData4d]>=5*365.25, 8] <- "y"
iv5Out[is.na(odk[ , indexData1y]) & odk[ , indexData2]=="child" &
odk[ , indexData4]=="months" & odk[ , indexData4m]< 15*12 &
odk[ , indexData4m]>=5*12, 8] <- "y"
iv5Out[is.na(odk[ , indexData1y]) & odk[ , indexData2]=="child" &
odk[ , indexData4]=="years" & odk[ , indexData4y]< 15 &
odk[ , indexData4y]>=5, 8] <- "y"
#9) Was s(he) aged 1 to 4 years at death? 1 to 4 (child)
iv5Out[odk[ , indexData1y]< 5 & odk[ , indexData1y]>=1, 9] <- "y"
iv5Out[is.na(odk[ , indexData1y]) & odk[ , indexData2]=="child" &
odk[ , indexData4]=="days" & odk[ , indexData4d]< 5*365.25 &
odk[ , indexData4d]>=1*365.25, 9] <- "y"
iv5Out[is.na(odk[ , indexData1y]) & odk[ , indexData2]=="child" &
odk[ , indexData4]=="months" & odk[ , indexData4m]< 5*12 &
odk[ , indexData4m]>=1*12, 9] <- "y"
iv5Out[is.na(odk[ , indexData1y]) & odk[ , indexData2]=="child" &
odk[ , indexData4]=="years" & odk[ , indexData4y]< 5 &
odk[ , indexData4y]>=1, 9] <- "y"
#10) Was s(he) aged 1 to 11 months at death? 1-11 months (child or neonate?)
iv5Out[odk[ , indexData1d]< 365.25 & odk[ , indexData1d]>=28, 10] <- "y"
iv5Out[is.na(odk[ , indexData1d]) & odk[ , indexData2]=="child" &
odk[ , indexData4]=="days" & odk[ , indexData4d]< 365.25 &
odk[ , indexData4d]>=28, 10] <- "y"
iv5Out[is.na(odk[ , indexData1m]) & odk[ , indexData2]=="child" &
odk[ , indexData4]=="months" & odk[ , indexData4m]< 12 &
odk[ , indexData4m]>=1, 10] <- "y"
#11) Was s(he) aged < 1 month (28 days) at death? 0 - 27 days (neonate)
iv5Out[odk[ , indexData1d]< 28, 11] <- "y"
iv5Out[is.na(odk[ , indexData1d]) & odk[ , indexData2]=="neonate", 11] <- "y"
#12) Was s(he) a live baby who died within 24 hours of birth? day0 iv5Names[12]
iv5Out[odk[ , indexData1d]< 1, 12] <- "y"
ageDays <- odk[ , indexData5d]
ageHours <- odk[ , indexData5h]/24
ageHours[is.na(ageHours)] <- 0
ageMinutes <- odk[ , indexData5m]/(24*12)
ageMinutes[is.na(ageMinutes)] <- 0
ageNeonate <- ageDays + ageHours + ageMinutes
iv5Out[odk[ , indexData2]=="neonate" & !is.na(odk[ , indexData5d]) &
ageNeonate< 1, 12] <- "y"
#13) Was s(he) a baby who died between 24 and 48 hours of birth? day1 iv5Names[13]
iv5Out[odk[ , indexData2]=="neonate" & !is.na(odk[ , indexData5d]) &
ageNeonate< 2 & ageNeonate>=1, 13] <- "y"
#14) Was s(he) a baby who died more than 48 hours from birth, but within the first week? day2-6 iv5Names[14]
iv5Out[odk[ , indexData2]=="neonate" & !is.na(odk[ , indexData5d]) &
ageNeonate< 7 & ageNeonate>=2, 14] <- "y"
#15) Was s(he) a baby who died after the first week, but within the first month? wk2-4 iv5Names[15]
iv5Out[odk[ , indexData2]=="neonate" & !is.na(odk[ , indexData5d]) &
ageNeonate< 28 & ageNeonate>=7, 15] <- "y"
# Finish coding age (5-15) -- if only one age has "y", recode all others to "n"
## e.g., if age 65 == "y", then age 50-64 == "n" and age 15-49 == "n" etc.
indexData6 <- iv5Out[ , 5:15] != "y" ## identify elements in age columns that do not equal "y"
##indexData7 <- rowSums(iv5Out[ , 5:15] == "y") ## identify with rows/records only have 1 "y" for all age columns
indexData7 <- rowSums(iv5Out[ , 5:15] == "y", na.rm = TRUE) ## identify which rows/records only have 1 "y" for all age columns
## Now recode all "n"
iv5Out[indexData7 == 1, 5:15][ indexData6[indexData7 == 1, ] ] <- "n"
## extra steps for less than a month #11 & first few weeks #12 - #15
y11_12 <- iv5Out[, 11] == "y" & iv5Out[, 12] == "y"
y11_13 <- iv5Out[, 11] == "y" & iv5Out[, 13] == "y"
y11_14 <- iv5Out[, 11] == "y" & iv5Out[, 14] == "y"
y11_15 <- iv5Out[, 11] == "y" & iv5Out[, 15] == "y"
iv5Out[indexData7 == 2 & y11_12, 5:15][ indexData6[indexData7 == 2 & y11_12, ] ] <- "n"
iv5Out[indexData7 == 2 & y11_13, 5:15][ indexData6[indexData7 == 2 & y11_13, ] ] <- "n"
iv5Out[indexData7 == 2 & y11_14, 5:15][ indexData6[indexData7 == 2 & y11_14, ] ] <- "n"
iv5Out[indexData7 == 2 & y11_15, 5:15][ indexData6[indexData7 == 2 & y11_15, ] ] <- "n"
#16) Was she a woman aged 12-19 years at death? f-19
iv5Out[ , 16] <- ifelse(odk[ , indexData_sex]=="female" &
odk[ , indexData1y]< 20 &
odk[ , indexData1y]>= 12, "y", ".")
