Nothing
R/odk2openVA_v141.R
In CrossVA: Verbal Autopsy Data Transformation for InSilicoVA and InterVA5 Algorithms
#' Map VA records (version 1.4.1) to InterVA5 and InSilico (with option data.type = "WHO2016").
#'
#' \code{odk2openVA} transforms data collected with the 2016 WHO VA instrument
#' (version 1.4.1) to serve as the input to the InterVA5 and InSilicoVA
#' alogrithms for coding cause of death.
#'
#' @param odk A dataframe, obtained from reading an ODK Briefcase
#' export of records collected with the WHO questionnaire.
#'
#' @param id_col A character string of the column name (in odk) with the
#' unique ID for each death.
#'
#' @examples
#' \dontrun{
#' record_f_name <- system.file("sample", "who141_odk_export.csv", package = "CrossVA")
#' records <- read.csv(record_f_name, stringsAsFactors = FALSE)
#' output <- odk2openVA_v141(records)
#' }
#'
#' @importFrom stringi stri_endswith_fixed
#'
#' @export
#'
odk2openVA_v141 <- function (odk, id_col = "meta.instanceID") {
## Input Data
odkNames <- tolower(names(odk))
## Output Variables
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", "Id10185",
"Id10186", "Id10187", "Id10188", "Id10189", "Id10190", "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)
# check for missing indicators
tmpMat <- matrix(sapply(whoNames, stri_endswith_fixed, str = odkNames), nrow = length(odkNames))
indexData <- apply(tmpMat, 2, which)
warnZeroMatch <- which(sapply(indexData, length) == 0)
if (length(warnZeroMatch) > 0) {
cat(
paste("Expecting indicator(s) with name(s): ",
whoNames[unique(warnZeroMatch)],
sep = ""),
sep = "\n"
)
stop("Problem with data: please add above columns to your data frame")
}
numNA <- 0 # used for tracking columns with NAs
indexNA <- NULL
flagNonNumeric <- function(x) {
return(tryCatch(as.numeric(x),
error = function(c) -9999,
warning = function(c) -9999)
)
}
# function for creating simple Y/N indicators
qYesNo <- c(20:40, 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, 142:143, 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]
cat(
paste("Duplicate column names containing:",
tmpNames[unlist(dups)],
sep = " "),
sep = "\n"
)
stop("Problem with data: please remove or rename one of the duplicate columns.")
}
iv5Out[ , qYesNo] <- as.matrix(odk[ , indexData])
iv5Out[iv5Out=="yes" | iv5Out=="Yes" | iv5Out=="YES"] <- "y"
iv5Out[iv5Out=="no" | iv5Out=="No" | iv5Out=="NO"] <- "n"
iv5Out[iv5Out=="dk" | iv5Out=="DK" | iv5Out=="Doesn't Know"] <- "."
iv5Out[iv5Out=="Doesn't know" | iv5Out=="doesn't know"] <- "."
iv5Out[iv5Out=="does not know" | iv5Out=="Does Not Know" | iv5Out=="Does not know"] <- "."
iv5Out[iv5Out=="ref" | iv5Out=="Ref" | iv5Out=="REF"] <- "."
iv5Out[iv5Out==""] <- "."
iv5Out[is.na(iv5Out)] <- "."
# Step through iv5 indicators to create new values
#1) Did s(he) die during the wet season? d wet & 2) Did s(he) die during the dry season? d dry
indexData <- which(stri_endswith_fixed(odkNames, whoNames[1]))
iv5Out[tolower(odk[ , indexData])=="wet" | tolower(odk[ , indexData])=="wet season", 1] <- "y" ## wet season
iv5Out[tolower(odk[ , indexData])=="dry" | tolower(odk[ , indexData])=="dry season", 1] <- "n"
iv5Out[tolower(odk[ , indexData])=="wet" | tolower(odk[ , indexData])=="wet season", 2] <- "n" ## dry season
iv5Out[tolower(odk[ , indexData])=="dry" | tolower(odk[ , indexData])=="dry season", 2] <- "y"
#3) Was he male? male & ##4) Was he female? female
indexData_sex <- which(stri_endswith_fixed(odkNames, whoNames[3]))
iv5Out[tolower(odk[ , indexData_sex])=="male", 3] <- "y"
