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R/odk2EAVA.R
In EAVA: Deterministic Verbal Autopsy Coding with Expert Algorithm Verbal Autopsy
Defines functions
odk2EAVA
Documented in
odk2EAVA
#' @title odk2EAVA
#' @description Converts 2016 WHO verbal autopsy (VA) data to an input file for Expert Algorithm Verbal Autopsy cause of death assignment by the codEAVA() function
#' @param odk A data frame which used open data kit (odk) to obtain 2016 WHO VA questionnaire responses
#' @param id_col A unique identifier for each record within the odk data frame
#' @returns A data frame that contains variable names and values which have been converted to openVA convention
#' @examples{
#' # load embedded example data or data from WHO 2016 Verbal Autopsy Questionnaire
#' data <- as.data.frame(data_public)
#' # run odk2EAVA()
#' output <- odk2EAVA(data, id_col = "comsa_id")
#' # view data converted for use in codEAVA()
#' head(output)
#' }
#' @references Thomas J, Choi E, Li Z, Maire N, McCormick T, Byass P, Clark S (2021). CrossVA: Verbal Autopsy Data Transformation for InSilicoVA and InterVA5 Algorithms_. R package version 1.0.0, <https://CRAN.R-project.org/package=CrossVA>.
#' @importFrom stringi stri_endswith_fixed
#' @importFrom stringr str_detect
#' @export
odk2EAVA <- function(odk, id_col) {
# Currently CrossVA requires all i022a-i022n variables, which public data does not have - improve errors to allow data management outdside function
names(odk) <- tolower(colnames(odk))
COMSAvariables <- as.vector(colnames(odk))
# Remove Stillbirths
odk$Stillbirth <- ifelse(odk$id10104 %in% c("no","dk") & odk$id10109 %in% c("no","dk") & odk$id10110 %in% c("no","dk"),1,0)
odk <- odk[odk$Stillbirth!=1,]
# convert id10022 -- need to add this manually
odk$id10022 <- odk$ageindaysnew
odk$i022a <- ifelse(is.na(odk$ageindaysnew),".", ifelse(odk$ageindaysnew >= 65*365.25, "y", "n"))
odk$i022b <- ifelse(is.na(odk$ageindaysnew),".", ifelse(odk$ageindaysnew >= 50*365.25 & odk$ageindaysnew < 65*365.25, "y","n"))
odk$i022c <- ifelse(is.na(odk$ageindaysnew),".", ifelse(odk$ageindaysnew >= 15*365.25 & odk$ageindaysnew < 50*365.25, "y", "n"))
odk$i022d <- ifelse(is.na(odk$ageindaysnew),".", ifelse(odk$ageindaysnew >= 5*365.25 & odk$ageindaysnew < 15*365.25, "y", "n"))
odk$i022e <- ifelse(is.na(odk$ageindaysnew),".", ifelse(odk$ageindaysnew >= 1*365.25 & odk$ageindaysnew < 5*365.25, "y", "n"))
odk$i022f <- ifelse(is.na(odk$ageindaysnew),".", ifelse(odk$ageindaysnew >= 28 & odk$ageindaysnew < 365.25, "y", "n"))
odk$i022g <- ifelse(is.na(odk$ageindaysnew),".", ifelse(odk$ageindaysnew < 28, "y", "n"))
odk$i022h <- ifelse(is.na(odk$ageindaysnew),".", ifelse(odk$ageindaysnew < 1, "y", "n"))
odk$i022i <- ifelse(is.na(odk$ageindaysnew),".", ifelse(odk$ageindaysnew %in% c(1:2), "y", "n"))
odk$i022j <- ifelse(is.na(odk$ageindaysnew),".", ifelse(odk$ageindaysnew %in% c(3:7), "y", "n"))
odk$i022k <- ifelse(is.na(odk$ageindaysnew),".", ifelse(odk$ageindaysnew %in% c(8:27), "y", "n"))
odk$i022l <- ifelse(is.na(odk$ageindaysnew),".", ifelse(odk$id10019b == "y" & odk$ageindaysnew >= 12*365.25 & odk$ageindaysnew < 20*365.25, "y", "n"))
odk$i022m <- ifelse(is.na(odk$ageindaysnew),".", ifelse(odk$id10019b == "y" & odk$ageindaysnew >= 20*365.25 & odk$ageindaysnew < 35*365.25, "y", "n"))
odk$i022n <- ifelse(is.na(odk$ageindaysnew),".", ifelse(odk$id10019b == "y" & odk$ageindaysnew >= 35*365.25 & odk$ageindaysnew < 49*365.25, "y", "n"))
# CrossVA starts here
odkNames <- tolower(names(odk))
whoNames <- c("Id10004", "Id10004", "Id10019", "Id10019",
"Id10022", "Id10022", "Id10022", "Id10022", "Id10022",
"Id10022", "Id10022", "Id10022", "Id10022", "Id10022",
"Id10022", "Id10022", "Id10022", "Id10022", "Id10059",
"Id10077", "Id10079", "Id10082", "Id10083", "Id10084",
"Id10085", "Id10086", "Id10087", "Id10089", "Id10090",
"Id10091", "Id10092", "Id10093", "Id10094", "Id10095",
"Id10096", "Id10098", "Id10099", "Id10100", "Id10104",
"Id10105", "Id10106", "Id10107", "Id10108", "Id10109",
"Id10110", "Id10111", "Id10112", "Id10113", "Id10114",
"Id10115", "Id10116", "Id10120", "Id10120", "Id10123",
"Id10125", "Id10127", "Id10128", "Id10129", "Id10130",
"Id10131", "Id10132", "Id10133", "Id10134", "Id10135",
"Id10136", "Id10137", "Id10138", "Id10139", "Id10140",
"Id10141", "Id10142", "Id10143", "Id10144", "Id10147",
"Id10148", "Id10148", "Id10148", "Id10149", "Id10150",
"Id10151", "Id10152", "Id10153", "Id10154", "Id10154",
"Id10155", "Id10156", "Id10157", "Id10158", "Id10159",
"Id10161", "Id10165", "Id10166", "Id10167", "Id10167",
"Id10168", "Id10169", "Id10169", "Id10170", "Id10171",
"Id10172", "Id10173", "Id10174", "Id10175", "Id10176",
"Id10178", "Id10181", "Id10182", "Id10182", "Id10182",
"Id10183", "Id10184_units", "Id10185", "Id10186", "Id10187",
"Id10188", "Id10189", "Id10190_units", "Id10191", "Id10192",
"Id10193", "Id10194", "Id10195", "Id10197", "Id10197",
"Id10199", "Id10199", "Id10200", "Id10201", "Id10201",
"Id10203", "Id10204", "Id10205", "Id10205", "Id10207",
"Id10208", "Id10209", "Id10209", "Id10210", "Id10211",
"Id10212", "Id10213", "Id10214", "Id10215", "Id10216",
"Id10217", "Id10218", "Id10219", "Id10220", "Id10221",
"Id10221", "Id10222", "Id10223", "Id10224", "Id10225",
"Id10226", "Id10227", "Id10228", "Id10229", "Id10230",
"Id10231", "Id10232", "Id10233", "Id10234", "Id10234",
"Id10235", "Id10235", "Id10235", "Id10235", "Id10236",
"Id10237", "Id10238", "Id10239", "Id10240", "Id10241",
"Id10242", "Id10243", "Id10244", "Id10245", "Id10246",
"Id10247", "Id10248", "Id10249", "Id10250", "Id10251",
"Id10252", "Id10253", "Id10254", "Id10255", "Id10256",
"Id10257", "Id10258", "Id10259", "Id10260", "Id10260",
"Id10260", "Id10260", "Id10260", "Id10260", "Id10260",
"Id10261", "Id10262", "Id10263", "Id10263", "Id10264",
"Id10265", "Id10266", "Id10267", "Id10268", "Id10269",
"Id10270", "Id10271", "Id10272", "Id10273", "Id10274",
"Id10275", "Id10276", "Id10277", "Id10278", "Id10279",
"Id10281", "Id10282", "Id10283", "Id10284", "Id10285",
"Id10286", "Id10287", "Id10288", "Id10289", "Id10290",
"Id10294", "Id10295", "Id10296", "Id10297", "Id10298",
"Id10299", "Id10300", "Id10301", "Id10302", "Id10303",
"Id10304", "Id10305", "Id10306", "Id10309", "Id10310",
"Id10312", "Id10313", "Id10314", "Id10315", "Id10316",
"Id10317", "Id10318", "Id10319", "Id10319", "Id10320",
"Id10321", "Id10322", "Id10323", "Id10324", "Id10325",
"Id10326", "Id10327", "Id10328", "Id10329", "Id10330",
"Id10331", "Id10332", "Id10333", "Id10334", "Id10335",
"Id10336", "Id10337", "Id10337", "Id10337", "Id10338",
"Id10340", "Id10342", "Id10343", "Id10344", "Id10347",
"Id10354", "Id10355", "Id10356", "Id10357", "Id10358",
"Id10360", "Id10360", "Id10360", "Id10361", "Id10362",
"Id10363", "Id10364", "Id10365", "Id10367", "Id10367",
"Id10367", "Id10368", "Id10369", "Id10370", "Id10371",
"Id10372", "Id10373", "Id10376", "Id10377", "Id10382",
"Id10383", "Id10384", "Id10385", "Id10387", "Id10388",
"Id10389", "Id10391", "Id10393", "Id10394", "Id10394",
"Id10395", "Id10396", "Id10397", "Id10398", "Id10399",
"Id10400", "Id10401", "Id10402", "Id10403", "Id10404",
"Id10405", "Id10406", "Id10408", "Id10411", "Id10412",
"Id10413", "Id10414", "Id10415", "Id10418", "Id10419",
"Id10420", "Id10421", "Id10422", "Id10423", "Id10424",
"Id10425", "Id10426", "Id10427", "Id10428", "Id10450",
"Id10451", "Id10452", "Id10453", "Id10454", "Id10455",
"Id10456", "Id10457", "Id10458", "Id10459")
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)
tmpMat <- matrix(sapply(whoNames, stri_endswith_fixed, str = odkNames),
nrow = length(odkNames))
indexData <- apply(tmpMat, 2, which)
warnZeroMatch <- which(sapply(indexData, length) == 0)
if (length(warnZeroMatch) > 0) {
message(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
indexNA <- NULL
flagNonNumeric <- function(x) {
return(tryCatch(as.numeric(x), error = function(c) -9999,
warning = function(c) -9999))
}
qYesNo <- c(20:40, 42, 44:51, 54:74, 78, 81:82, 85:89, 92,
95, 98:100, 102:103, 106, 112:116, 118:122, 127, 131,
134:135, 138, 140, 142, 145:148, 151:160, 162, 169:180,
182, 184:192, 200, 204:205, 207:213, 215:223, 225:238,
240:242, 244:251, 254:265, 267:270, 274:280, 282, 288:292,
296:303, 305:306, 308:312, 315:330, 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]
message(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)] <- "."
indexData <- which(stri_endswith_fixed(odkNames, whoNames[1]))
iv5Out[tolower(odk[, indexData]) == "wet" | tolower(odk[,
indexData]) == "wet season", 1] <- "y"
iv5Out[tolower(odk[, indexData]) == "dry" | tolower(odk[,
indexData]) == "dry season", 1] <- "n"
iv5Out[tolower(odk[, indexData]) == "wet" | tolower(odk[,
indexData]) == "wet season", 2] <- "n"
iv5Out[tolower(odk[, indexData]) == "dry" | tolower(odk[,
indexData]) == "dry season", 2] <- "y"
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"
indexData1y <- which(stri_endswith_fixed(odkNames, "ageinyears2"))
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])
indexData_isNeonatal <- which(stri_endswith_fixed(odkNames,
"isneonatal"))
indexData_isChild <- which(stri_endswith_fixed(odkNames,
"ischild"))
indexData_isAdult <- which(stri_endswith_fixed(odkNames,
"isadult"))
iv5Out[odk[, indexData1y] >= 65, 5] <- "y"
iv5Out[is.na(odk[, indexData1y]) & odk[, indexData2] == "adult" &
odk[, indexData3] >= 65, 5] <- "y"
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"
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"
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"
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"
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"
iv5Out[odk[, indexData1d] < 28, 11] <- "y"
iv5Out[is.na(odk[, indexData1d]) & odk[, indexData2] == "neonate",
11] <- "y"
iv5Out[odk[, indexData1d] < 1, 12] <- "y"
ageNeonate <- odk[, indexData5d]
iv5Out[odk[, indexData2] == "neonate" & !is.na(odk[, indexData5d]) &
ageNeonate < 1, 12] <- "y"
iv5Out[odk[, indexData1d] >= 1 & odk[, indexData1d] <= 2,
13] <- "y"
iv5Out[odk[, indexData2] == "neonate" & !is.na(odk[, indexData5d]) &
ageNeonate < 2 & ageNeonate >= 1, 13] <- "y"
iv5Out[odk[, indexData1d] > 2 & odk[, indexData1d] < 7, 14] <- "y"
iv5Out[odk[, indexData2] == "neonate" & !is.na(odk[, indexData5d]) &
ageNeonate < 7 & ageNeonate >= 2, 14] <- "y"
iv5Out[odk[, indexData1d] >= 7 & odk[, indexData1d] < 28,
15] <- "y"
iv5Out[odk[, indexData2] == "neonate" & !is.na(odk[, indexData5d]) &
ageNeonate < 28 & ageNeonate >= 7, 15] <- "y"
i022h_k_has_yes <- apply(iv5Out, 1, function(x) {
any(x[12:15] == "y")
})
iv5Out[i022h_k_has_yes, 11] <- "y"
neoIndexData6 <- iv5Out[, 12:15] != "y"
neoIndexData7 <- rowSums(iv5Out[, 12:15] == "y", na.rm = TRUE)
iv5Out[neoIndexData7 == 1, 12:15][neoIndexData6[neoIndexData7 ==
1, ]] <- "n"
indexData6 <- iv5Out[, 5:11] != "y"
indexData7 <- rowSums(iv5Out[, 5:11] == "y", na.rm = TRUE)
iv5Out[indexData7 == 1, 5:11][indexData6[indexData7 == 1,
]] <- "n"
indexData8 <- iv5Out[, 11] == "n"
iv5Out[indexData8, 12:15] <- "n"
iv5Out[, 16] <- ifelse(odk[, indexData_sex] == "female" &
odk[, indexData1y] < 20 & odk[, indexData1y] >= 12, "y",
".")