iv5Out[odk[ , indexData_sex]=="female" & odk[ , indexData1y]< 12, 16] <- "n"
iv5Out[odk[ , indexData_sex]=="female" & odk[ , indexData1y]> 19, 16] <- "n"
iv5Out[odk[ , indexData_sex]=="female" & is.na(odk[ , indexData1y]) &
odk[ , indexData2]=="adult" &
odk[ , indexData3]< 20 & odk[ , indexData3]>=12, 16] <- "y"
iv5Out[odk[ , indexData_sex]=="female" & is.na(odk[ , indexData1y]) &
odk[ , indexData2]=="adult" & odk[ , indexData3]< 12, 16] <- "n"
iv5Out[odk[ , indexData_sex]=="female" & is.na(odk[ , indexData1y]) &
odk[ , indexData2]=="adult" & odk[ , indexData3]> 19, 16] <- "n"
iv5Out[odk[ , indexData2]=="neonate", 16] <- "n"
iv5Out[odk[ , indexData_isNeonatal] == 1, 16] <- "n"
iv5Out[odk[ , indexData_isChild] == 1 & odk[ , indexData1y] < 12, 16] <- "n"
iv5Out[odk[ , indexData_isChild] == 1 & odk[ , indexData4y] < 12, 16] <- "n"
iv5Out[odk[ , indexData_isChild] == 1 &
odk[ , indexData4m] < 12*12, 16] <- "n"
iv5Out[odk[ , indexData_isChild] == 1 &
odk[ , indexData4d] < 12*365.25, 16] <- "n"
iv5Out[odk[ , indexData2] == "child" & odk[ , indexData1y] < 12, 16] <- "n"
iv5Out[odk[ , indexData2] == "child" & odk[ , indexData4y] < 12, 16] <- "n"
iv5Out[odk[ , indexData2] == "child" &
odk[ , indexData4m] < 12*12, 16] <- "n"
iv5Out[odk[ , indexData2] == "child" &
odk[ , indexData4d] < 12*365.25, 16] <- "n"
iv5Out[odk[ , indexData_sex]=="male", 16] <- "n"
#17) Was she a woman aged 20-34 years at death? f20-34
iv5Out[ , 17] <- ifelse(odk[ , indexData_sex]=="female" &
odk[ , indexData1y]< 35 &
odk[ , indexData1y]>= 20, "y", ".")
iv5Out[odk[ , indexData_sex]=="female" & odk[ , indexData1y]< 20, 17] <- "n"
iv5Out[odk[ , indexData_sex]=="female" & odk[ , indexData1y]> 34, 17] <- "n"
iv5Out[odk[ , indexData_sex]=="female" & is.na(odk[ , indexData1y]) &
odk[ , indexData2]=="adult" & odk[ , indexData3]< 35 &
odk[ , indexData3]>=20, 17] <- "y"
iv5Out[odk[ , indexData_sex]=="female" & is.na(odk[ , indexData1y]) &
odk[ , indexData2]=="adult" & odk[ , indexData3]< 20, 17] <- "n"
iv5Out[odk[ , indexData_sex]=="female" & is.na(odk[ , indexData1y]) &
odk[ , indexData2]=="adult" & odk[ , indexData3]> 34, 17] <- "n"
iv5Out[odk[ , indexData2]=="neonate", 17] <- "n"
iv5Out[odk[ , indexData2]=="child", 17] <- "n"
iv5Out[odk[ , indexData_isNeonatal] == 1, 17] <- "n"
iv5Out[odk[ , indexData_isChild] == 1, 17] <- "n"
iv5Out[odk[ , indexData_sex]=="male", 17] <- "n"
#18) Was she a woman aged 35 to 49 years at death? f35-49
iv5Out[ , 18] <- ifelse(odk[ , indexData_sex]=="female" &
odk[ , indexData1y]< 50 &
odk[ , indexData1y]>= 35, "y", ".")