iv5Out[tolower(odk[ , indexData_sex])=="female", 3] <- "n"
iv5Out[tolower(odk[ , indexData_sex])=="male", 4] <- "n"
iv5Out[tolower(odk[ , indexData_sex])=="female", 4] <- "y"
# age
indexData1y <- which(stri_endswith_fixed(odkNames, "ageinyears"))
nonNumeric <- lapply(odk[ , indexData1y], flagNonNumeric)
nonNumeric <- unlist(nonNumeric)
containsNA <- ifelse(
sum(nonNumeric < 0, na.rm = TRUE) > 0,
1, 0)
numNA <- numNA + containsNA
if (containsNA > 0) indexNA <- c(indexNA, odkNames[indexData1y])
nonNumeric[nonNumeric < 0] <- NA
odk[is.na(nonNumeric), indexData1y] <- NA
odk[, indexData1y] <- as.numeric(odk[, indexData1y])
indexData1m <- which(stri_endswith_fixed(odkNames, "ageinmonths"))
nonNumeric <- lapply(odk[ , indexData1m], flagNonNumeric)
nonNumeric <- unlist(nonNumeric)
containsNA <- ifelse(
sum(nonNumeric < 0, na.rm = TRUE) > 0,
1, 0)
numNA <- numNA + containsNA
if (containsNA > 0) indexNA <- c(indexNA, odkNames[indexData1m])
nonNumeric[nonNumeric < 0] <- NA
odk[is.na(nonNumeric), indexData1m] <- NA
odk[, indexData1m] <- as.numeric(odk[, indexData1m])
indexData1d <- which(stri_endswith_fixed(odkNames, "ageindays"))
nonNumeric <- lapply(odk[ , indexData1d], flagNonNumeric)
nonNumeric <- unlist(nonNumeric)
containsNA <- ifelse(
sum(nonNumeric < 0, na.rm = TRUE) > 0,
1, 0)
numNA <- numNA + containsNA
if (containsNA > 0) indexNA <- c(indexNA, odkNames[indexData1d])
nonNumeric[nonNumeric < 0] <- NA
odk[is.na(nonNumeric), indexData1d] <- NA
odk[, indexData1d] <- as.numeric(odk[, indexData1d])
indexData2 <- which(stri_endswith_fixed(odkNames, "age_group"))
indexData3 <- which(stri_endswith_fixed(odkNames, "age_adult"))
nonNumeric <- lapply(odk[ , indexData3], flagNonNumeric)
nonNumeric <- unlist(nonNumeric)
containsNA <- ifelse(
sum(nonNumeric < 0, na.rm = TRUE) > 0,
1, 0)
numNA <- numNA + containsNA
if (containsNA > 0) indexNA <- c(indexNA, odkNames[indexData3])
nonNumeric[nonNumeric < 0] <- NA
odk[is.na(nonNumeric), indexData3] <- NA
odk[, indexData3] <- as.numeric(odk[, indexData3])
indexData4 <- which(stri_endswith_fixed(odkNames, "age_child_unit"))
indexData4d <- which(stri_endswith_fixed(odkNames, "age_child_days"))
nonNumeric <- lapply(odk[ , indexData4d], flagNonNumeric)
nonNumeric <- unlist(nonNumeric)
containsNA <- ifelse(
sum(nonNumeric < 0, na.rm = TRUE) > 0,
1, 0)
numNA <- numNA + containsNA
if (containsNA > 0) indexNA <- c(indexNA, odkNames[indexData4d])
nonNumeric[nonNumeric < 0] <- NA
odk[is.na(nonNumeric), indexData4d] <- NA
odk[, indexData4d] <- as.numeric(odk[, indexData4d])
indexData4m <- which(stri_endswith_fixed(odkNames, "age_child_months"))
nonNumeric <- lapply(odk[ , indexData4m], flagNonNumeric)
nonNumeric <- unlist(nonNumeric)
containsNA <- ifelse(
sum(nonNumeric < 0, na.rm = TRUE) > 0,
1, 0)
numNA <- numNA + containsNA
if (containsNA > 0) indexNA <- c(indexNA, odkNames[indexData4m])
nonNumeric[nonNumeric < 0] <- NA
odk[is.na(nonNumeric), indexData4m] <- NA
odk[, indexData4m] <- as.numeric(odk[, indexData4m])
indexData4y <- which(stri_endswith_fixed(odkNames, "age_child_years"))
nonNumeric <- lapply(odk[ , indexData4y], flagNonNumeric)
nonNumeric <- unlist(nonNumeric)
containsNA <- ifelse(
sum(nonNumeric < 0, na.rm = TRUE) > 0,
1, 0)
numNA <- numNA + containsNA
if (containsNA > 0) indexNA <- c(indexNA, odkNames[indexData4y])
nonNumeric[nonNumeric < 0] <- NA
odk[is.na(nonNumeric), indexData4y] <- NA
odk[, indexData4y] <- as.numeric(odk[, indexData4y])
indexData5d <- which(stri_endswith_fixed(odkNames, "age_neonate_days"))
nonNumeric <- lapply(odk[ , indexData5d], flagNonNumeric)