iv5Out[odk[, indexData_sex] == "female" & is.na(odk[, indexData1y]) &
odk[, indexData2] == "adult" & odk[, indexData3] < 20 &
odk[, indexData3] >= 12, 16] <- "y"
iv5Out[odk[, indexData_isNeonatal] == 1, 16] <- "n"
iv5Out[odk[, indexData_isChild] == 1, 16] <- "n"
iv5Out[odk[, indexData_sex] == "male", 16] <- "n"
iv5Out[odk[, indexData1y] < 12, 16] <- "n"
iv5Out[odk[, indexData1y] > 19, 16] <- "n"
iv5Out[, 17] <- ifelse(odk[, indexData_sex] == "female" &
odk[, indexData1y] < 35 & odk[, indexData1y] >= 20, "y",
".")
iv5Out[odk[, indexData_sex] == "female" & is.na(odk[, indexData1y]) &
odk[, indexData2] == "adult" & odk[, indexData3] < 35 &
odk[, indexData3] >= 20, 17] <- "y"
iv5Out[odk[, indexData_isNeonatal] == 1, 17] <- "n"
iv5Out[odk[, indexData_isChild] == 1, 17] <- "n"
iv5Out[odk[, indexData_sex] == "male", 17] <- "n"
iv5Out[odk[, indexData1y] < 20, 17] <- "n"
iv5Out[odk[, indexData1y] > 34, 17] <- "n"
iv5Out[, 18] <- ifelse(odk[, indexData_sex] == "female" &
odk[, indexData1y] < 50 & odk[, indexData1y] >= 35, "y",
".")
iv5Out[odk[, indexData_sex] == "female" & is.na(odk[, indexData1y]) &
odk[, indexData2] == "adult" & odk[, indexData3] < 50 &
odk[, indexData3] >= 35, 18] <- "y"
iv5Out[odk[, indexData_isNeonatal] == 1, 18] <- "n"
iv5Out[odk[, indexData_isChild] == 1, 18] <- "n"
iv5Out[odk[, indexData_sex] == "male", 18] <- "n"
iv5Out[odk[, indexData1y] < 35, 18] <- "n"
iv5Out[odk[, indexData1y] > 49, 18] <- "n"
indexData <- which(stri_endswith_fixed(odkNames, whoNames[19]))
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] == "male", 19] <- "n"
indexData <- which(stri_endswith_fixed(odkNames, whoNames[41]))
iv5Out[odk[, indexData] > 5, 41] <- "y"
iv5Out[odk[, indexData] <= 5, 41] <- "n"
iv5Out[odk[, indexData] == 99, 41] <- "n"
iv5Out[odk[, indexData] == 88, 41] <- "n"
indexData <- which(stri_endswith_fixed(odkNames, whoNames[43]))
iv5Out[odk[, indexData] > 24, 43] <- "y"
iv5Out[odk[, indexData] <= 24, 43] <- "n"
iv5Out[odk[, indexData] == 99, 43] <- "."
iv5Out[odk[, indexData] == 88, 43] <- "."
indexDatad <- which(stri_endswith_fixed(odkNames, "id10120"))
iv5Out[odk[, indexDatad] < 21, 52] <- "y"
iv5Out[odk[, indexDatad] >= 21, 52] <- "n"
iv5Out[odk[, indexDatad] == 99, 52] <- "."
iv5Out[odk[, indexDatad] == 88, 52] <- "."
iv5Out[odk[, indexDatad] >= 21, 53] <- "y"
iv5Out[odk[, indexDatad] < 21, 53] <- "n"
indexData <- which(stri_endswith_fixed(odkNames, whoNames[74]))
indexData_days <- which(stri_endswith_fixed(odkNames, whoNames[75]))
iv5Out[odk[, indexData] == "yes" & odk[, indexData_days] <
7, 75] <- "y"
iv5Out[odk[, indexData] == "yes" & odk[, indexData_days] >=
7, 75] <- "n"
iv5Out[odk[, indexData] == "yes" & odk[, indexData_days] ==
99, 75] <- "."
iv5Out[odk[, indexData] == "yes" & odk[, indexData_days] ==
88, 75] <- "."
iv5Out[odk[, indexData] == "no", 75] <- "n"
iv5Out[odk[, indexData_days] >= 7 & odk[, indexData_days] <
14, 76] <- "y"
iv5Out[odk[, indexData_days] < 7, 76] <- "n"
iv5Out[odk[, indexData_days] >= 14, 76] <- "n"
iv5Out[odk[, indexData_days] == 99, 76] <- "."
iv5Out[odk[, indexData_days] == 88, 76] <- "."
iv5Out[odk[, indexData] == "no", 76] <- "n"
iv5Out[odk[, indexData_days] >= 14, 77] <- "y"
iv5Out[odk[, indexData_days] < 14, 77] <- "n"
iv5Out[odk[, indexData] == "no", 77] <- "n"
iv5Out[odk[, indexData] == "no", 78] <- "n"
indexData_sev <- which(stri_endswith_fixed(odkNames, whoNames[79]))
iv5Out[tolower(odk[, indexData_sev]) == "severe", 79] <- "y"
iv5Out[tolower(odk[, indexData_sev]) == "mild", 79] <- "n"
iv5Out[tolower(odk[, indexData_sev]) == "moderate", 79] <- "n"
iv5Out[odk[, indexData] == "no", 79] <- "n"
indexData_con <- which(stri_endswith_fixed(odkNames, whoNames[80]))
iv5Out[tolower(odk[, indexData_con]) == "continuous", 80] <- "y"
iv5Out[tolower(odk[, indexData_con]) == "nightly", 80] <- "n"
iv5Out[tolower(odk[, indexData_con]) == "on_and_off", 80] <- "n"
iv5Out[odk[, indexData] == "no", 80] <- "n"
indexData <- which(stri_endswith_fixed(odkNames, whoNames[82]))
indexData_days <- which(stri_endswith_fixed(odkNames, whoNames[83]))
iv5Out[odk[, indexData] == "yes" & odk[, indexData_days[1]] <
21, 83] <- "y"
iv5Out[odk[, indexData] == "yes" & odk[, indexData_days[1]] >=
21, 83] <- "n"
iv5Out[odk[, indexData] == "no", 83] <- "n"
iv5Out[odk[, indexData] == "yes" & odk[, indexData_days[1]] >=
21, 84] <- "y"
iv5Out[odk[, indexData] == "yes" & odk[, indexData_days[1]] <
21, 84] <- "n"
iv5Out[odk[, indexData] == "no", 84] <- "n"
indexDatad <- which(stri_endswith_fixed(odkNames, whoNames[90]))
indexDatam <- which(stri_endswith_fixed(odkNames, "id10162"))
indexDatay <- which(stri_endswith_fixed(odkNames, "id10163"))
iv5Out[odk[, indexDatad] >= 3, 90] <- "y"
iv5Out[odk[, indexDatad] < 3, 90] <- "n"
iv5Out[odk[, indexDatam] >= 1, 90] <- "y"
iv5Out[odk[, indexDatay] >= 1, 90] <- "y"
indexData <- which(stri_endswith_fixed(odkNames, whoNames[91]))
iv5Out[tolower(odk[, indexData]) == "continuous", 91] <- "y"
iv5Out[tolower(odk[, indexData]) == "on_and_off", 91] <- "n"
indexData <- which(stri_endswith_fixed(odkNames, whoNames[93]))
iv5Out[odk[, indexData[1]] < 14, 93] <- "y"
iv5Out[odk[, indexData[1]] >= 14, 93] <- "n"
iv5Out[odk[, indexData[1]] == 99, 93] <- "."
iv5Out[odk[, indexData[1]] == 88, 93] <- "."
iv5Out[odk[, indexData[1]] >= 14, 94] <- "y"
iv5Out[odk[, indexData[1]] < 14, 94] <- "n"
iv5Out[odk[, indexData[1]] == 99, 94] <- "."
iv5Out[odk[, indexData[1]] == 88, 94] <- "."
indexData <- which(stri_endswith_fixed(odkNames, whoNames[96]))
iv5Out[odk[, indexData[1]] < 14, 96] <- "y"
iv5Out[odk[, indexData[1]] >= 14, 96] <- "n"
iv5Out[odk[, indexData[1]] == 99, 96] <- "."
iv5Out[odk[, indexData[1]] == 88, 96] <- "."
iv5Out[odk[, indexData[1]] >= 14, 97] <- "y"
iv5Out[odk[, indexData[1]] < 14, 97] <- "n"
iv5Out[odk[, indexData[1]] == 99, 97] <- "."
iv5Out[odk[, indexData[1]] == 88, 97] <- "."
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"
indexData <- which(stri_endswith_fixed(odkNames, whoNames[104]))
iv5Out[odk[, indexData] >= 3, 104] <- "y"
iv5Out[odk[, indexData] < 3, 104] <- "n"
iv5Out[odk[, indexData] == 99, 104] <- "."
iv5Out[odk[, indexData] == 88, 104] <- "."
indexData_unit <- which(stri_endswith_fixed(odkNames, "id10178_unit"))
indexDatam <- which(stri_endswith_fixed(odkNames, "id10178"))
indexDatah <- which(stri_endswith_fixed(odkNames, "id10179"))
indexDatad <- which(stri_endswith_fixed(odkNames, "id10179_1"))
iv5Out[tolower(odk[, indexData_unit]) == "minutes" & odk[,
indexDatam] >= 30, 105] <- "y"
iv5Out[tolower(odk[, indexData_unit]) == "hours" & odk[,
indexDatah] >= 0.5, 105] <- "y"
iv5Out[tolower(odk[, indexData_unit]) == "days" & odk[, indexDatad] >=
1, 105] <- "y"
iv5Out[tolower(odk[, indexData_unit]) == "minutes" & odk[,
indexDatam] < 30, 105] <- "n"
iv5Out[tolower(odk[, indexData_unit]) == "hours" & odk[,
indexDatah] < 0.5, 105] <- "n"
indexData <- which(stri_endswith_fixed(odkNames, whoNames[107]))
iv5Out[odk[, indexData] < 14, 107] <- "y"
iv5Out[odk[, indexData] >= 14, 107] <- "n"
iv5Out[odk[, indexData] < 28 & odk[, indexData] >= 14, 108] <- "y"
iv5Out[odk[, indexData] < 14, 108] <- "n"
iv5Out[odk[, indexData] >= 28, 108] <- "n"
iv5Out[odk[, indexData] >= 28, 109] <- "y"
iv5Out[odk[, indexData] < 28, 109] <- "n"
indexData <- which(stri_endswith_fixed(odkNames, whoNames[110]))
iv5Out[odk[, indexData] >= 4 & odk[, indexData] < 999, 110] <- "y"
iv5Out[odk[, indexData] < 4, 110] <- "n"
iv5Out[odk[, indexData] == 99, 110] <- "."
iv5Out[odk[, indexData] == 88, 110] <- "."
indexData181 <- which(stri_endswith_fixed(odkNames, "id10181"))
indexDataIsNeonatal <- which(stri_endswith_fixed(odkNames,
"isneonatal"))
indexDataIsChild <- which(stri_endswith_fixed(odkNames, "ischild"))
indexData184_a <- which(stri_endswith_fixed(odkNames, "id10184_a"))
indexData184_units <- which(stri_endswith_fixed(odkNames,
"id10184_units"))
indexData184_b <- which(stri_endswith_fixed(odkNames, "id10184_b"))
indexData184_c <- which(stri_endswith_fixed(odkNames, "id10184_c"))
iv5Out[odk[, indexData184_a] >= 3 & tolower(odk[, indexData181]) ==
"yes" & tolower(odk[, indexDataIsNeonatal]) == "yes",
111] <- "y"
iv5Out[odk[, indexData184_a] < 3 & tolower(odk[, indexData181]) ==
"yes" & tolower(odk[, indexDataIsNeonatal]) == "yes",
111] <- "n"
iv5Out[odk[, indexData184_a] == 99, 111] <- "."
iv5Out[odk[, indexData184_a] == 88, 111] <- "."