iv5Out[odk[ , indexData_sex]=="female" & odk[ , indexData1y]< 35, 18] <- "n"
iv5Out[odk[ , indexData_sex]=="female" & odk[ , indexData1y]> 49, 18] <- "n"
iv5Out[odk[ , indexData_sex]=="female" & is.na(odk[ , indexData1y]) &
odk[ , indexData2]=="adult" & odk[ , indexData3]< 50 &
odk[ , indexData3]>=35, 18] <- "y"
iv5Out[odk[ , indexData_sex]=="female" & is.na(odk[ , indexData1y]) &
odk[ , indexData2]=="adult" & odk[ , indexData3]< 35, 18] <- "n"
iv5Out[odk[ , indexData_sex]=="female" & is.na(odk[ , indexData1y]) &
odk[ , indexData2]=="adult" & odk[ , indexData3]> 49, 18] <- "n"
iv5Out[odk[ , indexData2]=="neonate", 18] <- "n"
iv5Out[odk[ , indexData2]=="child", 18] <- "n"
iv5Out[odk[ , indexData_isNeonatal] == 1, 18] <- "n"
iv5Out[odk[ , indexData_isChild] == 1, 18] <- "n"
iv5Out[odk[ , indexData_sex]=="male", 18] <- "n"
#19) Was she married at the time of death? married
indexData <- which(stri_endswith_fixed(odkNames, whoNames[19]))
## table(odk[ , indexData])
iv5Out[odk[ , indexData_sex]=="female" & tolower(odk[ , indexData])=="married", 19] <- "y"
iv5Out[odk[ , indexData_sex]=="female" & tolower(odk[ , indexData])=="single", 19] <- "n"
iv5Out[odk[ , indexData_sex]=="female" & tolower(odk[ , indexData])=="partner", 19] <- "n"
iv5Out[odk[ , indexData_sex]=="female" & tolower(odk[ , indexData])=="divorced", 19] <- "n"
iv5Out[odk[ , indexData_sex]=="female" & tolower(odk[ , indexData])=="widowed", 19] <- "n"
iv5Out[odk[ , indexData_sex]=="female" & tolower(odk[ , indexData])=="too_young_to_be_married", 19] <- "n"
iv5Out[odk[ , indexData_sex]=="female" & tolower(odk[ , indexData])=="child", 19] <- "n"
iv5Out[odk[ , indexData_sex]=="male", 19] <- "n"
#22) Was (s)he injured in a non-road transport accident? inj nrta (NOT INCLUDED)
#26) Was (s)he injured by the bite or sting of a venomous animal? inj venom
indexData1 <- which(stri_endswith_fixed(odkNames, whoNames[26]))
indexData2 <- which(stri_endswith_fixed(odkNames, "id3e400"))
iv5Out[odk[ , indexData1] == "y" & odk[ , indexData2] == "snake", 26] <- "y"
iv5Out[odk[ , indexData1] == "y" & odk[ , indexData2] == "insect_or_scorpion", 26] <- "y"
#27) Was (s)he injured by an animal or insect (non-venomous) inj anim
iv5Out[odk[ , indexData2] == "dog", 27] <- "y"
#36) Was the injury accidental? inj accid
indexData1 <- which(stri_endswith_fixed(odkNames, whoNames[36]))
indexData2 <- which(stri_endswith_fixed(odkNames, "id3e335"))
iv5Out[odk[ , indexData1] == "y" | odk[ , indexData2] == "y", 36] <- "y"
#41) Was it more than 5 minutes after birth before the baby first cried? cry 5+m
indexData <- which(stri_endswith_fixed(odkNames, whoNames[41]))
iv5Out[odk[ , indexData]> 5, 41] <- "y"
iv5Out[odk[ , indexData]<=5, 41] <- "n"
#43) Did the baby stop crying more than a day before (s)he died? cry st 1+d
indexData <- which(stri_endswith_fixed(odkNames, whoNames[43]))
iv5Out[odk[ , indexData]> 24, 43] <- "y"
iv5Out[odk[ , indexData]<=24, 43] <- "n"
#47) Did the baby have a breathing problem? brth prob (NOT INCLUDED)
#52) Did the final illness last less than 3 weeks? ill <3w.
indexData <- which(stri_endswith_fixed(odkNames, whoNames[52]))
iv5Out[odk[ , indexData]< 21, 52] <- "y"
iv5Out[odk[ , indexData]>=21, 52] <- "n"
#53) Did the final illness last at least 3 weeks? ill 3+w
iv5Out[odk[ , indexData]>=21, 53] <- "y"
iv5Out[odk[ , indexData]< 21, 53] <- "n"
#75) Did the fever last less than a week before death? fev <1w
indexData <- which(stri_endswith_fixed(odkNames, whoNames[75]))
iv5Out[odk[ , indexData]< 7, 75] <- "y"
iv5Out[odk[ , indexData]>=7, 75] <- "n"
#76) Did the fever last at least one week, but less than 2 weeks before death? fev 1-2w
iv5Out[odk[ , indexData]>= 7 & odk[ , indexData]< 14, 76] <- "y"
iv5Out[odk[ , indexData]< 7, 76] <- "n"
#77) Did the fever last at least 2 weeks before death? fev 2+w
iv5Out[odk[ , indexData]>= 14, 77] <- "y"
iv5Out[odk[ , indexData]< 14, 77] <- "n"
#78) Did the fever continue until death? fev death (NOT INCLUDED)
#79) Was the fever severe? fev sev
indexData <- which(stri_endswith_fixed(odkNames, whoNames[79]))
iv5Out[tolower(odk[ , indexData])=="severe", 79] <- "y"
iv5Out[tolower(odk[ , indexData])=="mild", 79] <- "n"
iv5Out[tolower(odk[ , indexData])=="moderate", 79] <- "n"
#80) Was the fever continuous? fev cont (NOT INCLUDED)
#83) Did the cough last less than 3 weeks before death? cou <3w
indexData <- which(stri_endswith_fixed(odkNames, whoNames[83]))
iv5Out[odk[ , indexData[1]]< 21, 83] <- "y"
iv5Out[odk[ , indexData[1]]>=21, 83] <- "n"