nonNumeric <- unlist(nonNumeric)
containsNA <- ifelse(
sum(nonNumeric < 0, na.rm = TRUE) > 0,
1, 0)
numNA <- numNA + containsNA
if (containsNA > 0) indexNA <- c(indexNA, odkNames[indexData5d])
nonNumeric[nonNumeric < 0] <- NA
odk[is.na(nonNumeric), indexData5d] <- NA
odk[, indexData5d] <- as.numeric(odk[, indexData5d])
indexData5h <- which(stri_endswith_fixed(odkNames, "age_neonate_hours"))
nonNumeric <- lapply(odk[ , indexData5h], flagNonNumeric)
nonNumeric <- unlist(nonNumeric)
containsNA <- ifelse(
sum(nonNumeric < 0, na.rm = TRUE) > 0,
1, 0)
numNA <- numNA + containsNA
if (containsNA > 0) indexNA <- c(indexNA, odkNames[indexData5h])
nonNumeric[nonNumeric < 0] <- NA
odk[is.na(nonNumeric), indexData5h] <- NA
odk[, indexData5h] <- as.numeric(odk[, indexData5h])
indexData5m <- which(stri_endswith_fixed(odkNames, "age_neonate_minutes"))
nonNumeric <- lapply(odk[ , indexData5m], flagNonNumeric)
nonNumeric <- unlist(nonNumeric)
containsNA <- ifelse(
sum(nonNumeric < 0, na.rm = TRUE) > 0,
1, 0)
numNA <- numNA + containsNA
if (containsNA > 0) indexNA <- c(indexNA, odkNames[indexData5m])
nonNumeric[nonNumeric < 0] <- NA
odk[is.na(nonNumeric), indexData5m] <- NA
odk[, indexData5m] <- as.numeric(odk[, indexData5m])
indexData_isNeonatal <- which(stri_endswith_fixed(odkNames, "isneonatal"))
indexData_isChild <- which(stri_endswith_fixed(odkNames, "ischild"))
indexData_isAdult <- which(stri_endswith_fixed(odkNames, "isadult"))
#5) Was s(he) aged 65 years or more at death? 65+
iv5Out[odk[ , indexData1y]>=65, 5] <- "y"
iv5Out[is.na(odk[ , indexData1y]) & odk[ , indexData2]=="adult" &
odk[ , indexData3]>=65, 5] <- "y"
#6) Was s(he) aged 50 to 64 years at death? 50 to 64
iv5Out[odk[ , indexData1y]< 65 & odk[ , indexData1y]>=50, 6] <- "y"
iv5Out[is.na(odk[ , indexData1y]) & odk[ ,indexData2]=="adult" &
odk[ ,indexData3]< 65 & odk[ ,indexData3]>=50, 6] <- "y"
#7) Was s(he) aged 15 to 49 years at death? 15-49
iv5Out[odk[ , indexData1y]< 50 & odk[ , indexData1y]>=15, 7] <- "y"
iv5Out[is.na(odk[ , indexData1y]) & odk[ , indexData2]=="adult" &
odk[ , indexData3]< 50 & odk[ , indexData3]>=15, 7] <- "y"
#8) Was s(he) aged 5-14 years at death? 5-14 (adult or child)
iv5Out[odk[ , indexData1y]< 15 & odk[ , indexData1y]>= 5, 8] <- "y"
iv5Out[is.na(odk[ , indexData1y]) & odk[ , indexData2]=="adult" &
odk[ , indexData3]< 15 & odk[ , indexData3]>=5, 8] <- "y"
iv5Out[is.na(odk[ , indexData1y]) & odk[ , indexData2]=="child" &
odk[ , indexData4]=="days" & odk[ , indexData4d]< 15*365.25 &
odk[ , indexData4d]>=5*365.25, 8] <- "y"
iv5Out[is.na(odk[ , indexData1y]) & odk[ , indexData2]=="child" &
odk[ , indexData4]=="months" & odk[ , indexData4m]< 15*12 &
odk[ , indexData4m]>=5*12, 8] <- "y"
iv5Out[is.na(odk[ , indexData1y]) & odk[ , indexData2]=="child" &
odk[ , indexData4]=="years" & odk[ , indexData4y]< 15 &
odk[ , indexData4y]>=5, 8] <- "y"
#9) Was s(he) aged 1 to 4 years at death? 1 to 4 (child)
iv5Out[odk[ , indexData1y]< 5 & odk[ , indexData1y]>=1, 9] <- "y"
iv5Out[is.na(odk[ , indexData1y]) & odk[ , indexData2]=="child" &
odk[ , indexData4]=="days" & odk[ , indexData4d]< 5*365.25 &
odk[ , indexData4d]>=1*365.25, 9] <- "y"
iv5Out[is.na(odk[ , indexData1y]) & odk[ , indexData2]=="child" &
odk[ , indexData4]=="months" & odk[ , indexData4m]< 5*12 &
odk[ , indexData4m]>=1*12, 9] <- "y"
iv5Out[is.na(odk[ , indexData1y]) & odk[ , indexData2]=="child" &
odk[ , indexData4]=="years" & odk[ , indexData4y]< 5 &
odk[ , indexData4y]>=1, 9] <- "y"
#10) Was s(he) aged 1 to 11 months at death? 1-11 months (child or neonate?)