iv5Out[odk[, indexData184_b] >= 3 & tolower(odk[, indexData184_units]) ==
"days", 111] <- "y"
iv5Out[odk[, indexData184_b] < 3 & tolower(odk[, indexData184_units]) ==
"days", 111] <- "n"
iv5Out[odk[, indexData184_c] >= 1 & tolower(odk[, indexData184_units]) ==
"months", 111] <- "y"
indexData190_units <- which(stri_endswith_fixed(odkNames,
"id10190_units"))
indexData190_a <- which(stri_endswith_fixed(odkNames, "id10190_a"))
indexData190_b <- which(stri_endswith_fixed(odkNames, "id10190_b"))
iv5Out[odk[, indexData190_a] >= 3 & tolower(odk[, indexData190_units]) ==
"days", 117] <- "y"
iv5Out[odk[, indexData190_a] < 3 & tolower(odk[, indexData190_units]) ==
"days", 117] <- "n"
iv5Out[odk[, indexData190_b] >= 1 & tolower(odk[, indexData190_units]) ==
"months", 117] <- "y"
indexData <- which(stri_endswith_fixed(odkNames, "id10195"))
indexDatad <- which(stri_endswith_fixed(odkNames, "id10197"))
iv5Out[tolower(odk[, indexData]) == "yes" & odk[, indexDatad] <
14, 123] <- "y"
iv5Out[tolower(odk[, indexData]) == "yes" & odk[, indexDatad] >=
14, 123] <- "n"
iv5Out[tolower(odk[, indexData]) == "no", 123] <- "n"
iv5Out[tolower(odk[, indexData]) == "yes" & odk[, indexDatad] >=
14, 124] <- "y"
iv5Out[tolower(odk[, indexData]) == "yes" & odk[, indexDatad] <
14, 124] <- "n"
iv5Out[tolower(odk[, indexData]) == "no", 124] <- "n"
indexData <- which(stri_endswith_fixed(odkNames, "id10194"))
indexData_uplow <- which(stri_endswith_fixed(odkNames, whoNames[125]))
iv5Out[tolower(odk[, indexData_uplow]) == "upper_abdomen",
125] <- "y"
iv5Out[tolower(odk[, indexData_uplow]) == "upper_lower_abdomen",
125] <- "y"
iv5Out[tolower(odk[, indexData_uplow]) == "lower_abdomen",
125] <- "n"
iv5Out[tolower(odk[, indexData_uplow]) == "upper_abdomen",
126] <- "n"
iv5Out[tolower(odk[, indexData_uplow]) == "upper_lower_abdomen",
126] <- "y"
iv5Out[tolower(odk[, indexData_uplow]) == "lower_abdomen",
126] <- "y"
indexData <- which(stri_endswith_fixed(odkNames, "id10200"))
indexDatad <- which(stri_endswith_fixed(odkNames, whoNames[128]))
indexDatam <- which(stri_endswith_fixed(odkNames, "id10202"))
iv5Out[tolower(odk[, indexData]) == "yes" & odk[, indexDatad] <
14 & odk[, indexDatam] == 0, 128] <- "y"
iv5Out[tolower(odk[, indexData]) == "yes" & odk[, indexDatad] <
14 & is.na(odk[, indexDatam]), 128] <- "y"
iv5Out[tolower(odk[, indexData]) == "yes" & odk[, indexDatad] >=
14 & odk[, indexDatam] == 0, 128] <- "n"
iv5Out[tolower(odk[, indexData]) == "yes" & odk[, indexDatad] >=
14 & is.na(odk[, indexDatam]), 128] <- "n"
iv5Out[tolower(odk[, indexData]) == "yes" & odk[, indexDatam] >=
1, 128] <- "n"
iv5Out[tolower(odk[, indexData]) == "no", 128] <- "n"
iv5Out[tolower(odk[, indexData]) == "yes" & odk[, indexDatam] >=
1, 129] <- "y"
iv5Out[tolower(odk[, indexData]) == "yes" & odk[, indexDatad] >=
14 & odk[, indexDatam] == 0, 129] <- "y"
iv5Out[tolower(odk[, indexData]) == "yes" & odk[, indexDatad] >=
14 & is.na(odk[, indexDatam]), 129] <- "y"
iv5Out[tolower(odk[, indexData]) == "yes" & odk[, indexDatad] <
14 & odk[, indexDatam] == 0, 129] <- "n"
iv5Out[tolower(odk[, indexData]) == "yes" & odk[, indexDatad] <
14 & is.na(odk[, indexDatam]), 129] <- "n"
iv5Out[tolower(odk[, indexData]) == "no", 129] <- "n"
indexData <- which(stri_endswith_fixed(odkNames, whoNames[130]))
iv5Out[tolower(odk[, indexData]) == "rapidly", 130] <- "y"
iv5Out[tolower(odk[, indexData]) == "slowly", 130] <- "n"
indexData <- which(stri_endswith_fixed(odkNames, "id10204"))
indexDatad <- which(stri_endswith_fixed(odkNames, whoNames[132]))
indexDatam <- which(stri_endswith_fixed(odkNames, "id10206"))
iv5Out[tolower(odk[, indexData]) == "yes" & odk[, indexDatad] <
14 & odk[, indexDatam] == 0, 132] <- "y"
iv5Out[tolower(odk[, indexData]) == "yes" & odk[, indexDatad] <
14 & is.na(odk[, indexDatam]), 132] <- "y"
iv5Out[tolower(odk[, indexData]) == "yes" & odk[, indexDatad] >=
14 & odk[, indexDatam] == 0, 132] <- "n"
iv5Out[tolower(odk[, indexData]) == "yes" & odk[, indexDatad] >=
14 & is.na(odk[, indexDatam]), 132] <- "n"
iv5Out[tolower(odk[, indexData]) == "yes" & odk[, indexDatam] >=
1, 132] <- "n"
iv5Out[tolower(odk[, indexData]) == "no", 132] <- "n"
iv5Out[tolower(odk[, indexData]) == "yes" & odk[, indexDatad] <
14 & odk[, indexDatam] == 0, 133] <- "n"
iv5Out[tolower(odk[, indexData]) == "yes" & odk[, indexDatad] <
14 & is.na(odk[, indexDatam]), 133] <- "n"
iv5Out[tolower(odk[, indexData]) == "yes" & odk[, indexDatad] >=
14 & odk[, indexDatam] == 0, 133] <- "y"
iv5Out[tolower(odk[, indexData]) == "yes" & odk[, indexDatad] >=
14 & is.na(odk[, indexDatam]), 133] <- "y"
iv5Out[tolower(odk[, indexData]) == "yes" & odk[, indexDatam] >=
1, 133] <- "y"
iv5Out[tolower(odk[, indexData]) == "no", 133] <- "n"
indexData <- which(stri_endswith_fixed(odkNames, "id10208"))
indexDatad <- which(stri_endswith_fixed(odkNames, whoNames[136]))
iv5Out[tolower(odk[, indexData]) == "yes" & odk[, indexDatad] <
7, 136] <- "y"
iv5Out[tolower(odk[, indexData]) == "yes" & odk[, indexDatad] >=
7, 136] <- "n"
iv5Out[tolower(odk[, indexData]) == "no", 136] <- "n"
iv5Out[tolower(odk[, indexData]) == "yes" & odk[, indexDatad] >=
7, 137] <- "y"
iv5Out[tolower(odk[, indexData]) == "yes" & odk[, indexDatad] <
7, 137] <- "n"
iv5Out[tolower(odk[, indexData]) == "no", 137] <- "n"
indexData <- which(stri_endswith_fixed(odkNames, "id10210"))
indexDatad <- which(stri_endswith_fixed(odkNames, whoNames[139]))
iv5Out[tolower(odk[, indexData]) == "yes" & odk[, indexDatad] >=
7, 139] <- "y"
iv5Out[tolower(odk[, indexData]) == "yes" & odk[, indexDatad] <
7, 139] <- "n"
iv5Out[tolower(odk[, indexData]) == "no", 139] <- "n"
indexData <- which(stri_endswith_fixed(odkNames, whoNames[140]))
indexDatad <- which(stri_endswith_fixed(odkNames, whoNames[141]))
iv5Out[odk[, indexData] == "yes" & odk[, indexDatad] >= 3,
141] <- "y"
iv5Out[odk[, indexData] == "yes" & odk[, indexDatad] < 3,
141] <- "n"
iv5Out[odk[, indexData] == "no", 141] <- "n"
indexData_uncon <- which(stri_endswith_fixed(odkNames, whoNames[142]))
indexData_uncon24 <- which(stri_endswith_fixed(odkNames,
whoNames[143]))
iv5Out[odk[, indexData_uncon] == "yes" & odk[, indexData_uncon24] ==
"yes", 143] <- "y"
iv5Out[odk[, indexData_uncon] == "yes" & odk[, indexData_uncon24] ==
"no", 143] <- "n"
iv5Out[odk[, indexData_uncon] == "no", 143] <- "n"
indexData <- which(stri_endswith_fixed(odkNames, whoNames[143]))
indexData_hours <- which(stri_endswith_fixed(odkNames, whoNames[144]))
iv5Out[odk[, indexData] == "yes", 144] <- "y"
iv5Out[odk[, indexData] == "no" & odk[, indexData_hours] >=
6, 144] <- "y"
iv5Out[odk[, indexData] == "no" & odk[, indexData_hours] <
6, 144] <- "n"
iv5Out[odk[, indexData_uncon] == "no", 144] <- "n"
indexData <- which(stri_endswith_fixed(odkNames, whoNames[147]))
indexData_min <- which(stri_endswith_fixed(odkNames, whoNames[149]))
iv5Out[odk[, indexData] == "yes" & odk[, indexData_min] <
10, 149] <- "y"
iv5Out[odk[, indexData] == "yes" & odk[, indexData_min] >=
10, 149] <- "n"
iv5Out[odk[, indexData] == "yes" & odk[, indexData_min] ==
99, 149] <- "."
iv5Out[odk[, indexData] == "yes" & odk[, indexData_min] ==
88, 149] <- "."
iv5Out[odk[, indexData] == "yes" & odk[, indexData_min] <
10, 150] <- "n"
iv5Out[odk[, indexData] == "yes" & odk[, indexData_min] >=
10, 150] <- "y"
indexData <- which(stri_endswith_fixed(odkNames, whoNames[161]))
iv5Out[odk[, indexData] >= 14, 161] <- "y"
iv5Out[odk[, indexData] < 14, 161] <- "n"
indexData <- which(stri_endswith_fixed(odkNames, whoNames[163]))
iv5Out[odk[, indexData] < 7, 163] <- "y"
iv5Out[odk[, indexData] >= 7, 163] <- "n"
iv5Out[odk[, indexData] == 99, 163] <- "."
iv5Out[odk[, indexData] == 88, 163] <- "."
iv5Out[odk[, indexData] >= 7, 164] <- "y"
iv5Out[odk[, indexData] < 7, 164] <- "n"
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] <- "."
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] <- "."
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] <- "."
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] <- "."
indexData <- which(stri_endswith_fixed(odkNames, whoNames[181]))
iv5Out[odk[, indexData] >= 7, 181] <- "y"
iv5Out[odk[, indexData] < 7, 181] <- "n"
indexData <- which(stri_endswith_fixed(odkNames, whoNames[183]))
iv5Out[odk[, indexData] >= 3, 183] <- "y"
iv5Out[odk[, indexData] < 3, 183] <- "n"
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] <- "."
iv5Out[tolower(odk[, indexData]) == "left_side", 194] <- "y"
iv5Out[tolower(odk[, indexData]) != "left_side", 194] <- "n"
iv5Out[tolower(odk[, indexData]) == "", 194] <- "."
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] <- "."
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] <- "."
iv5Out[tolower(odk[, indexData]) == "one_leg_only", 197] <- "y"
iv5Out[tolower(odk[, indexData]) != "one_leg_only", 197] <- "n"
iv5Out[tolower(odk[, indexData]) == "", 197] <- "."
iv5Out[tolower(odk[, indexData]) == "one_arm_only", 198] <- "y"
iv5Out[tolower(odk[, indexData]) != "one_arm_only", 198] <- "n"
iv5Out[tolower(odk[, indexData]) == "", 198] <- "."
iv5Out[tolower(odk[, indexData]) == "whole_body", 199] <- "y"
iv5Out[tolower(odk[, indexData]) != "whole_body", 199] <- "n"
iv5Out[tolower(odk[, indexData]) == "", 199] <- "."
indexData <- which(stri_endswith_fixed(odkNames, whoNames[201]))
iv5Out[odk[, indexData] >= 7, 201] <- "y"
iv5Out[odk[, indexData] < 7, 201] <- "n"
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"
iv5Out[tolower(odk[, indexData]) == "solids", 203] <- "n"
iv5Out[tolower(odk[, indexData]) == "both", 203] <- "y"
iv5Out[tolower(odk[, indexData]) == "liquids", 203] <- "y"
indexData <- which(stri_endswith_fixed(odkNames, whoNames[206]))
iv5Out[odk[, indexData] >= 21, 206] <- "y"
iv5Out[odk[, indexData] < 21, 206] <- "n"
indexData <- which(stri_endswith_fixed(odkNames, whoNames[214]))
iv5Out[odk[, indexData[1]] >= 2, 214] <- "y"
iv5Out[odk[, indexData[1]] < 2, 214] <- "n"
iv5Out[odk[, indexData[1]] == 99, 214] <- "."
iv5Out[odk[, indexData[1]] == 88, 214] <- "."
indexData <- which(stri_endswith_fixed(odkNames, whoNames[224]))
iv5Out[odk[, indexData] > 3, 224] <- "y"
iv5Out[odk[, indexData] <= 3, 224] <- "n"
iv5Out[odk[, indexData] == 99, 224] <- "."
iv5Out[odk[, indexData] == 88, 224] <- "."
indexData <- which(stri_endswith_fixed(odkNames, whoNames[239]))
iv5Out[odk[, indexData] >= 4, 239] <- "y"
iv5Out[odk[, indexData] < 4, 239] <- "n"
iv5Out[odk[, indexData] == 99, 239] <- "."
iv5Out[odk[, indexData] == 88, 239] <- "."
indexData <- which(stri_endswith_fixed(odkNames, whoNames[243]))
iv5Out[odk[, indexData] < 6, 243] <- "y"
iv5Out[odk[, indexData] >= 6, 243] <- "n"
iv5Out[odk[, indexData] == 99, 243] <- "."
iv5Out[odk[, indexData] == 88, 243] <- "."
indexData <- which(stri_endswith_fixed(odkNames, whoNames[252]))
iv5Out[odk[, indexData] == 0, 252] <- "y"
iv5Out[odk[, indexData] > 0, 252] <- "n"
iv5Out[odk[, indexData] == 99, 252] <- "."
iv5Out[odk[, indexData] == 88, 252] <- "."
iv5Out[odk[, indexData] >= 4, 253] <- "y"
iv5Out[odk[, indexData] < 4, 253] <- "n"
indexData <- which(stri_endswith_fixed(odkNames, whoNames[266]))
iv5Out[odk[, indexData] > 24, 266] <- "y"
iv5Out[odk[, indexData] <= 24, 266] <- "n"
iv5Out[odk[, indexData] == 99, 266] <- "."
iv5Out[odk[, indexData] == 88, 266] <- "."