#84) Did the cough last at least 3 weeks before death? cou 3+w
iv5Out[odk[ , indexData[1]]>=21, 84] <- "y"
iv5Out[odk[ , indexData[1]]< 21, 84] <- "n"
#90) Did the difficult breathing last for at least 3 days before death? dif br 3d
indexDatad <- which(stri_endswith_fixed(odkNames, whoNames[90]))
iv5Out[odk[ , indexDatad]>=3, 90] <- "y"
iv5Out[odk[ , indexDatad]< 3, 90] <- "n"
#91) Was the difficult breathing continuous during this period? dif br con
indexData <- which(stri_endswith_fixed(odkNames, whoNames[91]))
iv5Out[tolower(odk[ , indexData])=="continuous", 91] <- "y"
iv5Out[tolower(odk[ , indexData])=="on_and_off", 91] <- "n"
#93) Did the fast breathing last for less than two weeks before death? br fs <2w
indexData <- which(stri_endswith_fixed(odkNames, whoNames[93]))
iv5Out[odk[ , indexData]< 14, 93] <- "y"
iv5Out[odk[ , indexData]>=14, 93] <- "n"
#94) Did the fast breathing last for at least 2 weeks before death? br fs 2+w
iv5Out[odk[ , indexData]>=14, 94] <- "y"
iv5Out[odk[ , indexData]< 14, 94] <- "n"
#96) Did the breathlessness last for less than 2 weeks before death? brl <2w
indexData <- which(stri_endswith_fixed(odkNames, whoNames[96]))
iv5Out[odk[ , indexData]< 2, 96] <- "y"
iv5Out[odk[ , indexData]>=2, 96] <- "n"
#97) Did the breathlessness last for at least 2 weeks before death? brl 2+w
iv5Out[odk[ , indexData]>=2, 97] <- "y"
iv5Out[odk[ , indexData]< 2, 97] <- "n"
#101) Did his/her breathing sound like wheezing or grunting? whz grun
indexData <- which(stri_endswith_fixed(odkNames, whoNames[101]))
iv5Out[stri_endswith_fixed(tolower(odk[ , indexData]), "grunting"), 101] <- "y"
iv5Out[stri_endswith_fixed(tolower(odk[ , indexData]), "stridor"), 101] <- "y"
iv5Out[stri_endswith_fixed(tolower(odk[ , indexData]), "wheezing"), 101] <- "y"
iv5Out[stri_endswith_fixed(tolower(odk[ , indexData]), "no"), 101] <- "n"
#102) During the illness that led to death, did (s)he have chest pain? ch pain (NOT INCLUDED)
#104) Did (s)he experience chest pain at least 3 days before death? chp 3d
indexData <- which(stri_endswith_fixed(odkNames, whoNames[104]))
iv5Out[odk[ , indexData]>=3, 104] <- "y"
iv5Out[odk[ , indexData]< 3, 104] <- "n"
#105) Did the chest pain last for at least 30 minutes? chp 30m
indexDatam <- which(stri_endswith_fixed(odkNames, whoNames[105]))
iv5Out[odk[ , indexDatam]>=30, 105] <- "y"
iv5Out[odk[ , indexDatam]< 30, 105] <- "n"
#107) Did (s)he have diarrhoea for less than 2 weeks before death? drr <2w
indexData <- which(stri_endswith_fixed(odkNames, whoNames[107]))
iv5Out[odk[ , indexData]< 14, 107] <- "y"
iv5Out[odk[ , indexData]>=14, 107] <- "n"
#108) Did (s)he have diarrhoea for at least 2 weeks but less than 4 weeks before death? drr 2-4w
iv5Out[odk[ , indexData]< 28 & odk[ , indexData]>=14, 108] <- "y"
iv5Out[odk[ , indexData]< 14, 108] <- "n"
iv5Out[odk[ , indexData]>=28, 108] <- "n"
#109) Did (s)he have diarrhoea for at least 4 weeks before death? drr 4+w
iv5Out[odk[ , indexData]>=28, 109] <- "y"
iv5Out[odk[ , indexData]< 28, 109] <- "n"
#110) Did the baby or child have at least 4 stools on the day that loose liquid stools were most frequent? 4+ stls
indexData <- which(stri_endswith_fixed(odkNames, whoNames[110]))
iv5Out[odk[ , indexData]>= 4 & odk[ , indexData]< 999, 110] <- "y"
iv5Out[odk[ , indexData]< 4, 110] <- "n"
#111) Did the frequent loose or liquid stools start at least 3 days before death? drr 3d
indexData <- which(stri_endswith_fixed(odkNames, whoNames[111]))
iv5Out[odk[ , indexData]>= 3 & odk[ , indexData]< 999, 111] <- "y"
iv5Out[odk[ , indexData]< 3, 111] <- "n"
#116)Did (s)he vomit in the week preceding the death? vom bd (NOT INCLUDED)
#117) Did (s)he vomit for at least 3 days before death? vom 3d
indexData <- which(stri_endswith_fixed(odkNames, whoNames[117]))
iv5Out[odk[ , indexData]>= 3 & odk[ , indexData]< 999, 117] <- "y"
iv5Out[odk[ , indexData]< 3, 117] <- "n"
#121) Did (s)he have abdominal pain? abd pain (NOT INCLUDED)
#123) Did (s)he have severe abdominal pain for less than 2 weeks before death? abd p <2w
indexData <- which(stri_endswith_fixed(odkNames, whoNames[123]))
iv5Out[odk[ , indexData]< 14, 123] <- "y"
iv5Out[odk[ , indexData]>=14, 123] <- "n"
#124) Did (s)he have severe abdominal pain for at least 2 weeks before death? abd p 2+w
iv5Out[odk[ , indexData]>=14, 124] <- "y"
iv5Out[odk[ , indexData]< 14, 124] <- "n"
#125) Was the pain in the upper abdomen? abd p up
indexData <- which(stri_endswith_fixed(odkNames, whoNames[125]))
iv5Out[tolower(odk[ , indexData])=="upper_abdomen", 125] <- "y"