iv5Out[odk[ , indexData1d]< 365.25 & odk[ , indexData1d]>=28, 10] <- "y"
iv5Out[is.na(odk[ , indexData1d]) & odk[ , indexData2]=="child" &
odk[ , indexData4]=="days" & odk[ , indexData4d]< 365.25 &
odk[ , indexData4d]>=28, 10] <- "y"
#11) Was s(he) aged < 1 month (28 days) at death? 0 - 27 days (neonate)
iv5Out[odk[ , indexData1d]< 28, 11] <- "y"
iv5Out[is.na(odk[ , indexData1d]) & odk[ , indexData2]=="neonate", 11] <- "y"
#12) Was s(he) a live baby who died within 24 hours of birth? day0 iv5Names[12]
iv5Out[odk[ , indexData1d]< 1, 12] <- "y"
ageDays <- odk[ , indexData5d]
ageHours <- odk[ , indexData5h]/24;
ageHours[is.na(ageHours)] <- 0
ageMinutes <- odk[ , indexData5m]/(24*12)
ageMinutes[is.na(ageMinutes)] <- 0
ageNeonate <- ageDays + ageHours + ageMinutes
iv5Out[odk[ , indexData2]=="neonate" & !is.na(odk[ , indexData5d]) &
ageNeonate< 1, 12] <- "y"
#13) Was s(he) a baby who died between 24 and 48 hours of birth? day1 iv5Names[13]
iv5Out[odk[ , indexData2]=="neonate" & !is.na(odk[ , indexData5d]) &
ageNeonate< 2 & ageNeonate>=1, 13] <- "y"
#14) Was s(he) a baby who died more than 48 hours from birth, but within the first week? day2-6 iv5Names[14]
iv5Out[odk[ , indexData2]=="neonate" & !is.na(odk[ , indexData5d]) &
ageNeonate< 7 & ageNeonate>=2, 14] <- "y"
#15) Was s(he) a baby who died after the first week, but within the first month? wk2-4 iv5Names[15]
iv5Out[odk[ , indexData2]=="neonate" & !is.na(odk[ , indexData5d]) &
ageNeonate< 28 & ageNeonate>=7, 15] <- "y"
# Finish coding age (5-15) -- if only only one age has "y", recode all others to "n"
## e.g., if age 65 == "y", then age 50-64 == "n" and age 15-49 == "n" etc.
indexData6 <-iv5Out[ , 5:11] != "y" ## identify elements in age columns that do not equal "y"
##indexData7 <- rowSums(iv5Out[ , 5:15] == "y") ## identify with rows/records only have 1 "y" for all age columns
indexData7 <- rowSums(iv5Out[ , 5:11] == "y", na.rm = TRUE) ## identify with rows/records only have 1 "y" for all age columns
## Now recode all "n"
iv5Out[indexData7 == 1, 5:11][ indexData6[indexData7 == 1, ] ] <- "n"
## Extend "n" to neonates sub-categories (if not a neonate)
indexData8 <- iv5Out[ , 11] == "n"
iv5Out[indexData8, 12:15] <- "n"
#16) Was she a woman aged 12-19 years at death? f-19
iv5Out[ , 16] <- ifelse(odk[ , indexData_sex]=="female" &
odk[ , indexData1y]< 20 &
odk[ , indexData1y]>= 12, "y", ".")
iv5Out[odk[ , indexData_sex]=="female" & odk[ , indexData1y]< 12, 16] <- "n"
iv5Out[odk[ , indexData_sex]=="female" & odk[ , indexData1y]> 19, 16] <- "n"
iv5Out[odk[ , indexData_sex]=="female" & is.na(odk[ , indexData1y]) &
odk[ , indexData2]=="adult" & odk[ , indexData3]< 20 &
odk[ , indexData3]>=12, 16] <- "y"
iv5Out[odk[ , indexData_sex]=="female" & is.na(odk[ , indexData1y]) &
odk[ , indexData2]=="adult" & odk[ , indexData3]< 12, 16] <- "n"
iv5Out[odk[ , indexData_sex]=="female" & is.na(odk[ , indexData1y]) &
odk[ , indexData2]=="adult" & odk[ , indexData3]> 19, 16] <- "n"
iv5Out[odk[ , indexData2]=="neonate", 16] <- "n"
iv5Out[odk[ , indexData_isNeonatal] == 1, 16] <- "n"
iv5Out[odk[ , indexData_isChild] == 1 & odk[ , indexData1y] < 12, 16] <- "n"
iv5Out[odk[ , indexData_isChild] == 1 & odk[ , indexData4y] < 12, 16] <- "n"
iv5Out[odk[ , indexData_isChild] == 1 &
odk[ , indexData4m] < 12*12, 16] <- "n"
iv5Out[odk[ , indexData_isChild] == 1 &
odk[ , indexData4d] < 12*365.25, 16] <- "n"
iv5Out[odk[ , indexData_sex]=="male", 16] <- "n"
#17) Was she a woman aged 20-34 years at death? f20-34
iv5Out[ , 17] <- ifelse(odk[ , indexData_sex]=="female" &
odk[ , indexData1y]< 35 &
odk[ , indexData1y]>= 20, "y", ".")