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"
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"
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"
indexData <- which(stri_endswith_fixed(odkNames, whoNames[281]))
iv5Out[tolower(odk[, indexData]) == "first", 281] <- "y"
iv5Out[tolower(odk[, indexData]) == "second_or_later", 281] <- "n"
indexData <- which(stri_endswith_fixed(odkNames, whoNames[283]))
iv5Out[tolower(odk[, indexData]) == "after_delivery", 283] <- "y"
iv5Out[tolower(odk[, indexData]) == "during_delivery", 283] <- "y"
indexDataM <- which(stri_endswith_fixed(odkNames, whoNames[284]))
indexDataD <- which(stri_endswith_fixed(odkNames, "id10359"))
nMonths <- odk[, indexDataM]
nDays <- odk[, indexDataD]
nMonths[is.na(odk[, indexDataM]) & !is.na(odk[, indexDataD])] <- 0
nDays[is.na(odk[, indexDataD]) & !is.na(odk[, indexDataM])] <- 0
naMonthsAndDays <- is.na(odk[, indexDataM]) & is.na(odk[,
indexDataD])
iv5Out[nMonths + nDays/30.4 <= 12 & !naMonthsAndDays, 284] <- "y"
iv5Out[nMonths + nDays/30.4 > 12 & !naMonthsAndDays, 284] <- "n"
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"
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"
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"
indexData <- which(stri_endswith_fixed(odkNames, whoNames[293]))
iv5Out[odk[, indexData] >= 9 & odk[, indexData] < 88, 293] <- "y"
iv5Out[odk[, indexData] < 9, 293] <- "n"
iv5Out[odk[, indexData] == 99, 293] <- "."
iv5Out[odk[, indexData] == 88, 293] <- "."
iv5Out[odk[, indexData] > 8 & odk[, indexData] < 88, 294] <- "n"
iv5Out[odk[, indexData] == 8, 294] <- "y"
iv5Out[odk[, indexData] < 8, 294] <- "n"
iv5Out[odk[, indexData] >= 8 & odk[, indexData] < 88, 295] <- "n"
iv5Out[odk[, indexData] < 8, 295] <- "y"
indexData <- which(stri_endswith_fixed(odkNames, whoNames[304]))
iv5Out[odk[, indexData] > 24, 304] <- "y"
iv5Out[odk[, indexData] <= 24, 304] <- "n"
iv5Out[odk[, indexData] == 99, 304] <- "."
iv5Out[odk[, indexData] == 88, 304] <- "."
indexData <- which(stri_endswith_fixed(odkNames, whoNames[307]))
iv5Out[tolower(odk[, indexData]) == "green_or_brown", 307] <- "y"
iv5Out[tolower(odk[, indexData]) == "clear", 307] <- "n"
iv5Out[tolower(odk[, indexData]) == "other", 307] <- "n"
indexData <- which(stri_endswith_fixed(odkNames, whoNames[313]))
iv5Out[odk[, indexData] == 0, 313] <- "y"
iv5Out[odk[, indexData] > 0, 313] <- "n"
iv5Out[odk[, indexData] == 99, 313] <- "."
iv5Out[odk[, indexData] == 88, 313] <- "."
iv5Out[odk[, indexData] >= 4, 314] <- "y"
iv5Out[odk[, indexData] < 4, 314] <- "n"
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"
indexData <- which(stri_endswith_fixed(odkNames, whoNames[332]))
iv5Out[odk[, indexData] >= 10, 332] <- "y"
iv5Out[odk[, indexData] < 10, 332] <- "n"
iv5Out[odk[, indexData] == 99, 332] <- "."
iv5Out[odk[, indexData] == 88, 332] <- "."
if (numNA > 0) {
warning("Found unexpected input values (coded as missing)",
call. = FALSE)
message("Unexpected values found in: ", sep = "\n")
message(paste(indexNA), sep = ", ")
message("\n")
}
numNA <- colSums(is.na(iv5Out))
indexNA <- which(numNA > 0)
if (length(indexNA) > 0) {
warning("NA's included in output", call. = FALSE)
message(paste("odk2openVA produced NA's in the following columns",
" (this may cause errors with openVA)", sep = ""),
sep = "\n")
message(paste(iv5Names[indexNA], " Probably associated with WHO column containing: ",
whoNames[indexNA], sep = ""), sep = "\n")
}
indexID <- which(stri_endswith_fixed(odkNames, id_col))
# indexID <- odkNames[4]
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)
}
colnames(iv5Out) <- c("ID", iv5Names)
# EAVA-specific variables
names(odk) <- tolower(colnames(odk))
# odk$ageatdeath <- NULL
# odk$ageatdeath <- odk$ageindays
# odk$ageatdeath <- ifelse(is.na(odk$ageatdeath) & !is.na(odk$age_neonate_minutes) & !is.na(odk$isneonatal), odk$age_neonate_minutes/(60*24), odk$ageatdeath)
# odk$ageatdeath <- ifelse(is.na(odk$ageatdeath) & !is.na(odk$age_neonate_hours) & !is.na(odk$isneonatal), odk$age_neonate_hours/(24), odk$ageatdeath)
# odk$ageatdeath <- ifelse(is.na(odk$ageatdeath) & !is.na(odk$age_neonate_days) & !is.na(odk$isneonatal), odk$age_neonate_days, odk$ageatdeath)
# odk$ageatdeath <- ifelse(is.na(odk$ageatdeath) & !is.na(odk$ageindaysneonate) & !is.na(odk$isneonatal), odk$ageindaysneonate, odk$ageatdeath)
# odk$ageatdeath <- ifelse(is.na(odk$ageatdeath) & !is.na(odk$age_child_months) & !is.na(odk$ischild), odk$age_child_months*30.4, odk$ageatdeath)
# odk$ageatdeath <- ifelse(is.na(odk$ageatdeath) & !is.na(odk$age_child_years) & !is.na(odk$ischild), odk$age_child_years*365.25, odk$ageatdeath)
# odk$ageatdeath <- ifelse(is.na(odk$ageatdeath) & !is.na(odk$age_adult) & !is.na(odk$isadult), odk$age_adult*365.25, odk$ageatdeath)
# odk$ageatdeath <- ifelse(is.na(odk$ageatdeath) & !is.na(odk$ageinyears) & !is.na(odk$isadult), odk$ageinyears*365.25, odk$ageatdeath)
# odk$ageatdeath <- ifelse(is.na(odk$ageatdeath) & !is.na(odk$ageinmonths) & !is.na(odk$isadult), odk$ageinmonths*30.4, odk$ageatdeath)
#
# odk$age <- odk$ageatdeath
odk$age <- odk$ageindaysnew
odkNames <- tolower(names(odk))
whoNames_add <- c("Id10183","Id10167","Id10173","Id10161","Id10250","Id10120","Id10182","Id10148","Id10234",
"Id10126","Id10446","Id10151","Id10154")
whoNames_add <- tolower(whoNames_add)
eavaNames <- c("i183b","fb_day0","i173b","i167c","i161b","i250b","i120c","i182d","i148d","i234c",
"i126o","i446o","i183c","i182e","i151b","i148e","i234d","i173b","i154c","i154d","i173c",
"i167d","i120d")
eavaOut <- matrix(".", nrow = nrow(odk), ncol = length(eavaNames))
# i183b
indexData <- which(stri_endswith_fixed(odkNames, whoNames_add[1]))
eavaOut[odk[, indexData] > 4, 1] <- "y"
eavaOut[odk[, indexData] <= 4, 1] <- "n"
eavaOut[odk[, indexData] == 99, 1] <- "."
eavaOut[odk[, indexData] == 88, 1] <- "."
# fb_day0
indexData <- which(stri_endswith_fixed(odkNames, whoNames_add[2]))
eavaOut[odk[,"age"] - odk[,indexData] == 0, 2] <- "y"
eavaOut[odk[,"age"] - odk[,indexData] > 0, 2] <- "n"
eavaOut[odk[,"age"] - odk[,indexData] < 0, 2] <- "."
# i173b
indexData <- which(stri_endswith_fixed(odkNames, whoNames_add[3]))
eavaOut[str_detect(tolower(odk[, indexData]), "grunting"), 3] <- "y"
eavaOut[!str_detect(tolower(odk[, indexData]), "grunting"), 3] <- "n"
eavaOut[odk[, indexData] == "", 3] <- "."
# i167c
indexData <- which(stri_endswith_fixed(odkNames, whoNames_add[2]))
eavaOut[odk[, indexData] > 0, 4] <- "y"
eavaOut[odk[, indexData] == 0, 4] <- "n"
eavaOut[is.na(odk[, indexData]), 4] <- "."
# i161b
indexData <- which(stri_endswith_fixed(odkNames, whoNames_add[4]))
eavaOut[odk[, indexData] > 0, 5] <- "y"
eavaOut[odk[, indexData] == 0, 5] <- "n"
eavaOut[is.na(odk[, indexData]), 5] <- "."
# i250b
indexData <- which(stri_endswith_fixed(odkNames, whoNames_add[5]))
eavaOut[, 5] <- odk[, indexData]
eavaOut[is.na(odk[, indexData]), 6] <- "."
# i120c
indexData <- which(stri_endswith_fixed(odkNames, whoNames_add[6]))
eavaOut[, 7] <- odk[, indexData]
eavaOut[is.na(odk[, indexData]), 7] <- "."
# i182d
indexData <- which(stri_endswith_fixed(odkNames, whoNames_add[7]))
eavaOut[odk[, indexData] > 30, 8] <- "y"
eavaOut[odk[, indexData] <=30, 8] <- "n"
eavaOut[is.na(odk[, indexData]), 8] <- "."
# i148d
indexData <- which(stri_endswith_fixed(odkNames, whoNames_add[8]))
eavaOut[odk[, indexData] > 30, 9] <- "y"
eavaOut[odk[, indexData] <=30, 9] <- "n"
eavaOut[is.na(odk[, indexData]), 9] <- "."
# i234c
indexData <- which(stri_endswith_fixed(odkNames, whoNames_add[9]))
eavaOut[odk[, indexData] > 30, 10] <- "y"
eavaOut[odk[, indexData] <=30, 10] <- "n"
eavaOut[is.na(odk[, indexData]), 10] <- "."
# # i126o
indexData <- which(stri_endswith_fixed(odkNames, whoNames_add[10]))
eavaOut[, 11] <- odk[, indexData]
# # i446o
indexData <- which(stri_endswith_fixed(odkNames, whoNames_add[11]))
eavaOut[, 12] <- odk[, indexData]
# i183c
indexData <- which(stri_endswith_fixed(odkNames, whoNames_add[1]))
eavaOut[odk[, indexData] > 5, 13] <- "y"
eavaOut[odk[, indexData] <= 5, 13] <- "n"
eavaOut[odk[, indexData] == 99, 13] <- "."
eavaOut[odk[, indexData] == 88, 13] <- "."
# i182d
indexData <- which(stri_endswith_fixed(odkNames, whoNames_add[7]))
eavaOut[odk[, indexData] > 14, 14] <- "y"
eavaOut[odk[, indexData] <= 14, 14] <- "n"
eavaOut[is.na(odk[, indexData]), 14] <- "."
# i151b
indexData <- which(stri_endswith_fixed(odkNames, whoNames_add[12]))
eavaOut[str_detect(tolower(odk[, indexData]), "on_and_off"), 15] <- "y"
eavaOut[!str_detect(tolower(odk[, indexData]), "on_and_off"), 15] <- "n"
eavaOut[odk[, indexData] %in% c("dk","DK","Doesn't Know","Doesn't know","doesn't know",
"does not know","Does Not Know","Does not know",""), 15] <- "."
# i148e
indexData <- which(stri_endswith_fixed(odkNames, whoNames_add[8]))
eavaOut[odk[, indexData] > 2, 16] <- "y"
eavaOut[odk[, indexData] <=2, 16] <- "n"
eavaOut[is.na(odk[, indexData]), 16] <- "."
# i234d
indexData <- which(stri_endswith_fixed(odkNames, whoNames_add[9]))
eavaOut[odk[, indexData] > 2, 17] <- "y"
eavaOut[odk[, indexData] <=2, 17] <- "n"
eavaOut[is.na(odk[, indexData]), 17] <- "."
# i154c
indexData <- which(stri_endswith_fixed(odkNames, whoNames_add[13]))
eavaOut[odk[, indexData] > 14, 18] <- "y"
eavaOut[odk[, indexData] <=14, 18] <- "n"
eavaOut[is.na(odk[, indexData]), 18] <- "."
# i173b
indexData <- which(stri_endswith_fixed(odkNames, whoNames_add[3]))
eavaOut[str_detect(tolower(odk[, indexData]), "stridor"), 19] <- "y"
eavaOut[!str_detect(tolower(odk[, indexData]), "stridor"), 19] <- "n"
eavaOut[odk[, indexData] %in% c("dk","DK","Doesn't Know","Doesn't know","doesn't know",
"does not know","Does Not Know","Does not know",""), 19] <- "."
# i154d
indexData <- which(stri_endswith_fixed(odkNames, whoNames_add[13]))
eavaOut[odk[, indexData] > 2, 20] <- "y"
eavaOut[odk[, indexData] <=2, 20] <- "n"
eavaOut[is.na(odk[, indexData]), 20] <- "."
# i173c
indexData <- which(stri_endswith_fixed(odkNames, whoNames_add[3]))
eavaOut[str_detect(tolower(odk[, indexData]), "stridor"), 21] <- "y"
eavaOut[str_detect(tolower(odk[, indexData]), "grunting"), 21] <- "y"
eavaOut[str_detect(tolower(odk[, indexData]), "wheezing"), 21] <- "y"
eavaOut[str_detect(tolower(odk[, indexData]), "no"), 21] <- "n"
eavaOut[str_detect(tolower(odk[, indexData]), "dk|DK|Doesn't Know|doesn't know|does not know|Does Not Know|Does not know"), 21] <- "."
eavaOut[odk[, indexData] == "", 21] <- "."
# i167d
indexData <- which(stri_endswith_fixed(odkNames, whoNames_add[2]))
eavaOut[odk[, indexData] > 2, 22] <- "y"
eavaOut[odk[, indexData] <=2, 22] <- "n"
eavaOut[is.na(odk[, indexData]), 22] <- "."