iv5Out[tolower(odk[ , indexData])=="lower_abdomen", 125] <- "n"
#126) Was the pain in the lower abdomen? abd p lo
iv5Out[tolower(odk[ , indexData])=="upper_abdomen", 126] <- "n"
iv5Out[tolower(odk[ , indexData])=="lower_abdomen", 126] <- "y"
#128) Did (s)he have a more than usually protruding abdomen for less than 2 weeks before death? abd pr <2w
indexData <- which(stri_endswith_fixed(odkNames, whoNames[128]))
iv5Out[odk[ , indexData]< 14, 128] <- "y"
iv5Out[odk[ , indexData]>=14, 128] <- "n"
#129) Did (s)he have a more than usually protruding abdomen for at least 2 weeks before death? abd pr 2+w
iv5Out[odk[ , indexData]>=14, 129] <- "y"
iv5Out[odk[ , indexData]< 14, 129] <- "n"
#130) Did (s)he develop the protruding abdomen rapidly? abd pr rap
indexData <- which(stri_endswith_fixed(odkNames, whoNames[130]))
iv5Out[tolower(odk[ , indexData])=="rapidly", 130] <- "y"
iv5Out[tolower(odk[ , indexData])=="slowly", 130] <- "n"
#132) Did (s)he have a mass in the abdomen for less than 2 weeks before death? ab ms <2w
indexData <- which(stri_endswith_fixed(odkNames, whoNames[132]))
iv5Out[odk[ , indexData]< 14, 132] <- "y"
iv5Out[odk[ , indexData]>=14, 132] <- "n"
#133) Did (s)he have a mass in the abdomen for at least 2 weeks before death? ab ms 2+w
iv5Out[odk[ , indexData]< 14, 133] <- "n"
iv5Out[odk[ , indexData]>=14, 133] <- "y"
#136) Did (s)he have a stiff neck for less than one week before death? st n <1w
indexData <- which(stri_endswith_fixed(odkNames, whoNames[136]))
iv5Out[odk[ , indexData]< 7, 136] <- "y"
iv5Out[odk[ , indexData]>=7, 136] <- "n"
#137) Did (s)he have a stiff neck for at least one week before death? st n 1+w
iv5Out[odk[ , indexData]>=7, 137] <- "y"
iv5Out[odk[ , indexData]< 7, 137] <- "n"
#139) Did (s)he have a painful neck for at least one week before death? pa n 1+w
indexData <- which(stri_endswith_fixed(odkNames, whoNames[139]))
iv5Out[odk[ , indexData]>=7, 139] <- "y"
iv5Out[odk[ , indexData]< 7, 139] <- "n"
#141) Did (s)he have mental confusion for at least 3 months before death? menc 3+m
indexData <- which(stri_endswith_fixed(odkNames, whoNames[141]))
iv5Out[odk[ , indexData]>=3, 141] <- "y"
iv5Out[odk[ , indexData]< 3, 141] <- "n"
#142) Did (s)he have mental confusion for at least 3 months before death? menc 3+m (NOT INCLUDED)
#144) Was (s)he unsconscious for at least 6 hours before death? unc 6+h
indexData <- which(stri_endswith_fixed(odkNames, whoNames[144]))
iv5Out[odk[ , indexData]>=6, 144] <- "y"
iv5Out[odk[ , indexData]< 6, 144] <- "n"
#149) Did the convulsions last for less than 10 minutes? conv <10m
indexData <- which(stri_endswith_fixed(odkNames, whoNames[149]))
iv5Out[odk[ , indexData]< 10, 149] <- "y"
iv5Out[odk[ , indexData]>=10, 149] <- "n"
#150) Did the convulsions last for at least 10 minutes? conv 10+m
iv5Out[odk[ , indexData]< 10, 150] <- "n"
iv5Out[odk[ , indexData]>=10, 150] <- "y"
#161) Did the ulcer ooze pus for at least 2 weeks? sk ul 2+w
indexData <- which(stri_endswith_fixed(odkNames, whoNames[161]))
iv5Out[odk[ , indexData]>=14, 161] <- "y"
iv5Out[odk[ , indexData]< 14, 161] <- "n"
#163) Did (s)he have the skin rash for less than one week? sk ra <1w
indexData <- which(stri_endswith_fixed(odkNames, whoNames[163]))
iv5Out[odk[ , indexData]< 7, 163] <- "y"
iv5Out[odk[ , indexData]>=7, 163] <- "n"
#164) Did (s)he have the skin rash for at least one week? sk ra 1+w
iv5Out[odk[ , indexData]>=7, 164] <- "y"
iv5Out[odk[ , indexData]< 7, 164] <- "n"
#165) Did (s)he have a rash on the face? sk ra face
indexData <- which(stri_endswith_fixed(odkNames, whoNames[165]))
iv5Out[stri_endswith_fixed(tolower(odk[ , indexData]), "face"), 165] <- "y"
iv5Out[stri_endswith_fixed(tolower(odk[ , indexData]), negate = TRUE, "face"), 165] <- "n"
iv5Out[tolower(odk[ , indexData])=="", 165] <- "."
#166) Did (s)he have a rash on the trunk or abdomen? sk ra abd
indexData <- which(stri_endswith_fixed(odkNames, whoNames[166]))
iv5Out[stri_endswith_fixed(tolower(odk[ , indexData]), "abdomen|trunk"), 166] <- "y"
iv5Out[stri_endswith_fixed(tolower(odk[ , indexData]), negate = TRUE, "abdomen|trunk"), 166] <- "n"
iv5Out[tolower(odk[ , indexData])=="", 166] <- "."
#167) Did (s)he have a rash on the extremities? sk ra ext
indexData <- which(stri_endswith_fixed(odkNames, whoNames[167]))
iv5Out[stri_endswith_fixed(tolower(odk[ , indexData]), "extremities"), 167] <- "y"
iv5Out[stri_endswith_fixed(tolower(odk[ , indexData]), negate = TRUE, "extremities"), 167] <- "n"
iv5Out[tolower(odk[ , indexData])=="", 167] <- "."