iv5Out[odk[ , indexData_sex]=="female" & odk[ , indexData1y]< 20, 17] <- "n"
iv5Out[odk[ , indexData_sex]=="female" & odk[ , indexData1y]> 34, 17] <- "n"
iv5Out[odk[ , indexData_sex]=="female" & is.na(odk[ , indexData1y]) &
odk[ , indexData2]=="adult" & odk[ , indexData3]< 35 &
odk[ , indexData3]>=20, 17] <- "y"
iv5Out[odk[ , indexData_sex]=="female" & is.na(odk[ , indexData1y]) &
odk[ , indexData2]=="adult" & odk[ , indexData3]< 20, 17] <- "n"
iv5Out[odk[ , indexData_sex]=="female" & is.na(odk[ , indexData1y]) &
odk[ , indexData2]=="adult" & odk[ , indexData3]> 34, 17] <- "n"
iv5Out[odk[ , indexData2]=="neonate", 17] <- "n"
iv5Out[odk[ , indexData_isNeonatal] == 1, 17] <- "n"
iv5Out[odk[ , indexData_isChild] == 1, 17] <- "n"
iv5Out[odk[ , indexData_sex]=="male", 17] <- "n"
#18) Was she a woman aged 35 to 49 years at death? f35-49
iv5Out[ , 18] <- ifelse(odk[ , indexData_sex]=="female" &
odk[ , indexData1y]< 50 &
odk[ , indexData1y]>= 35, "y", ".")
iv5Out[odk[ , indexData_sex]=="female" & odk[ , indexData1y]< 35, 18] <- "n"
iv5Out[odk[ , indexData_sex]=="female" & odk[ , indexData1y]> 49, 18] <- "n"
iv5Out[odk[ , indexData_sex]=="female" & is.na(odk[ , indexData1y]) &
odk[ , indexData2]=="adult" & odk[ , indexData3]< 50 &
odk[ , indexData3]>=35, 18] <- "y"
iv5Out[odk[ , indexData_sex]=="female" & is.na(odk[ , indexData1y]) &
odk[ , indexData2]=="adult" & odk[ , indexData3]< 35, 18] <- "n"
iv5Out[odk[ , indexData_sex]=="female" & is.na(odk[ , indexData1y]) &
odk[ , indexData2]=="adult" & odk[ , indexData3]> 49, 18] <- "n"
iv5Out[odk[ , indexData2]=="neonate", 18] <- "n"
iv5Out[odk[ , indexData_isNeonatal] == 1, 18] <- "n"
iv5Out[odk[ , indexData_isChild] == 1, 18] <- "n"
iv5Out[odk[ , indexData_sex]=="male", 18] <- "n"
#19) Was she married at the time of death? married
indexData <- which(stri_endswith_fixed(odkNames, whoNames[19]))
## table(odk[ , indexData])
iv5Out[odk[ , indexData_sex]=="female" & tolower(odk[ , indexData])=="married", 19] <- "y"
iv5Out[odk[ , indexData_sex]=="female" & tolower(odk[ , indexData])=="single", 19] <- "n"
iv5Out[odk[ , indexData_sex]=="female" & tolower(odk[ , indexData])=="partner", 19] <- "n"
iv5Out[odk[ , indexData_sex]=="female" & tolower(odk[ , indexData])=="divorced", 19] <- "n"
iv5Out[odk[ , indexData_sex]=="female" & tolower(odk[ , indexData])=="widowed", 19] <- "n"
iv5Out[odk[ , indexData_sex]=="female" & tolower(odk[ , indexData])=="too_young_to_be_married", 19] <- "n"
iv5Out[odk[ , indexData_sex]=="female" & tolower(odk[ , indexData])=="child", 19] <- "n"
iv5Out[odk[ , indexData_sex]=="male", 19] <- "n"
#41) Was it more than 5 minutes after birth before the baby first cried? cry 5+m
indexData <- which(stri_endswith_fixed(odkNames, whoNames[41]))
iv5Out[odk[ , indexData]> 5, 41] <- "y"
iv5Out[odk[ , indexData]<=5, 41] <- "n"
#43) Did the baby stop crying more than a day before (s)he died? cry st 1+d
indexData <- which(stri_endswith_fixed(odkNames, whoNames[43]))
iv5Out[odk[ , indexData]> 24, 43] <- "y"
iv5Out[odk[ , indexData]<=24, 43] <- "n"
#52) Did the final illness last less than 3 weeks? ill <3w.