# i120d
indexData <- which(stri_endswith_fixed(odkNames, whoNames_add[6]))
eavaOut[odk[, indexData] <= 1, 23] <- "y"
eavaOut[odk[, indexData] > 1, 23] <- "n"
eavaOut[is.na(odk[, indexData]), 23] <- "."
colnames(eavaOut) <- c(eavaNames)
indexID <- which(stri_endswith_fixed(odkNames, id_col))
# odkOut <- odk[,c(indexID,"age")]
# odkOut <- cbind(as.character(odk[, indexID]), odk[,"age"])
odkOut <- as.data.frame(odk[,"age"])
colnames(odkOut) <- c("age")
# eavaOut <- as.data.frame(cbind(iv5Out,odk[,"age"], eavaOut))
eavaOut <- as.data.frame(cbind(iv5Out,odkOut, eavaOut))
return(as.data.frame(eavaOut, stringsAsFactors = FALSE))
}
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Defines functions odk2EAVA
Documented in odk2EAVA
#' @title odk2EAVA
#' @description Converts 2016 WHO verbal autopsy (VA) data to an input file for Expert Algorithm Verbal Autopsy cause of death assignment by the codEAVA() function
#' @param odk A data frame which used open data kit (odk) to obtain 2016 WHO VA questionnaire responses
#' @param id_col A unique identifier for each record within the odk data frame
#' @returns A data frame that contains variable names and values which have been converted to openVA convention
#' @examples{
#' # load embedded example data or data from WHO 2016 Verbal Autopsy Questionnaire
#' data <- as.data.frame(data_public)
#' # run odk2EAVA()
#' output <- odk2EAVA(data, id_col = "comsa_id")
#' # view data converted for use in codEAVA()
#' head(output)
#' }
#' @references Thomas J, Choi E, Li Z, Maire N, McCormick T, Byass P, Clark S (2021). CrossVA: Verbal Autopsy Data Transformation for InSilicoVA and InterVA5 Algorithms_. R package version 1.0.0, <https://CRAN.R-project.org/package=CrossVA>.
#' @importFrom stringi stri_endswith_fixed
#' @importFrom stringr str_detect
#' @export
odk2EAVA <- function(odk, id_col) {
# Currently CrossVA requires all i022a-i022n variables, which public data does not have - improve errors to allow data management outdside function
names(odk) <- tolower(colnames(odk))
COMSAvariables <- as.vector(colnames(odk))
# Remove Stillbirths
odk$Stillbirth <- ifelse(odk$id10104 %in% c("no","dk") & odk$id10109 %in% c("no","dk") & odk$id10110 %in% c("no","dk"),1,0)
odk <- odk[odk$Stillbirth!=1,]
# convert id10022 -- need to add this manually
odk$id10022 <- odk$ageindaysnew
odk$i022a <- ifelse(is.na(odk$ageindaysnew),".", ifelse(odk$ageindaysnew >= 65*365.25, "y", "n"))
odk$i022b <- ifelse(is.na(odk$ageindaysnew),".", ifelse(odk$ageindaysnew >= 50*365.25 & odk$ageindaysnew < 65*365.25, "y","n"))
odk$i022c <- ifelse(is.na(odk$ageindaysnew),".", ifelse(odk$ageindaysnew >= 15*365.25 & odk$ageindaysnew < 50*365.25, "y", "n"))
odk$i022d <- ifelse(is.na(odk$ageindaysnew),".", ifelse(odk$ageindaysnew >= 5*365.25 & odk$ageindaysnew < 15*365.25, "y", "n"))
odk$i022e <- ifelse(is.na(odk$ageindaysnew),".", ifelse(odk$ageindaysnew >= 1*365.25 & odk$ageindaysnew < 5*365.25, "y", "n"))
odk$i022f <- ifelse(is.na(odk$ageindaysnew),".", ifelse(odk$ageindaysnew >= 28 & odk$ageindaysnew < 365.25, "y", "n"))
odk$i022g <- ifelse(is.na(odk$ageindaysnew),".", ifelse(odk$ageindaysnew < 28, "y", "n"))
odk$i022h <- ifelse(is.na(odk$ageindaysnew),".", ifelse(odk$ageindaysnew < 1, "y", "n"))
odk$i022i <- ifelse(is.na(odk$ageindaysnew),".", ifelse(odk$ageindaysnew %in% c(1:2), "y", "n"))
odk$i022j <- ifelse(is.na(odk$ageindaysnew),".", ifelse(odk$ageindaysnew %in% c(3:7), "y", "n"))
odk$i022k <- ifelse(is.na(odk$ageindaysnew),".", ifelse(odk$ageindaysnew %in% c(8:27), "y", "n"))
odk$i022l <- ifelse(is.na(odk$ageindaysnew),".", ifelse(odk$id10019b == "y" & odk$ageindaysnew >= 12*365.25 & odk$ageindaysnew < 20*365.25, "y", "n"))
odk$i022m <- ifelse(is.na(odk$ageindaysnew),".", ifelse(odk$id10019b == "y" & odk$ageindaysnew >= 20*365.25 & odk$ageindaysnew < 35*365.25, "y", "n"))
odk$i022n <- ifelse(is.na(odk$ageindaysnew),".", ifelse(odk$id10019b == "y" & odk$ageindaysnew >= 35*365.25 & odk$ageindaysnew < 49*365.25, "y", "n"))
# CrossVA starts here
odkNames <- tolower(names(odk))
whoNames <- c("Id10004", "Id10004", "Id10019", "Id10019",
"Id10022", "Id10022", "Id10022", "Id10022", "Id10022",
"Id10022", "Id10022", "Id10022", "Id10022", "Id10022",
"Id10022", "Id10022", "Id10022", "Id10022", "Id10059",
"Id10077", "Id10079", "Id10082", "Id10083", "Id10084",
"Id10085", "Id10086", "Id10087", "Id10089", "Id10090",
"Id10091", "Id10092", "Id10093", "Id10094", "Id10095",
"Id10096", "Id10098", "Id10099", "Id10100", "Id10104",
"Id10105", "Id10106", "Id10107", "Id10108", "Id10109",
"Id10110", "Id10111", "Id10112", "Id10113", "Id10114",
"Id10115", "Id10116", "Id10120", "Id10120", "Id10123",
"Id10125", "Id10127", "Id10128", "Id10129", "Id10130",
"Id10131", "Id10132", "Id10133", "Id10134", "Id10135",
"Id10136", "Id10137", "Id10138", "Id10139", "Id10140",
"Id10141", "Id10142", "Id10143", "Id10144", "Id10147",
"Id10148", "Id10148", "Id10148", "Id10149", "Id10150",
"Id10151", "Id10152", "Id10153", "Id10154", "Id10154",
"Id10155", "Id10156", "Id10157", "Id10158", "Id10159",
"Id10161", "Id10165", "Id10166", "Id10167", "Id10167",
"Id10168", "Id10169", "Id10169", "Id10170", "Id10171",
"Id10172", "Id10173", "Id10174", "Id10175", "Id10176",
"Id10178", "Id10181", "Id10182", "Id10182", "Id10182",
"Id10183", "Id10184_units", "Id10185", "Id10186", "Id10187",
"Id10188", "Id10189", "Id10190_units", "Id10191", "Id10192",
"Id10193", "Id10194", "Id10195", "Id10197", "Id10197",
"Id10199", "Id10199", "Id10200", "Id10201", "Id10201",
"Id10203", "Id10204", "Id10205", "Id10205", "Id10207",
"Id10208", "Id10209", "Id10209", "Id10210", "Id10211",
"Id10212", "Id10213", "Id10214", "Id10215", "Id10216",
"Id10217", "Id10218", "Id10219", "Id10220", "Id10221",
"Id10221", "Id10222", "Id10223", "Id10224", "Id10225",
"Id10226", "Id10227", "Id10228", "Id10229", "Id10230",
"Id10231", "Id10232", "Id10233", "Id10234", "Id10234",
"Id10235", "Id10235", "Id10235", "Id10235", "Id10236",
"Id10237", "Id10238", "Id10239", "Id10240", "Id10241",
"Id10242", "Id10243", "Id10244", "Id10245", "Id10246",
"Id10247", "Id10248", "Id10249", "Id10250", "Id10251",
"Id10252", "Id10253", "Id10254", "Id10255", "Id10256",
"Id10257", "Id10258", "Id10259", "Id10260", "Id10260",
"Id10260", "Id10260", "Id10260", "Id10260", "Id10260",
"Id10261", "Id10262", "Id10263", "Id10263", "Id10264",
"Id10265", "Id10266", "Id10267", "Id10268", "Id10269",
"Id10270", "Id10271", "Id10272", "Id10273", "Id10274",
"Id10275", "Id10276", "Id10277", "Id10278", "Id10279",
"Id10281", "Id10282", "Id10283", "Id10284", "Id10285",
"Id10286", "Id10287", "Id10288", "Id10289", "Id10290",
"Id10294", "Id10295", "Id10296", "Id10297", "Id10298",
"Id10299", "Id10300", "Id10301", "Id10302", "Id10303",
"Id10304", "Id10305", "Id10306", "Id10309", "Id10310",
"Id10312", "Id10313", "Id10314", "Id10315", "Id10316",
"Id10317", "Id10318", "Id10319", "Id10319", "Id10320",
"Id10321", "Id10322", "Id10323", "Id10324", "Id10325",
"Id10326", "Id10327", "Id10328", "Id10329", "Id10330",
"Id10331", "Id10332", "Id10333", "Id10334", "Id10335",
"Id10336", "Id10337", "Id10337", "Id10337", "Id10338",
"Id10340", "Id10342", "Id10343", "Id10344", "Id10347",
"Id10354", "Id10355", "Id10356", "Id10357", "Id10358",
"Id10360", "Id10360", "Id10360", "Id10361", "Id10362",
"Id10363", "Id10364", "Id10365", "Id10367", "Id10367",
"Id10367", "Id10368", "Id10369", "Id10370", "Id10371",
"Id10372", "Id10373", "Id10376", "Id10377", "Id10382",
"Id10383", "Id10384", "Id10385", "Id10387", "Id10388",
"Id10389", "Id10391", "Id10393", "Id10394", "Id10394",
"Id10395", "Id10396", "Id10397", "Id10398", "Id10399",
"Id10400", "Id10401", "Id10402", "Id10403", "Id10404",
"Id10405", "Id10406", "Id10408", "Id10411", "Id10412",
"Id10413", "Id10414", "Id10415", "Id10418", "Id10419",
"Id10420", "Id10421", "Id10422", "Id10423", "Id10424",
"Id10425", "Id10426", "Id10427", "Id10428", "Id10450",
"Id10451", "Id10452", "Id10453", "Id10454", "Id10455",
"Id10456", "Id10457", "Id10458", "Id10459")
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)
tmpMat <- matrix(sapply(whoNames, stri_endswith_fixed, str = odkNames),
nrow = length(odkNames))
indexData <- apply(tmpMat, 2, which)
warnZeroMatch <- which(sapply(indexData, length) == 0)
if (length(warnZeroMatch) > 0) {
message(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
indexNA <- NULL
flagNonNumeric <- function(x) {
return(tryCatch(as.numeric(x), error = function(c) -9999,
warning = function(c) -9999))
}
qYesNo <- c(20:40, 42, 44:51, 54:74, 78, 81:82, 85:89, 92,
95, 98:100, 102:103, 106, 112:116, 118:122, 127, 131,
134:135, 138, 140, 142, 145:148, 151:160, 162, 169:180,
182, 184:192, 200, 204:205, 207:213, 215:223, 225:238,
240:242, 244:251, 254:265, 267:270, 274:280, 282, 288:292,
296:303, 305:306, 308:312, 315:330, 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]
message(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)] <- "."
indexData <- which(stri_endswith_fixed(odkNames, whoNames[1]))
iv5Out[tolower(odk[, indexData]) == "wet" | tolower(odk[,
indexData]) == "wet season", 1] <- "y"
iv5Out[tolower(odk[, indexData]) == "dry" | tolower(odk[,
indexData]) == "dry season", 1] <- "n"
iv5Out[tolower(odk[, indexData]) == "wet" | tolower(odk[,
indexData]) == "wet season", 2] <- "n"
iv5Out[tolower(odk[, indexData]) == "dry" | tolower(odk[,
indexData]) == "dry season", 2] <- "y"
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"
indexData1y <- which(stri_endswith_fixed(odkNames, "ageinyears2"))
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])
indexData_isNeonatal <- which(stri_endswith_fixed(odkNames,
"isneonatal"))
indexData_isChild <- which(stri_endswith_fixed(odkNames,
"ischild"))
indexData_isAdult <- which(stri_endswith_fixed(odkNames,
"isadult"))
iv5Out[odk[, indexData1y] >= 65, 5] <- "y"
iv5Out[is.na(odk[, indexData1y]) & odk[, indexData2] == "adult" &
odk[, indexData3] >= 65, 5] <- "y"
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"
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"
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"
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"
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"
iv5Out[odk[, indexData1d] < 28, 11] <- "y"
iv5Out[is.na(odk[, indexData1d]) & odk[, indexData2] == "neonate",
11] <- "y"
iv5Out[odk[, indexData1d] < 1, 12] <- "y"
ageNeonate <- odk[, indexData5d]
iv5Out[odk[, indexData2] == "neonate" & !is.na(odk[, indexData5d]) &
ageNeonate < 1, 12] <- "y"
iv5Out[odk[, indexData1d] >= 1 & odk[, indexData1d] <= 2,
13] <- "y"
iv5Out[odk[, indexData2] == "neonate" & !is.na(odk[, indexData5d]) &
ageNeonate < 2 & ageNeonate >= 1, 13] <- "y"
iv5Out[odk[, indexData1d] > 2 & odk[, indexData1d] < 7, 14] <- "y"
iv5Out[odk[, indexData2] == "neonate" & !is.na(odk[, indexData5d]) &
ageNeonate < 7 & ageNeonate >= 2, 14] <- "y"
iv5Out[odk[, indexData1d] >= 7 & odk[, indexData1d] < 28,
15] <- "y"
iv5Out[odk[, indexData2] == "neonate" & !is.na(odk[, indexData5d]) &
ageNeonate < 28 & ageNeonate >= 7, 15] <- "y"
i022h_k_has_yes <- apply(iv5Out, 1, function(x) {
any(x[12:15] == "y")
})
iv5Out[i022h_k_has_yes, 11] <- "y"
neoIndexData6 <- iv5Out[, 12:15] != "y"
neoIndexData7 <- rowSums(iv5Out[, 12:15] == "y", na.rm = TRUE)
iv5Out[neoIndexData7 == 1, 12:15][neoIndexData6[neoIndexData7 ==
1, ]] <- "n"
indexData6 <- iv5Out[, 5:11] != "y"
indexData7 <- rowSums(iv5Out[, 5:11] == "y", na.rm = TRUE)
iv5Out[indexData7 == 1, 5:11][indexData6[indexData7 == 1,
]] <- "n"
indexData8 <- iv5Out[, 11] == "n"
iv5Out[indexData8, 12:15] <- "n"
iv5Out[, 16] <- ifelse(odk[, indexData_sex] == "female" &
odk[, indexData1y] < 20 & odk[, indexData1y] >= 12, "y",
".")