#168) Did (s)he have a rash everywhere? sk ra all
indexData <- which(stri_endswith_fixed(odkNames, whoNames[168]))
iv5Out[stri_endswith_fixed(tolower(odk[ , indexData]), "everywhere"), 168] <- "y"
iv5Out[stri_endswith_fixed(tolower(odk[ , indexData]), negate = TRUE, "everywhere"), 168] <- "n"
iv5Out[tolower(odk[ , indexData])=="", 168] <- "."
#173) During the illness that led to death, did he/she have areas of the skin with redness and swelling? sk red
# (NOT INCLUDED)
#181) Did (s)he have puffiness of the face for at least one week before death? sw p f 1+w
indexData <- which(stri_endswith_fixed(odkNames, whoNames[181]))
iv5Out[odk[ , indexData]>=7, 181] <- "y"
iv5Out[odk[ , indexData]< 7, 181] <- "n"
#183) Did the swelling last for at least 3 days before death? sw lf 3+d
indexData <- which(stri_endswith_fixed(odkNames, whoNames[183]))
iv5Out[odk[ , indexData]>=3, 183] <- "y"
iv5Out[odk[ , indexData]< 3, 183] <- "n"
#193) Was only the right side of the body paralysed? par rs
indexData <- which(stri_endswith_fixed(odkNames, whoNames[193]))
iv5Out[tolower(odk[ , indexData])=="right_side", 193] <- "y"
iv5Out[tolower(odk[ , indexData])!="right_side", 193] <- "n"
iv5Out[tolower(odk[ , indexData])=="", 193] <- "."
#194) Was only the left side of the body paralysed? par ls
iv5Out[tolower(odk[ , indexData])=="left_side", 194] <- "y"
iv5Out[tolower(odk[ , indexData])!="left_side", 194] <- "n"
iv5Out[tolower(odk[ , indexData])=="", 194] <- "."
#195) Was only the lower part of the body paralysed? par lo
iv5Out[tolower(odk[ , indexData])=="lower_part_of_body", 195] <- "y"
iv5Out[tolower(odk[ , indexData])!="lower_part_of_body", 195] <- "n"
iv5Out[tolower(odk[ , indexData])=="", 195] <- "."
#196) Was only the upper part of the body paralysed? par up
iv5Out[tolower(odk[ , indexData])=="upper_part_of_body", 196] <- "y"
iv5Out[tolower(odk[ , indexData])!="upper_part_of_body", 196] <- "n"
iv5Out[tolower(odk[ , indexData])=="", 196] <- "."
#197) Was only one leg paralysed? par leg
iv5Out[tolower(odk[ , indexData])=="one_leg_only", 197] <- "y"
iv5Out[tolower(odk[ , indexData])!="one_leg_only", 197] <- "n"
iv5Out[tolower(odk[ , indexData])=="", 197] <- "."
#198) Was only one arm paralysed? par arm
iv5Out[tolower(odk[ , indexData])=="one_arm_only", 198] <- "y"
iv5Out[tolower(odk[ , indexData])!="one_arm_only", 198] <- "n"
iv5Out[tolower(odk[ , indexData])=="", 198] <- "."
#199) Was the entire body paralysed? par all
iv5Out[tolower(odk[ , indexData])=="whole_body", 199] <- "y"
iv5Out[tolower(odk[ , indexData])!="whole_body", 199] <- "n"
iv5Out[tolower(odk[ , indexData])=="", 199] <- "."
#201) Did (s)he have difficulty swallowing for at least one week before death? swa 1+w
indexData <- which(stri_endswith_fixed(odkNames, whoNames[201]))
iv5Out[odk[ , indexData]>=7, 201] <- "y"
iv5Out[odk[ , indexData]< 7, 201] <- "n"
#202) Did (s)he have difficulty with swallowing solids? swa sol
indexData <- which(stri_endswith_fixed(odkNames, whoNames[202]))
iv5Out[tolower(odk[ , indexData])=="solids", 202] <- "y"
iv5Out[tolower(odk[ , indexData])=="both", 202] <- "y"
iv5Out[tolower(odk[ , indexData])=="liquids", 202] <- "n"
#203) Did (s)he have difficulty with swallowing liquids? swa liq
iv5Out[tolower(odk[ , indexData])=="solids", 203] <- "n"
iv5Out[tolower(odk[ , indexData])=="both", 203] <- "y"
iv5Out[tolower(odk[ , indexData])=="liquids", 203] <- "y"
#206) Did (s)he have the yellow discolouration for at least 3 weeks before death? yell 3+w
indexData <- which(stri_endswith_fixed(odkNames, whoNames[206]))
iv5Out[odk[ , indexData]>=21, 206] <- "y"
iv5Out[odk[ , indexData]< 21, 206] <- "n"
#212) Did the baby ever suckle in a normal way? suck ev (NOT INCLUDED)
#214) Did the baby stop suckling on the 2nd day of life or later? suck st d1
indexData <- which(stri_endswith_fixed(odkNames, whoNames[214]))
iv5Out[odk[ , indexData[1]]>=2, 214] <- "y"
iv5Out[odk[ , indexData[1]]< 2, 214] <- "n"
#220) During the illness that led to death, did the baby become unresponsive or unconscious? unresp
# (NOT INCLUDED)
#224) Was the baby more than 3 days old when it started feeling cold to touch? cold 3+d
indexData <- which(stri_endswith_fixed(odkNames, whoNames[224]))
iv5Out[odk[ , indexData]> 3, 224] <- "y"
iv5Out[odk[ , indexData]<=3, 224] <- "n"
#224) Was the baby more than 3 days old when it started feeling cold to touch? cold 3+d (NOT INCLUDED)
#233) During the illness that led to death, did she have excessive vaginal bleeding in between menstrual periods? men betw
# (NOT INCLUDED)
#239) Had her period been overdue for at least 4 weeks? men l 4+w
indexData <- which(stri_endswith_fixed(odkNames, whoNames[239]))
iv5Out[odk[ , indexData]>=4, 239] <- "y"
iv5Out[odk[ , indexData]< 4, 239] <- "n"
#243) Was she, or had she been, pregnant for less than 6 months when she died? d <6m pr
indexData <- which(stri_endswith_fixed(odkNames, whoNames[243]))
iv5Out[odk[ , indexData]< 6, 243] <- "y"
iv5Out[odk[ , indexData]>=6, 243] <- "n"
#248) Did she die within 6 weeks of childbirth? d <6w chb
indexData_a <- which(stri_endswith_fixed(odkNames, whoNames[248]))
indexData_b <- which(stri_endswith_fixed(odkNames, "id3c212"))
iv5Out[odk[ , indexData_a] == "y" & odk[ , indexData_b] == "y", 248] <- "y"
iv5Out[odk[ , indexData_a] == "n" | odk[ , indexData_b] == "n", 248] <- "n"
#252) Did she die during or after her first pregnancy? 1st pr.