indexDatad <- which(stri_endswith_fixed(odkNames, "id10120"))
indexDataw <- which(stri_endswith_fixed(odkNames, "id10122")) ## should this be "years"?
indexDatam <- which(stri_endswith_fixed(odkNames, "id10121"))
iv5Out[odk[ , indexDatad]< 21, 52] <- "y"
iv5Out[odk[ , indexDatad]>=21, 52] <- "n"
iv5Out[odk[ , indexDataw]< 3, 52] <- "y"
iv5Out[odk[ , indexDataw]>=3, 52] <- "n"
#iv5Out[odk[ , indexDatam]< 1, 52] <- "y"
iv5Out[odk[ , indexDatam]>=1, 52] <- "n"
#53) Did the final illness last at least 3 weeks? ill 3+w
iv5Out[odk[ , indexDatad]>=21, 53] <- "y"
iv5Out[odk[ , indexDatad]< 21, 53] <- "n"
iv5Out[odk[ , indexDataw]>= 3, 53] <- "y"
iv5Out[odk[ , indexDataw]< 3, 53] <- "n"
iv5Out[odk[ , indexDatam]>= 1, 53] <- "y"
#iv5Out[odk[ , indexDatam]< 1, 53] <- "y"
#75) Did the fever last less than a week before death? fev <1w
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]=="no", 75] <- "n"
#76) Did the fever last at least one week, but less than 2 weeks before death? fev 1-2w
iv5Out[odk[ , indexData]=="yes" & odk[ , indexData_days]< 7, 76] <- "n"
iv5Out[odk[ , indexData]=="yes" & odk[ , indexData_days]>= 7 & odk[ , indexData_days]< 14, 76] <- "y"
iv5Out[odk[ , indexData]=="yes" & odk[ , indexData_days]>=14, 76] <- "n"
iv5Out[odk[ , indexData]=="no", 76] <- "n"
#77) Did the fever last at least 2 weeks before death? fev 2+w
iv5Out[odk[ , indexData]=="yes" & odk[ , indexData_days]>= 14, 77] <- "y"
iv5Out[odk[ , indexData]=="yes" & odk[ , indexData_days]< 14, 77] <- "n"
iv5Out[odk[ , indexData]=="no", 77] <- "n"
#78) Did the fever continue until death
iv5Out[odk[ , indexData]=="no", 78] <- "n"
#79) Was the fever severe? fev sev
indexData_sev <- which(stri_endswith_fixed(odkNames, whoNames[79]))
iv5Out[odk[ , indexData]=="yes" & tolower(odk[ , indexData_sev])=="severe", 79] <- "y"
iv5Out[odk[ , indexData]=="yes" & tolower(odk[ , indexData_sev])=="mild", 79] <- "n"
iv5Out[odk[ , indexData]=="yes" & tolower(odk[ , indexData_sev])=="moderate", 79] <- "n"
iv5Out[odk[ , indexData]=="no", 79] <- "n"
#80) Was the fever continuous? fev cont
indexData_cont <- which(stri_endswith_fixed(odkNames, whoNames[80]))
iv5Out[odk[ , indexData]=="yes" & tolower(odk[ , indexData_cont])=="continuous", 80] <- "y"
iv5Out[odk[ , indexData]=="yes" & tolower(odk[ , indexData_cont])=="nightly", 80] <- "n"
iv5Out[odk[ , indexData]=="yes" & tolower(odk[ , indexData_cont])=="on_and_off", 80] <- "n"
iv5Out[odk[ , indexData]=="no", 80] <- "n"
#83) Did the cough last less than 3 weeks before death? cou <3w
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"
#84) Did the cough last at least 3 weeks before death? cou 3+w
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"
#90) Did the difficult breathing last for at least 3 days before death? dif br 3d
indexDatad <- which(stri_endswith_fixed(odkNames, whoNames[90]))
indexDatam <- which(stri_endswith_fixed(odkNames, "id10162"))
indexDatay <- which(stri_endswith_fixed(odkNames, "id10163"))
## indexDatad; odkNames[indexDatad]. #
iv5Out[odk[ , indexDatad]>=3, 90] <- "y"
iv5Out[odk[ , indexDatad]< 3, 90] <- "n"
iv5Out[odk[ , indexDatam]>=1, 90] <- "y"
iv5Out[odk[ , indexDatay]>=1, 90] <- "y"
#91) Was the difficult breathing continuous during this period? dif br con
indexData <- which(stri_endswith_fixed(odkNames, whoNames[91]))
iv5Out[tolower(odk[ , indexData])=="continuous", 91] <- "y"
iv5Out[tolower(odk[ , indexData])=="on_and_off", 91] <- "n"
#93) Did the fast breathing last for less than two weeks before death? br fs <2w
indexData <- which(stri_endswith_fixed(odkNames, whoNames[93]))