iv5Out[odk[, indexData_sex] == "female" & is.na(odk[, indexData1y]) &
odk[, indexData2] == "adult" & odk[, indexData3] < 20 &
odk[, indexData3] >= 12, 16] <- "y"
iv5Out[odk[, indexData_isNeonatal] == 1, 16] <- "n"
iv5Out[odk[, indexData_isChild] == 1, 16] <- "n"
iv5Out[odk[, indexData_sex] == "male", 16] <- "n"
iv5Out[odk[, indexData1y] < 12, 16] <- "n"
iv5Out[odk[, indexData1y] > 19, 16] <- "n"
iv5Out[, 17] <- ifelse(odk[, indexData_sex] == "female" &
odk[, indexData1y] < 35 & odk[, indexData1y] >= 20, "y",
".")
iv5Out[odk[, indexData_sex] == "female" & is.na(odk[, indexData1y]) &
odk[, indexData2] == "adult" & odk[, indexData3] < 35 &
odk[, indexData3] >= 20, 17] <- "y"
iv5Out[odk[, indexData_isNeonatal] == 1, 17] <- "n"
iv5Out[odk[, indexData_isChild] == 1, 17] <- "n"
iv5Out[odk[, indexData_sex] == "male", 17] <- "n"
iv5Out[odk[, indexData1y] < 20, 17] <- "n"
iv5Out[odk[, indexData1y] > 34, 17] <- "n"
iv5Out[, 18] <- ifelse(odk[, indexData_sex] == "female" &
odk[, indexData1y] < 50 & odk[, indexData1y] >= 35, "y",
".")
iv5Out[odk[, indexData_sex] == "female" & is.na(odk[, indexData1y]) &
odk[, indexData2] == "adult" & odk[, indexData3] < 50 &
odk[, indexData3] >= 35, 18] <- "y"
iv5Out[odk[, indexData_isNeonatal] == 1, 18] <- "n"
iv5Out[odk[, indexData_isChild] == 1, 18] <- "n"
iv5Out[odk[, indexData_sex] == "male", 18] <- "n"
iv5Out[odk[, indexData1y] < 35, 18] <- "n"
iv5Out[odk[, indexData1y] > 49, 18] <- "n"
indexData <- which(stri_endswith_fixed(odkNames, whoNames[19]))
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] == "male", 19] <- "n"
indexData <- which(stri_endswith_fixed(odkNames, whoNames[41]))
iv5Out[odk[, indexData] > 5, 41] <- "y"
iv5Out[odk[, indexData] <= 5, 41] <- "n"
iv5Out[odk[, indexData] == 99, 41] <- "n"
iv5Out[odk[, indexData] == 88, 41] <- "n"
indexData <- which(stri_endswith_fixed(odkNames, whoNames[43]))
iv5Out[odk[, indexData] > 24, 43] <- "y"
iv5Out[odk[, indexData] <= 24, 43] <- "n"
iv5Out[odk[, indexData] == 99, 43] <- "."
iv5Out[odk[, indexData] == 88, 43] <- "."
indexDatad <- which(stri_endswith_fixed(odkNames, "id10120"))
iv5Out[odk[, indexDatad] < 21, 52] <- "y"
iv5Out[odk[, indexDatad] >= 21, 52] <- "n"
iv5Out[odk[, indexDatad] == 99, 52] <- "."
iv5Out[odk[, indexDatad] == 88, 52] <- "."
iv5Out[odk[, indexDatad] >= 21, 53] <- "y"
iv5Out[odk[, indexDatad] < 21, 53] <- "n"
indexData <- which(stri_endswith_fixed(odkNames, whoNames[74]))
indexData_days <- which(stri_endswith_fixed(odkNames, whoNames[75]))
iv5Out[odk[, indexData] == "yes" & odk[, indexData_days] <
7, 75] <- "y"
iv5Out[odk[, indexData] == "yes" & odk[, indexData_days] >=
7, 75] <- "n"
iv5Out[odk[, indexData] == "yes" & odk[, indexData_days] ==
99, 75] <- "."
iv5Out[odk[, indexData] == "yes" & odk[, indexData_days] ==
88, 75] <- "."
iv5Out[odk[, indexData] == "no", 75] <- "n"
iv5Out[odk[, indexData_days] >= 7 & odk[, indexData_days] <
14, 76] <- "y"
iv5Out[odk[, indexData_days] < 7, 76] <- "n"
iv5Out[odk[, indexData_days] >= 14, 76] <- "n"
iv5Out[odk[, indexData_days] == 99, 76] <- "."
iv5Out[odk[, indexData_days] == 88, 76] <- "."
iv5Out[odk[, indexData] == "no", 76] <- "n"
iv5Out[odk[, indexData_days] >= 14, 77] <- "y"
iv5Out[odk[, indexData_days] < 14, 77] <- "n"
iv5Out[odk[, indexData] == "no", 77] <- "n"
iv5Out[odk[, indexData] == "no", 78] <- "n"
indexData_sev <- which(stri_endswith_fixed(odkNames, whoNames[79]))
iv5Out[tolower(odk[, indexData_sev]) == "severe", 79] <- "y"
iv5Out[tolower(odk[, indexData_sev]) == "mild", 79] <- "n"
iv5Out[tolower(odk[, indexData_sev]) == "moderate", 79] <- "n"
iv5Out[odk[, indexData] == "no", 79] <- "n"
indexData_con <- which(stri_endswith_fixed(odkNames, whoNames[80]))
iv5Out[tolower(odk[, indexData_con]) == "continuous", 80] <- "y"
iv5Out[tolower(odk[, indexData_con]) == "nightly", 80] <- "n"
iv5Out[tolower(odk[, indexData_con]) == "on_and_off", 80] <- "n"
iv5Out[odk[, indexData] == "no", 80] <- "n"
indexData <- which(stri_endswith_fixed(odkNames, whoNames[82]))
indexData_days <- which(stri_endswith_fixed(odkNames, whoNames[83]))
iv5Out[odk[, indexData] == "yes" & odk[, indexData_days[1]] <
21, 83] <- "y"
iv5Out[odk[, indexData] == "yes" & odk[, indexData_days[1]] >=
21, 83] <- "n"
iv5Out[odk[, indexData] == "no", 83] <- "n"
iv5Out[odk[, indexData] == "yes" & odk[, indexData_days[1]] >=
21, 84] <- "y"
iv5Out[odk[, indexData] == "yes" & odk[, indexData_days[1]] <
21, 84] <- "n"
iv5Out[odk[, indexData] == "no", 84] <- "n"
indexDatad <- which(stri_endswith_fixed(odkNames, whoNames[90]))
indexDatam <- which(stri_endswith_fixed(odkNames, "id10162"))
indexDatay <- which(stri_endswith_fixed(odkNames, "id10163"))
iv5Out[odk[, indexDatad] >= 3, 90] <- "y"
iv5Out[odk[, indexDatad] < 3, 90] <- "n"
iv5Out[odk[, indexDatam] >= 1, 90] <- "y"
iv5Out[odk[, indexDatay] >= 1, 90] <- "y"
indexData <- which(stri_endswith_fixed(odkNames, whoNames[91]))
iv5Out[tolower(odk[, indexData]) == "continuous", 91] <- "y"
iv5Out[tolower(odk[, indexData]) == "on_and_off", 91] <- "n"
indexData <- which(stri_endswith_fixed(odkNames, whoNames[93]))
iv5Out[odk[, indexData[1]] < 14, 93] <- "y"
iv5Out[odk[, indexData[1]] >= 14, 93] <- "n"
iv5Out[odk[, indexData[1]] == 99, 93] <- "."
iv5Out[odk[, indexData[1]] == 88, 93] <- "."
iv5Out[odk[, indexData[1]] >= 14, 94] <- "y"
iv5Out[odk[, indexData[1]] < 14, 94] <- "n"
iv5Out[odk[, indexData[1]] == 99, 94] <- "."
iv5Out[odk[, indexData[1]] == 88, 94] <- "."
indexData <- which(stri_endswith_fixed(odkNames, whoNames[96]))
iv5Out[odk[, indexData[1]] < 14, 96] <- "y"
iv5Out[odk[, indexData[1]] >= 14, 96] <- "n"
iv5Out[odk[, indexData[1]] == 99, 96] <- "."
iv5Out[odk[, indexData[1]] == 88, 96] <- "."
iv5Out[odk[, indexData[1]] >= 14, 97] <- "y"
iv5Out[odk[, indexData[1]] < 14, 97] <- "n"
iv5Out[odk[, indexData[1]] == 99, 97] <- "."
iv5Out[odk[, indexData[1]] == 88, 97] <- "."
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"
indexData <- which(stri_endswith_fixed(odkNames, whoNames[104]))
iv5Out[odk[, indexData] >= 3, 104] <- "y"
iv5Out[odk[, indexData] < 3, 104] <- "n"
iv5Out[odk[, indexData] == 99, 104] <- "."
iv5Out[odk[, indexData] == 88, 104] <- "."
indexData_unit <- which(stri_endswith_fixed(odkNames, "id10178_unit"))
indexDatam <- which(stri_endswith_fixed(odkNames, "id10178"))
indexDatah <- which(stri_endswith_fixed(odkNames, "id10179"))
indexDatad <- which(stri_endswith_fixed(odkNames, "id10179_1"))
iv5Out[tolower(odk[, indexData_unit]) == "minutes" & odk[,
indexDatam] >= 30, 105] <- "y"
iv5Out[tolower(odk[, indexData_unit]) == "hours" & odk[,
indexDatah] >= 0.5, 105] <- "y"
iv5Out[tolower(odk[, indexData_unit]) == "days" & odk[, indexDatad] >=
1, 105] <- "y"
iv5Out[tolower(odk[, indexData_unit]) == "minutes" & odk[,
indexDatam] < 30, 105] <- "n"
iv5Out[tolower(odk[, indexData_unit]) == "hours" & odk[,
indexDatah] < 0.5, 105] <- "n"
indexData <- which(stri_endswith_fixed(odkNames, whoNames[107]))
iv5Out[odk[, indexData] < 14, 107] <- "y"
iv5Out[odk[, indexData] >= 14, 107] <- "n"
iv5Out[odk[, indexData] < 28 & odk[, indexData] >= 14, 108] <- "y"
iv5Out[odk[, indexData] < 14, 108] <- "n"
iv5Out[odk[, indexData] >= 28, 108] <- "n"
iv5Out[odk[, indexData] >= 28, 109] <- "y"
iv5Out[odk[, indexData] < 28, 109] <- "n"
indexData <- which(stri_endswith_fixed(odkNames, whoNames[110]))
iv5Out[odk[, indexData] >= 4 & odk[, indexData] < 999, 110] <- "y"
iv5Out[odk[, indexData] < 4, 110] <- "n"
iv5Out[odk[, indexData] == 99, 110] <- "."
iv5Out[odk[, indexData] == 88, 110] <- "."
indexData181 <- which(stri_endswith_fixed(odkNames, "id10181"))
indexDataIsNeonatal <- which(stri_endswith_fixed(odkNames,
"isneonatal"))
indexDataIsChild <- which(stri_endswith_fixed(odkNames, "ischild"))
indexData184_a <- which(stri_endswith_fixed(odkNames, "id10184_a"))
indexData184_units <- which(stri_endswith_fixed(odkNames,
"id10184_units"))
indexData184_b <- which(stri_endswith_fixed(odkNames, "id10184_b"))
indexData184_c <- which(stri_endswith_fixed(odkNames, "id10184_c"))
iv5Out[odk[, indexData184_a] >= 3 & tolower(odk[, indexData181]) ==
"yes" & tolower(odk[, indexDataIsNeonatal]) == "yes",
111] <- "y"
iv5Out[odk[, indexData184_a] < 3 & tolower(odk[, indexData181]) ==
"yes" & tolower(odk[, indexDataIsNeonatal]) == "yes",
111] <- "n"
iv5Out[odk[, indexData184_a] == 99, 111] <- "."
iv5Out[odk[, indexData184_a] == 88, 111] <- "."