# WHO question is "How many births, including stillbirths, did she/the mother have before this baby?"
indexData <- which(stri_endswith_fixed(odkNames, whoNames[252]))
iv5Out[odk[ , indexData]==0, 252] <- "y"
iv5Out[odk[ , indexData]> 0, 252] <- "n"
#253) Did she have four or more pregnancies before this one? 4+ pr
iv5Out[odk[ , indexData]>=4, 253] <- "y"
iv5Out[odk[ , indexData]< 4, 253] <- "n"
#266) Did her labour last longer than 24 hours? lab 24+h
indexData <- which(stri_endswith_fixed(odkNames, whoNames[266]))
iv5Out[odk[ , indexData]> 24, 266] <- "y"
iv5Out[odk[ , indexData]<=24, 266] <- "n"
#271) Did the mother deliver at a health facility or clinic? del hfac
indexData <- which(stri_endswith_fixed(odkNames, whoNames[271]))
iv5Out[tolower(odk[ , indexData])=="hospital", 271] <- "y"
iv5Out[tolower(odk[ , indexData])=="other_health_facility", 271] <- "y"
iv5Out[tolower(odk[ , indexData])=="home", 271] <- "n"
iv5Out[tolower(odk[ , indexData])=="on_route_to_hospital_or_facility", 271] <- "n"
iv5Out[tolower(odk[ , indexData])=="other", 271] <- "n"
#272) Did the mother deliver at home? del home
iv5Out[tolower(odk[ , indexData])=="hospital", 272] <- "n"
iv5Out[tolower(odk[ , indexData])=="other_health_facility", 272] <- "n"
iv5Out[tolower(odk[ , indexData])=="home", 272] <- "y"
iv5Out[tolower(odk[ , indexData])=="on_route_to_hospital_or_facility", 272] <- "n"
iv5Out[tolower(odk[ , indexData])=="other", 272] <- "n"
#273) Did the mother deliver elsewhere (not at a health facility nor at home)? del else
iv5Out[tolower(odk[ , indexData])=="hospital", 273] <- "n"
iv5Out[tolower(odk[ , indexData])=="other_health_facility", 273] <- "n"
iv5Out[tolower(odk[ , indexData])=="home", 273] <- "n"
iv5Out[tolower(odk[ , indexData])=="on_route_to_hospital_or_facility", 273] <- "y"
iv5Out[tolower(odk[ , indexData])=="other", 273] <- "y"
#281) If the child was part of a multiple birth, was it born first? mult fir
indexData <- which(stri_endswith_fixed(odkNames, whoNames[281]))
iv5Out[tolower(odk[ , indexData])=="first", 281] <- "y"
iv5Out[tolower(odk[ , indexData])=="second_or_later", 281] <- "n"
#283) Did the child's mother die during or shortly after the delivery? moth d del
indexData <- which(stri_endswith_fixed(odkNames, whoNames[283]))
iv5Out[tolower(odk[ , indexData])=="after_delivery", 283] <- "y"
iv5Out[tolower(odk[ , indexData])=="during_delivery" , 283] <- "y"
#284) Did the child's mother die in the baby's first year of life? moth d y1
indexDatam <- which(stri_endswith_fixed(odkNames, whoNames[284]))
indexDatad <- which(stri_endswith_fixed(odkNames, "id3d108b"))
nMonths <- odk[ , indexDatam]
nDays <- odk[ , indexDatad]
nMonths[is.na(nMonths) & !is.na(nDays)] <- 0
nDays[is.na(nDays) & !is.na(nMonths)] <- 0
iv5Out[nMonths + nDays/30.4 <=12, 284] <- "y"
iv5Out[nMonths + nDays/30.4 > 12, 284] <- "n"
#285) Was the baby born in a health facility or clinic? born fac
indexData <- which(stri_endswith_fixed(odkNames, whoNames[285]))
iv5Out[tolower(odk[ , indexData])=="hospital", 285] <- "y"
iv5Out[tolower(odk[ , indexData])=="other_health_facility", 285] <- "y"
iv5Out[tolower(odk[ , indexData])=="home", 285] <- "n"
iv5Out[tolower(odk[ , indexData])=="other", 285] <- "n"
iv5Out[tolower(odk[ , indexData])=="on_route_to_hospital_or_facility", 285] <- "n"
#286) Was the baby born at home? born home
iv5Out[tolower(odk[ , indexData])=="hospital", 286] <- "n"
iv5Out[tolower(odk[ , indexData])=="other_health_facility", 286] <- "n"
iv5Out[tolower(odk[ , indexData])=="home", 286] <- "y"
iv5Out[tolower(odk[ , indexData])=="other", 286] <- "n"
iv5Out[tolower(odk[ , indexData])=="on_route_to_hospital_or_facility", 286] <- "n"
#287) Was the baby born somewhere else (e.g. on the way to a clinic)? born on way
iv5Out[tolower(odk[ , indexData])=="hospital", 287] <- "n"
iv5Out[tolower(odk[ , indexData])=="other_health_facility", 287] <- "n"
iv5Out[tolower(odk[ , indexData])=="home", 287] <- "n"
iv5Out[tolower(odk[ , indexData])=="other", 287] <- "y"