iv5Out[odk[ , indexData[1]]< 14, 93] <- "y"
iv5Out[odk[ , indexData[1]]>=14, 93] <- "n"
#94) Did the fast breathing last for at least 2 weeks before death? br fs 2+w
iv5Out[odk[ , indexData[1]]>=14, 94] <- "y"
iv5Out[odk[ , indexData[1]]< 14, 94] <- "n"
#96) Did the breathlessness last for less than 2 weeks before death? brl <2w
indexData <- which(stri_endswith_fixed(odkNames, whoNames[96]))
iv5Out[odk[ , indexData[1]]< 14, 96] <- "y"
iv5Out[odk[ , indexData[1]]>=14, 96] <- "n"
#97) Did the breathlessness last for at least 2 weeks before death? brl 2+w
iv5Out[odk[ , indexData[1]]>=14, 97] <- "y"
iv5Out[odk[ , indexData[1]]< 14, 97] <- "n"
#101) Did his/her breathing sound like wheezing or grunting? whz grun
indexData <- which(stri_endswith_fixed(odkNames, whoNames[101]))
iv5Out[stri_endswith_fixed(tolower(odk[ , indexData]), "grunting"), 101] <- "y"
iv5Out[stri_endswith_fixed(tolower(odk[ , indexData]), "stridor"), 101] <- "y"
iv5Out[stri_endswith_fixed(tolower(odk[ , indexData]), "wheezing"), 101] <- "y"
iv5Out[stri_endswith_fixed(tolower(odk[ , indexData]), "no"), 101] <- "n"
#104) Did (s)he experience chest pain at least 3 days before death? chp 3d
indexData <- which(stri_endswith_fixed(odkNames, whoNames[104]))
iv5Out[odk[ , indexData]>=3, 104] <- "y"
iv5Out[odk[ , indexData]< 3, 104] <- "n"
#105) Did the chest pain last for at least 30 minutes? chp 30m
indexDatam <- which(stri_endswith_fixed(odkNames, whoNames[105]))
indexDatah <- which(stri_endswith_fixed(odkNames, "id10179"))
iv5Out[odk[ , indexDatam]>=30, 105] <- "y"
iv5Out[odk[ , indexDatah]>=.5, 105] <- "y"
iv5Out[odk[ , indexDatam]< 30, 105] <- "n"
iv5Out[odk[ , indexDatah]< .5, 105] <- "n"
#107) Did (s)he have diarrhoea for less than 2 weeks before death? drr <2w
indexData <- which(stri_endswith_fixed(odkNames, whoNames[107]))
iv5Out[odk[ , indexData]< 14, 107] <- "y"
iv5Out[odk[ , indexData]>=14, 107] <- "n"
#108) Did (s)he have diarrhoea for at least 2 weeks but less than 4 weeks before death? drr 2-4w
iv5Out[odk[ , indexData]< 28 & odk[ , indexData]>=14, 108] <- "y"
iv5Out[odk[ , indexData]< 14, 108] <- "n"
iv5Out[odk[ , indexData]>=28, 108] <- "n"
#109) Did (s)he have diarrhoea for at least 4 weeks before death? drr 4+w
iv5Out[odk[ , indexData]>=28, 109] <- "y"
iv5Out[odk[ , indexData]< 28, 109] <- "n"
#110) Did the baby or child have at least 4 stools on the day that loose liquid stools were most frequent? 4+ stls
indexData <- which(stri_endswith_fixed(odkNames, whoNames[110]))
iv5Out[odk[ , indexData]>= 4 & odk[ , indexData]< 999, 110] <- "y"
iv5Out[odk[ , indexData]< 4, 110] <- "n"
#111) Did the frequent loose or liquid stools start at least 3 days before death? drr 3d
indexData <- which(stri_endswith_fixed(odkNames, whoNames[111]))
iv5Out[odk[ , indexData]>= 3 & odk[ , indexData]< 999, 111] <- "y"
iv5Out[odk[ , indexData]< 3, 111] <- "n"
#117) Did (s)he vomit for at least 3 days before death? vom 3d
indexData <- which(stri_endswith_fixed(odkNames, whoNames[117]))
iv5Out[odk[ , indexData]>= 3 & odk[ , indexData]< 999, 117] <- "y"
iv5Out[odk[ , indexData]< 3, 117] <- "n"
#123) Did (s)he have severe abdominal pain for less than 2 weeks before death? abd p <2w
## indexData <- which(stri_endswith_fixed(odkNames, whoNames[122]))
indexFilter <- which(stri_endswith_fixed(odkNames, "id10194"))
indexData <- which(stri_endswith_fixed(odkNames, "id10195"))
indexDatad <- which(stri_endswith_fixed(odkNames, "id10197"))
indexDatah <- which(stri_endswith_fixed(odkNames, "id10196"))
indexDataw <- which(stri_endswith_fixed(odkNames, "id10197b"))