iv5Out[odk[, indexData184_b] >= 3 & tolower(odk[, indexData184_units]) ==
"days", 111] <- "y"
iv5Out[odk[, indexData184_b] < 3 & tolower(odk[, indexData184_units]) ==
"days", 111] <- "n"
iv5Out[odk[, indexData184_c] >= 1 & tolower(odk[, indexData184_units]) ==
"months", 111] <- "y"
indexData190_units <- which(stri_endswith_fixed(odkNames,
"id10190_units"))
indexData190_a <- which(stri_endswith_fixed(odkNames, "id10190_a"))
indexData190_b <- which(stri_endswith_fixed(odkNames, "id10190_b"))
iv5Out[odk[, indexData190_a] >= 3 & tolower(odk[, indexData190_units]) ==
"days", 117] <- "y"
iv5Out[odk[, indexData190_a] < 3 & tolower(odk[, indexData190_units]) ==
"days", 117] <- "n"
iv5Out[odk[, indexData190_b] >= 1 & tolower(odk[, indexData190_units]) ==
"months", 117] <- "y"
indexData <- which(stri_endswith_fixed(odkNames, "id10195"))
indexDatad <- which(stri_endswith_fixed(odkNames, "id10197"))
iv5Out[tolower(odk[, indexData]) == "yes" & odk[, indexDatad] <
14, 123] <- "y"
iv5Out[tolower(odk[, indexData]) == "yes" & odk[, indexDatad] >=
14, 123] <- "n"
iv5Out[tolower(odk[, indexData]) == "no", 123] <- "n"
iv5Out[tolower(odk[, indexData]) == "yes" & odk[, indexDatad] >=
14, 124] <- "y"
iv5Out[tolower(odk[, indexData]) == "yes" & odk[, indexDatad] <
14, 124] <- "n"
iv5Out[tolower(odk[, indexData]) == "no", 124] <- "n"
indexData <- which(stri_endswith_fixed(odkNames, "id10194"))
indexData_uplow <- which(stri_endswith_fixed(odkNames, whoNames[125]))
iv5Out[tolower(odk[, indexData_uplow]) == "upper_abdomen",
125] <- "y"
iv5Out[tolower(odk[, indexData_uplow]) == "upper_lower_abdomen",
125] <- "y"
iv5Out[tolower(odk[, indexData_uplow]) == "lower_abdomen",
125] <- "n"
iv5Out[tolower(odk[, indexData_uplow]) == "upper_abdomen",
126] <- "n"
iv5Out[tolower(odk[, indexData_uplow]) == "upper_lower_abdomen",
126] <- "y"
iv5Out[tolower(odk[, indexData_uplow]) == "lower_abdomen",
126] <- "y"
indexData <- which(stri_endswith_fixed(odkNames, "id10200"))
indexDatad <- which(stri_endswith_fixed(odkNames, whoNames[128]))
indexDatam <- which(stri_endswith_fixed(odkNames, "id10202"))
iv5Out[tolower(odk[, indexData]) == "yes" & odk[, indexDatad] <
14 & odk[, indexDatam] == 0, 128] <- "y"
iv5Out[tolower(odk[, indexData]) == "yes" & odk[, indexDatad] <
14 & is.na(odk[, indexDatam]), 128] <- "y"
iv5Out[tolower(odk[, indexData]) == "yes" & odk[, indexDatad] >=
14 & odk[, indexDatam] == 0, 128] <- "n"
iv5Out[tolower(odk[, indexData]) == "yes" & odk[, indexDatad] >=
14 & is.na(odk[, indexDatam]), 128] <- "n"
iv5Out[tolower(odk[, indexData]) == "yes" & odk[, indexDatam] >=
1, 128] <- "n"
iv5Out[tolower(odk[, indexData]) == "no", 128] <- "n"
iv5Out[tolower(odk[, indexData]) == "yes" & odk[, indexDatam] >=
1, 129] <- "y"
iv5Out[tolower(odk[, indexData]) == "yes" & odk[, indexDatad] >=
14 & odk[, indexDatam] == 0, 129] <- "y"
iv5Out[tolower(odk[, indexData]) == "yes" & odk[, indexDatad] >=
14 & is.na(odk[, indexDatam]), 129] <- "y"
iv5Out[tolower(odk[, indexData]) == "yes" & odk[, indexDatad] <
14 & odk[, indexDatam] == 0, 129] <- "n"
iv5Out[tolower(odk[, indexData]) == "yes" & odk[, indexDatad] <
14 & is.na(odk[, indexDatam]), 129] <- "n"
iv5Out[tolower(odk[, indexData]) == "no", 129] <- "n"
indexData <- which(stri_endswith_fixed(odkNames, whoNames[130]))
iv5Out[tolower(odk[, indexData]) == "rapidly", 130] <- "y"
iv5Out[tolower(odk[, indexData]) == "slowly", 130] <- "n"
indexData <- which(stri_endswith_fixed(odkNames, "id10204"))
indexDatad <- which(stri_endswith_fixed(odkNames, whoNames[132]))
indexDatam <- which(stri_endswith_fixed(odkNames, "id10206"))
iv5Out[tolower(odk[, indexData]) == "yes" & odk[, indexDatad] <
14 & odk[, indexDatam] == 0, 132] <- "y"
iv5Out[tolower(odk[, indexData]) == "yes" & odk[, indexDatad] <
14 & is.na(odk[, indexDatam]), 132] <- "y"
iv5Out[tolower(odk[, indexData]) == "yes" & odk[, indexDatad] >=
14 & odk[, indexDatam] == 0, 132] <- "n"
iv5Out[tolower(odk[, indexData]) == "yes" & odk[, indexDatad] >=
14 & is.na(odk[, indexDatam]), 132] <- "n"
iv5Out[tolower(odk[, indexData]) == "yes" & odk[, indexDatam] >=
1, 132] <- "n"
iv5Out[tolower(odk[, indexData]) == "no", 132] <- "n"
iv5Out[tolower(odk[, indexData]) == "yes" & odk[, indexDatad] <
14 & odk[, indexDatam] == 0, 133] <- "n"
iv5Out[tolower(odk[, indexData]) == "yes" & odk[, indexDatad] <
14 & is.na(odk[, indexDatam]), 133] <- "n"
iv5Out[tolower(odk[, indexData]) == "yes" & odk[, indexDatad] >=
14 & odk[, indexDatam] == 0, 133] <- "y"
iv5Out[tolower(odk[, indexData]) == "yes" & odk[, indexDatad] >=
14 & is.na(odk[, indexDatam]), 133] <- "y"
iv5Out[tolower(odk[, indexData]) == "yes" & odk[, indexDatam] >=
1, 133] <- "y"
iv5Out[tolower(odk[, indexData]) == "no", 133] <- "n"
indexData <- which(stri_endswith_fixed(odkNames, "id10208"))
indexDatad <- which(stri_endswith_fixed(odkNames, whoNames[136]))
iv5Out[tolower(odk[, indexData]) == "yes" & odk[, indexDatad] <
7, 136] <- "y"
iv5Out[tolower(odk[, indexData]) == "yes" & odk[, indexDatad] >=
7, 136] <- "n"
iv5Out[tolower(odk[, indexData]) == "no", 136] <- "n"
iv5Out[tolower(odk[, indexData]) == "yes" & odk[, indexDatad] >=
7, 137] <- "y"
iv5Out[tolower(odk[, indexData]) == "yes" & odk[, indexDatad] <
7, 137] <- "n"
iv5Out[tolower(odk[, indexData]) == "no", 137] <- "n"
indexData <- which(stri_endswith_fixed(odkNames, "id10210"))
indexDatad <- which(stri_endswith_fixed(odkNames, whoNames[139]))
iv5Out[tolower(odk[, indexData]) == "yes" & odk[, indexDatad] >=
7, 139] <- "y"
iv5Out[tolower(odk[, indexData]) == "yes" & odk[, indexDatad] <
7, 139] <- "n"
iv5Out[tolower(odk[, indexData]) == "no", 139] <- "n"
indexData <- which(stri_endswith_fixed(odkNames, whoNames[140]))
indexDatad <- which(stri_endswith_fixed(odkNames, whoNames[141]))
iv5Out[odk[, indexData] == "yes" & odk[, indexDatad] >= 3,
141] <- "y"
iv5Out[odk[, indexData] == "yes" & odk[, indexDatad] < 3,
141] <- "n"
iv5Out[odk[, indexData] == "no", 141] <- "n"
indexData_uncon <- which(stri_endswith_fixed(odkNames, whoNames[142]))
indexData_uncon24 <- which(stri_endswith_fixed(odkNames,
whoNames[143]))
iv5Out[odk[, indexData_uncon] == "yes" & odk[, indexData_uncon24] ==
"yes", 143] <- "y"
iv5Out[odk[, indexData_uncon] == "yes" & odk[, indexData_uncon24] ==
"no", 143] <- "n"
iv5Out[odk[, indexData_uncon] == "no", 143] <- "n"
indexData <- which(stri_endswith_fixed(odkNames, whoNames[143]))
indexData_hours <- which(stri_endswith_fixed(odkNames, whoNames[144]))
iv5Out[odk[, indexData] == "yes", 144] <- "y"
iv5Out[odk[, indexData] == "no" & odk[, indexData_hours] >=
6, 144] <- "y"
iv5Out[odk[, indexData] == "no" & odk[, indexData_hours] <
6, 144] <- "n"
iv5Out[odk[, indexData_uncon] == "no", 144] <- "n"
indexData <- which(stri_endswith_fixed(odkNames, whoNames[147]))
indexData_min <- which(stri_endswith_fixed(odkNames, whoNames[149]))
iv5Out[odk[, indexData] == "yes" & odk[, indexData_min] <
10, 149] <- "y"
iv5Out[odk[, indexData] == "yes" & odk[, indexData_min] >=
10, 149] <- "n"
iv5Out[odk[, indexData] == "yes" & odk[, indexData_min] ==
99, 149] <- "."
iv5Out[odk[, indexData] == "yes" & odk[, indexData_min] ==
88, 149] <- "."
iv5Out[odk[, indexData] == "yes" & odk[, indexData_min] <
10, 150] <- "n"
iv5Out[odk[, indexData] == "yes" & odk[, indexData_min] >=
10, 150] <- "y"
indexData <- which(stri_endswith_fixed(odkNames, whoNames[161]))
iv5Out[odk[, indexData] >= 14, 161] <- "y"
iv5Out[odk[, indexData] < 14, 161] <- "n"
indexData <- which(stri_endswith_fixed(odkNames, whoNames[163]))
iv5Out[odk[, indexData] < 7, 163] <- "y"
iv5Out[odk[, indexData] >= 7, 163] <- "n"
iv5Out[odk[, indexData] == 99, 163] <- "."
iv5Out[odk[, indexData] == 88, 163] <- "."
iv5Out[odk[, indexData] >= 7, 164] <- "y"
iv5Out[odk[, indexData] < 7, 164] <- "n"
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] <- "."
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] <- "."
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] <- "."
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] <- "."
indexData <- which(stri_endswith_fixed(odkNames, whoNames[181]))
iv5Out[odk[, indexData] >= 7, 181] <- "y"
iv5Out[odk[, indexData] < 7, 181] <- "n"
indexData <- which(stri_endswith_fixed(odkNames, whoNames[183]))
iv5Out[odk[, indexData] >= 3, 183] <- "y"
iv5Out[odk[, indexData] < 3, 183] <- "n"
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] <- "."
iv5Out[tolower(odk[, indexData]) == "left_side", 194] <- "y"
iv5Out[tolower(odk[, indexData]) != "left_side", 194] <- "n"
iv5Out[tolower(odk[, indexData]) == "", 194] <- "."
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] <- "."
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] <- "."
iv5Out[tolower(odk[, indexData]) == "one_leg_only", 197] <- "y"
iv5Out[tolower(odk[, indexData]) != "one_leg_only", 197] <- "n"
iv5Out[tolower(odk[, indexData]) == "", 197] <- "."
iv5Out[tolower(odk[, indexData]) == "one_arm_only", 198] <- "y"
iv5Out[tolower(odk[, indexData]) != "one_arm_only", 198] <- "n"
iv5Out[tolower(odk[, indexData]) == "", 198] <- "."
iv5Out[tolower(odk[, indexData]) == "whole_body", 199] <- "y"
iv5Out[tolower(odk[, indexData]) != "whole_body", 199] <- "n"
iv5Out[tolower(odk[, indexData]) == "", 199] <- "."
indexData <- which(stri_endswith_fixed(odkNames, whoNames[201]))
iv5Out[odk[, indexData] >= 7, 201] <- "y"
iv5Out[odk[, indexData] < 7, 201] <- "n"
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"
iv5Out[tolower(odk[, indexData]) == "solids", 203] <- "n"
iv5Out[tolower(odk[, indexData]) == "both", 203] <- "y"
iv5Out[tolower(odk[, indexData]) == "liquids", 203] <- "y"
indexData <- which(stri_endswith_fixed(odkNames, whoNames[206]))
iv5Out[odk[, indexData] >= 21, 206] <- "y"
iv5Out[odk[, indexData] < 21, 206] <- "n"
indexData <- which(stri_endswith_fixed(odkNames, whoNames[214]))
iv5Out[odk[, indexData[1]] >= 2, 214] <- "y"
iv5Out[odk[, indexData[1]] < 2, 214] <- "n"
iv5Out[odk[, indexData[1]] == 99, 214] <- "."
iv5Out[odk[, indexData[1]] == 88, 214] <- "."
indexData <- which(stri_endswith_fixed(odkNames, whoNames[224]))
iv5Out[odk[, indexData] > 3, 224] <- "y"
iv5Out[odk[, indexData] <= 3, 224] <- "n"
iv5Out[odk[, indexData] == 99, 224] <- "."
iv5Out[odk[, indexData] == 88, 224] <- "."
indexData <- which(stri_endswith_fixed(odkNames, whoNames[239]))
iv5Out[odk[, indexData] >= 4, 239] <- "y"
iv5Out[odk[, indexData] < 4, 239] <- "n"
iv5Out[odk[, indexData] == 99, 239] <- "."
iv5Out[odk[, indexData] == 88, 239] <- "."
indexData <- which(stri_endswith_fixed(odkNames, whoNames[243]))
iv5Out[odk[, indexData] < 6, 243] <- "y"
iv5Out[odk[, indexData] >= 6, 243] <- "n"
iv5Out[odk[, indexData] == 99, 243] <- "."
iv5Out[odk[, indexData] == 88, 243] <- "."
indexData <- which(stri_endswith_fixed(odkNames, whoNames[252]))
iv5Out[odk[, indexData] == 0, 252] <- "y"
iv5Out[odk[, indexData] > 0, 252] <- "n"
iv5Out[odk[, indexData] == 99, 252] <- "."
iv5Out[odk[, indexData] == 88, 252] <- "."
iv5Out[odk[, indexData] >= 4, 253] <- "y"
iv5Out[odk[, indexData] < 4, 253] <- "n"
indexData <- which(stri_endswith_fixed(odkNames, whoNames[266]))
iv5Out[odk[, indexData] > 24, 266] <- "y"
iv5Out[odk[, indexData] <= 24, 266] <- "n"
iv5Out[odk[, indexData] == 99, 266] <- "."
iv5Out[odk[, indexData] == 88, 266] <- "."