iv5Out[tolower(odk[ , indexData])=="on_route_to_hospital_or_facility", 287] <- "y"
#291) At birth, was the baby very much smaller than usual, (weighing under 1 kg)? bwt vsmall
indexData <- which(stri_endswith_fixed(odkNames, whoNames[291]))
iv5Out[odk[ , indexData]< 1000, 291] <- "y"
iv5Out[odk[ , indexData]>=1000, 291] <- "n"
#293) Was the baby born during the ninth month (at least 37 weeks) of pregnancy? gest 9m
indexData <- which(stri_endswith_fixed(odkNames, whoNames[293]))
iv5Out[odk[ , indexData]>=9, 293] <- "y"
iv5Out[odk[ , indexData]< 9, 293] <- "n"
#294) Was the baby born during the eighth month (34 to 37 weeks) of pregnancy? gest 8m
iv5Out[odk[ , indexData]> 8, 294] <- "n"
iv5Out[odk[ , indexData]==8, 294] <- "y"
iv5Out[odk[ , indexData]< 8, 294] <- "n"
#295) Was the baby born before the eighth month (less than 34 weeks) of pregnancy? gest 7m
iv5Out[odk[ , indexData]>=8, 295] <- "n"
iv5Out[odk[ , indexData]< 8, 295] <- "y"
#302) Was the baby moving in the last few days before the birth? bab mov (NOT INCLUDED)
#304) Did labour and delivery take more than 24 hours? lab 24+h (NOT INCLUDED)
#307) Was the liquor a green or brown colour when the waters broke? liq gr-br (NOT INCLUDED)
#313) Was this baby born from the mother's first pregnancy? born 1st pr
indexData <- which(stri_endswith_fixed(odkNames, whoNames[313]))
iv5Out[odk[ , indexData]==0, 313] <- "y"
iv5Out[odk[ , indexData]> 0, 313] <- "n"
#314) Did the baby's mother have four or more births before this one? born 4+ pr
iv5Out[odk[ , indexData]>=4, 314] <- "y"
iv5Out[odk[ , indexData]< 4, 314] <- "n"
#315) During labour, did the baby's mother suffer from fever? moth fev (NOT INCLUDED)
#317) Did the baby's mother have diabetes mellitus? moth diab (NOT INCLUDED)
#321) Did the baby's mother have severe anaemia? moth anaem (NOT INCLUDED)
#325) Was the umbilical cord delivered first? cord first (NOT INCLUDED)
#330) Did (s)he smoke tobacco? tobac ns
indexData <- which(stri_endswith_fixed(odkNames, whoNames[330]))
iv5Out[tolower(odk[ , indexData])=="chewing_tobacco", 330] <- "n"
iv5Out[tolower(odk[ , indexData])=="cigarettes", 330] <- "y"
iv5Out[tolower(odk[ , indexData])=="pipe", 330] <- "y"
#331) Did (s)he use non-smoking tobacco? tobac ns
indexData <- which(stri_endswith_fixed(odkNames, whoNames[331]))
iv5Out[tolower(odk[ , indexData])=="chewing_tobacco", 331] <- "y"
iv5Out[tolower(odk[ , indexData])=="cigarettes", 331] <- "n"
iv5Out[tolower(odk[ , indexData])=="pipe", 331] <- "n"
iv5Out[tolower(odk[ , indexData])=="local_form_of_tobacco", 331] <- "n"
iv5Out[tolower(odk[ , indexData])=="other", 331] <- "n"
#332) Did (s)he smoke at least 10 cigarettes daily? cigs >10
indexData <- which(stri_endswith_fixed(odkNames, whoNames[332]))
iv5Out[odk[ , indexData]>=10, 332] <- "y"
iv5Out[odk[ , indexData]< 10, 332] <- "n"
# check for NAs
if (numNA > 0) {
warning("Found unexpected input values (coded as missing)", call. = FALSE)
cat("Unexpected values found in: ", sep = "\n")
cat(paste(indexNA), sep = ", ")
cat("\n")
}
numNA <- colSums(is.na(iv5Out))
indexNA <- which(numNA > 0)
if (length(indexNA) > 0) {
warning("NA's included in output", call. = FALSE)
cat(
paste("odk2openVA produced NA's in the following columns",
" (this may cause errors with openVA)",
sep = ""),
sep = "\n"
)
cat(
paste(iv5Names[indexNA], ## subtract 1 since ID is omitted
" Probably associated with WHO column containing: ",
whoNames[indexNA], ## subtract 1 since ID is omitted
sep = ""),
sep = "\n"
)
}
# Add ID as first column
indexID <- which(stri_endswith_fixed(odkNames, tolower(id_col)))
if (length(indexID)) {
iv5Out <- cbind(as.character(odk[, indexID]), iv5Out)
} else {
message("Did not find id_col, so assigning row numbers for IDs.",
call. = FALSE)
iv5Out <- cbind(as.character(1:nrow(iv5Out)), iv5Out)
}
# Attach column names
colnames(iv5Out) <- c("ID", iv5Names)
# That's all folks!
return(as.data.frame(iv5Out, stringsAsFactors = FALSE))
}
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