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"
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"
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"
indexData <- which(stri_endswith_fixed(odkNames, whoNames[281]))
iv5Out[tolower(odk[, indexData]) == "first", 281] <- "y"
iv5Out[tolower(odk[, indexData]) == "second_or_later", 281] <- "n"
indexData <- which(stri_endswith_fixed(odkNames, whoNames[283]))
iv5Out[tolower(odk[, indexData]) == "after_delivery", 283] <- "y"
iv5Out[tolower(odk[, indexData]) == "during_delivery", 283] <- "y"
indexDataM <- which(stri_endswith_fixed(odkNames, whoNames[284]))
indexDataD <- which(stri_endswith_fixed(odkNames, "id10359"))
nMonths <- odk[, indexDataM]
nDays <- odk[, indexDataD]
nMonths[is.na(odk[, indexDataM]) & !is.na(odk[, indexDataD])] <- 0
nDays[is.na(odk[, indexDataD]) & !is.na(odk[, indexDataM])] <- 0
naMonthsAndDays <- is.na(odk[, indexDataM]) & is.na(odk[,
indexDataD])
iv5Out[nMonths + nDays/30.4 <= 12 & !naMonthsAndDays, 284] <- "y"
iv5Out[nMonths + nDays/30.4 > 12 & !naMonthsAndDays, 284] <- "n"
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"
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"
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"
indexData <- which(stri_endswith_fixed(odkNames, whoNames[293]))
iv5Out[odk[, indexData] >= 9 & odk[, indexData] < 88, 293] <- "y"
iv5Out[odk[, indexData] < 9, 293] <- "n"
iv5Out[odk[, indexData] == 99, 293] <- "."
iv5Out[odk[, indexData] == 88, 293] <- "."
iv5Out[odk[, indexData] > 8 & odk[, indexData] < 88, 294] <- "n"
iv5Out[odk[, indexData] == 8, 294] <- "y"
iv5Out[odk[, indexData] < 8, 294] <- "n"
iv5Out[odk[, indexData] >= 8 & odk[, indexData] < 88, 295] <- "n"
iv5Out[odk[, indexData] < 8, 295] <- "y"
indexData <- which(stri_endswith_fixed(odkNames, whoNames[304]))
iv5Out[odk[, indexData] > 24, 304] <- "y"
iv5Out[odk[, indexData] <= 24, 304] <- "n"
iv5Out[odk[, indexData] == 99, 304] <- "."
iv5Out[odk[, indexData] == 88, 304] <- "."
indexData <- which(stri_endswith_fixed(odkNames, whoNames[307]))
iv5Out[tolower(odk[, indexData]) == "green_or_brown", 307] <- "y"
iv5Out[tolower(odk[, indexData]) == "clear", 307] <- "n"
iv5Out[tolower(odk[, indexData]) == "other", 307] <- "n"
indexData <- which(stri_endswith_fixed(odkNames, whoNames[313]))
iv5Out[odk[, indexData] == 0, 313] <- "y"
iv5Out[odk[, indexData] > 0, 313] <- "n"
iv5Out[odk[, indexData] == 99, 313] <- "."
iv5Out[odk[, indexData] == 88, 313] <- "."
iv5Out[odk[, indexData] >= 4, 314] <- "y"
iv5Out[odk[, indexData] < 4, 314] <- "n"
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"
indexData <- which(stri_endswith_fixed(odkNames, whoNames[332]))
iv5Out[odk[, indexData] >= 10, 332] <- "y"
iv5Out[odk[, indexData] < 10, 332] <- "n"
iv5Out[odk[, indexData] == 99, 332] <- "."
iv5Out[odk[, indexData] == 88, 332] <- "."
if (numNA > 0) {
warning("Found unexpected input values (coded as missing)",
call. = FALSE)
message("Unexpected values found in: ", sep = "\n")
message(paste(indexNA), sep = ", ")
message("\n")
}
numNA <- colSums(is.na(iv5Out))
indexNA <- which(numNA > 0)
if (length(indexNA) > 0) {
warning("NA's included in output", call. = FALSE)
message(paste("odk2openVA produced NA's in the following columns",
" (this may cause errors with openVA)", sep = ""),
sep = "\n")
message(paste(iv5Names[indexNA], " Probably associated with WHO column containing: ",
whoNames[indexNA], sep = ""), sep = "\n")
}
indexID <- which(stri_endswith_fixed(odkNames, id_col))
# indexID <- odkNames[4]
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)
}
colnames(iv5Out) <- c("ID", iv5Names)
# EAVA-specific variables
names(odk) <- tolower(colnames(odk))
# odk$ageatdeath <- NULL
# odk$ageatdeath <- odk$ageindays
# odk$ageatdeath <- ifelse(is.na(odk$ageatdeath) & !is.na(odk$age_neonate_minutes) & !is.na(odk$isneonatal), odk$age_neonate_minutes/(60*24), odk$ageatdeath)
# odk$ageatdeath <- ifelse(is.na(odk$ageatdeath) & !is.na(odk$age_neonate_hours) & !is.na(odk$isneonatal), odk$age_neonate_hours/(24), odk$ageatdeath)
# odk$ageatdeath <- ifelse(is.na(odk$ageatdeath) & !is.na(odk$age_neonate_days) & !is.na(odk$isneonatal), odk$age_neonate_days, odk$ageatdeath)
# odk$ageatdeath <- ifelse(is.na(odk$ageatdeath) & !is.na(odk$ageindaysneonate) & !is.na(odk$isneonatal), odk$ageindaysneonate, odk$ageatdeath)
# odk$ageatdeath <- ifelse(is.na(odk$ageatdeath) & !is.na(odk$age_child_months) & !is.na(odk$ischild), odk$age_child_months*30.4, odk$ageatdeath)
# odk$ageatdeath <- ifelse(is.na(odk$ageatdeath) & !is.na(odk$age_child_years) & !is.na(odk$ischild), odk$age_child_years*365.25, odk$ageatdeath)
# odk$ageatdeath <- ifelse(is.na(odk$ageatdeath) & !is.na(odk$age_adult) & !is.na(odk$isadult), odk$age_adult*365.25, odk$ageatdeath)
# odk$ageatdeath <- ifelse(is.na(odk$ageatdeath) & !is.na(odk$ageinyears) & !is.na(odk$isadult), odk$ageinyears*365.25, odk$ageatdeath)
# odk$ageatdeath <- ifelse(is.na(odk$ageatdeath) & !is.na(odk$ageinmonths) & !is.na(odk$isadult), odk$ageinmonths*30.4, odk$ageatdeath)
#
# odk$age <- odk$ageatdeath
odk$age <- odk$ageindaysnew
odkNames <- tolower(names(odk))
whoNames_add <- c("Id10183","Id10167","Id10173","Id10161","Id10250","Id10120","Id10182","Id10148","Id10234",
"Id10126","Id10446","Id10151","Id10154")
whoNames_add <- tolower(whoNames_add)
eavaNames <- c("i183b","fb_day0","i173b","i167c","i161b","i250b","i120c","i182d","i148d","i234c",
"i126o","i446o","i183c","i182e","i151b","i148e","i234d","i173b","i154c","i154d","i173c",
"i167d","i120d")
eavaOut <- matrix(".", nrow = nrow(odk), ncol = length(eavaNames))
# i183b
indexData <- which(stri_endswith_fixed(odkNames, whoNames_add[1]))
eavaOut[odk[, indexData] > 4, 1] <- "y"
eavaOut[odk[, indexData] <= 4, 1] <- "n"
eavaOut[odk[, indexData] == 99, 1] <- "."
eavaOut[odk[, indexData] == 88, 1] <- "."
# fb_day0
indexData <- which(stri_endswith_fixed(odkNames, whoNames_add[2]))
eavaOut[odk[,"age"] - odk[,indexData] == 0, 2] <- "y"
eavaOut[odk[,"age"] - odk[,indexData] > 0, 2] <- "n"
eavaOut[odk[,"age"] - odk[,indexData] < 0, 2] <- "."
# i173b
indexData <- which(stri_endswith_fixed(odkNames, whoNames_add[3]))
eavaOut[str_detect(tolower(odk[, indexData]), "grunting"), 3] <- "y"
eavaOut[!str_detect(tolower(odk[, indexData]), "grunting"), 3] <- "n"
eavaOut[odk[, indexData] == "", 3] <- "."
# i167c
indexData <- which(stri_endswith_fixed(odkNames, whoNames_add[2]))
eavaOut[odk[, indexData] > 0, 4] <- "y"
eavaOut[odk[, indexData] == 0, 4] <- "n"
eavaOut[is.na(odk[, indexData]), 4] <- "."
# i161b
indexData <- which(stri_endswith_fixed(odkNames, whoNames_add[4]))
eavaOut[odk[, indexData] > 0, 5] <- "y"
eavaOut[odk[, indexData] == 0, 5] <- "n"
eavaOut[is.na(odk[, indexData]), 5] <- "."
# i250b
indexData <- which(stri_endswith_fixed(odkNames, whoNames_add[5]))
eavaOut[, 5] <- odk[, indexData]
eavaOut[is.na(odk[, indexData]), 6] <- "."
# i120c
indexData <- which(stri_endswith_fixed(odkNames, whoNames_add[6]))
eavaOut[, 7] <- odk[, indexData]
eavaOut[is.na(odk[, indexData]), 7] <- "."
# i182d
indexData <- which(stri_endswith_fixed(odkNames, whoNames_add[7]))
eavaOut[odk[, indexData] > 30, 8] <- "y"
eavaOut[odk[, indexData] <=30, 8] <- "n"
eavaOut[is.na(odk[, indexData]), 8] <- "."
# i148d
indexData <- which(stri_endswith_fixed(odkNames, whoNames_add[8]))
eavaOut[odk[, indexData] > 30, 9] <- "y"
eavaOut[odk[, indexData] <=30, 9] <- "n"
eavaOut[is.na(odk[, indexData]), 9] <- "."
# i234c
indexData <- which(stri_endswith_fixed(odkNames, whoNames_add[9]))
eavaOut[odk[, indexData] > 30, 10] <- "y"
eavaOut[odk[, indexData] <=30, 10] <- "n"
eavaOut[is.na(odk[, indexData]), 10] <- "."
# # i126o
indexData <- which(stri_endswith_fixed(odkNames, whoNames_add[10]))
eavaOut[, 11] <- odk[, indexData]
# # i446o
indexData <- which(stri_endswith_fixed(odkNames, whoNames_add[11]))
eavaOut[, 12] <- odk[, indexData]
# i183c
indexData <- which(stri_endswith_fixed(odkNames, whoNames_add[1]))
eavaOut[odk[, indexData] > 5, 13] <- "y"
eavaOut[odk[, indexData] <= 5, 13] <- "n"
eavaOut[odk[, indexData] == 99, 13] <- "."
eavaOut[odk[, indexData] == 88, 13] <- "."
# i182d
indexData <- which(stri_endswith_fixed(odkNames, whoNames_add[7]))
eavaOut[odk[, indexData] > 14, 14] <- "y"
eavaOut[odk[, indexData] <= 14, 14] <- "n"
eavaOut[is.na(odk[, indexData]), 14] <- "."
# i151b
indexData <- which(stri_endswith_fixed(odkNames, whoNames_add[12]))
eavaOut[str_detect(tolower(odk[, indexData]), "on_and_off"), 15] <- "y"
eavaOut[!str_detect(tolower(odk[, indexData]), "on_and_off"), 15] <- "n"
eavaOut[odk[, indexData] %in% c("dk","DK","Doesn't Know","Doesn't know","doesn't know",
"does not know","Does Not Know","Does not know",""), 15] <- "."
# i148e
indexData <- which(stri_endswith_fixed(odkNames, whoNames_add[8]))
eavaOut[odk[, indexData] > 2, 16] <- "y"
eavaOut[odk[, indexData] <=2, 16] <- "n"
eavaOut[is.na(odk[, indexData]), 16] <- "."
# i234d
indexData <- which(stri_endswith_fixed(odkNames, whoNames_add[9]))
eavaOut[odk[, indexData] > 2, 17] <- "y"
eavaOut[odk[, indexData] <=2, 17] <- "n"
eavaOut[is.na(odk[, indexData]), 17] <- "."
# i154c
indexData <- which(stri_endswith_fixed(odkNames, whoNames_add[13]))
eavaOut[odk[, indexData] > 14, 18] <- "y"
eavaOut[odk[, indexData] <=14, 18] <- "n"
eavaOut[is.na(odk[, indexData]), 18] <- "."
# i173b
indexData <- which(stri_endswith_fixed(odkNames, whoNames_add[3]))
eavaOut[str_detect(tolower(odk[, indexData]), "stridor"), 19] <- "y"
eavaOut[!str_detect(tolower(odk[, indexData]), "stridor"), 19] <- "n"
eavaOut[odk[, indexData] %in% c("dk","DK","Doesn't Know","Doesn't know","doesn't know",
"does not know","Does Not Know","Does not know",""), 19] <- "."
# i154d
indexData <- which(stri_endswith_fixed(odkNames, whoNames_add[13]))
eavaOut[odk[, indexData] > 2, 20] <- "y"
eavaOut[odk[, indexData] <=2, 20] <- "n"
eavaOut[is.na(odk[, indexData]), 20] <- "."
# i173c
indexData <- which(stri_endswith_fixed(odkNames, whoNames_add[3]))
eavaOut[str_detect(tolower(odk[, indexData]), "stridor"), 21] <- "y"
eavaOut[str_detect(tolower(odk[, indexData]), "grunting"), 21] <- "y"
eavaOut[str_detect(tolower(odk[, indexData]), "wheezing"), 21] <- "y"
eavaOut[str_detect(tolower(odk[, indexData]), "no"), 21] <- "n"
eavaOut[str_detect(tolower(odk[, indexData]), "dk|DK|Doesn't Know|doesn't know|does not know|Does Not Know|Does not know"), 21] <- "."
eavaOut[odk[, indexData] == "", 21] <- "."
# i167d
indexData <- which(stri_endswith_fixed(odkNames, whoNames_add[2]))
eavaOut[odk[, indexData] > 2, 22] <- "y"
eavaOut[odk[, indexData] <=2, 22] <- "n"
eavaOut[is.na(odk[, indexData]), 22] <- "."
# i120d
indexData <- which(stri_endswith_fixed(odkNames, whoNames_add[6]))
eavaOut[odk[, indexData] <= 1, 23] <- "y"
eavaOut[odk[, indexData] > 1, 23] <- "n"
eavaOut[is.na(odk[, indexData]), 23] <- "."
colnames(eavaOut) <- c(eavaNames)
indexID <- which(stri_endswith_fixed(odkNames, id_col))
# odkOut <- odk[,c(indexID,"age")]
# odkOut <- cbind(as.character(odk[, indexID]), odk[,"age"])
odkOut <- as.data.frame(odk[,"age"])
colnames(odkOut) <- c("age")
# eavaOut <- as.data.frame(cbind(iv5Out,odk[,"age"], eavaOut))
eavaOut <- as.data.frame(cbind(iv5Out,odkOut, eavaOut))
return(as.data.frame(eavaOut, stringsAsFactors = FALSE))
}
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