indexDatam <- which(stri_endswith_fixed(odkNames, "id10198"))
iv5Out[tolower(odk[ , indexData])=="yes" & odk[ , indexDatad]< 14, 123] <- "y"
iv5Out[tolower(odk[ , indexData])=="yes" & odk[ , indexDatad]>=14, 123] <- "n"
iv5Out[tolower(odk[ , indexData])=="yes" & odk[ , indexDatah]< (24*14), 123] <- "y"
iv5Out[tolower(odk[ , indexData])=="yes" & odk[ , indexDatah]>=(24*14), 123] <- "n"
iv5Out[tolower(odk[ , indexData])=="yes" & odk[ , indexDataw]< 2, 123] <- "y"
iv5Out[tolower(odk[ , indexData])=="yes" & odk[ , indexDataw]>=2, 123] <- "n"
iv5Out[tolower(odk[ , indexData])=="yes" & odk[ , indexDatam]< 1, 123] <- "y"
iv5Out[tolower(odk[ , indexData])=="no", 123] <- "n"
iv5Out[tolower(odk[ , indexFilter])=="no", 123] <- "n"
#124) Did (s)he have severe abdominal pain for at least 2 weeks before death? abd p 2+w
iv5Out[tolower(odk[ , indexData])=="yes" & odk[ , indexDatad]>=14, 124] <- "y"
iv5Out[tolower(odk[ , indexData])=="yes" & odk[ , indexDatad]< 14, 124] <- "n"
iv5Out[tolower(odk[ , indexData])=="yes" & odk[ , indexDatah]>=(24*14), 124] <- "y"
iv5Out[tolower(odk[ , indexData])=="yes" & odk[ , indexDatah]< (24*14), 124] <- "n"
iv5Out[tolower(odk[ , indexData])=="yes" & odk[ , indexDataw]>=2, 124] <- "y"
iv5Out[tolower(odk[ , indexData])=="yes" & odk[ , indexDataw]< 2, 124] <- "n"
iv5Out[tolower(odk[ , indexData])=="yes" & odk[ , indexDatam]>=1, 124] <- "y"
iv5Out[tolower(odk[ , indexData])=="no", 124] <- "n"
iv5Out[tolower(odk[ , indexFilter])=="no", 124] <- "n"
#125) Was the pain in the upper abdomen? abd p up
indexData <- which(stri_endswith_fixed(odkNames, whoNames[125]))
iv5Out[tolower(odk[ , indexData])=="upper_abdomen", 125] <- "y"
iv5Out[tolower(odk[ , indexData])=="upper_lower_abdomen", 125] <- "y"
iv5Out[tolower(odk[ , indexData])=="lower_abdomen", 125] <- "n"
#126) Was the pain in the lower abdomen? abd p lo
iv5Out[tolower(odk[ , indexData])=="upper_abdomen", 126] <- "n"
iv5Out[tolower(odk[ , indexData])=="upper_lower_abdomen", 126] <- "y"
iv5Out[tolower(odk[ , indexData])=="lower_abdomen", 126] <- "y"
#128) Did (s)he have a more than usually protruding abdomen for less than 2 weeks before death? abd pr <2w
indexData <- which(stri_endswith_fixed(odkNames, "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"
#129) Did (s)he have a more than usually protruding abdomen for at least 2 weeks before death? abd pr 2+w
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"
#130) Did (s)he develop the protruding abdomen rapidly? abd pr rap
indexData <- which(stri_endswith_fixed(odkNames, whoNames[130]))
iv5Out[tolower(odk[ , indexData])=="rapidly", 130] <- "y"
iv5Out[tolower(odk[ , indexData])=="slowly", 130] <- "n"
#132) Did (s)he have a mass in the abdomen for less than 2 weeks before death? ab ms <2w
indexData <- which(stri_endswith_fixed(odkNames, "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"
#133) Did (s)he have a mass in the abdomen for at least 2 weeks before death? ab ms 2+w
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"
#136) Did (s)he have a stiff neck for less than one week before death? st n <1w
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"
#137) Did (s)he have a stiff neck for at least one week before death? st n 1+w
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"
#139) Did (s)he have a painful neck for at least one week before death? pa n 1+w
indexData <- which(stri_endswith_fixed(odkNames, "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"
#141) Did (s)he have mental confusion for at least 3 months before death? menc 3+m
indexData <- which(stri_endswith_fixed(odkNames, whoNames[140]))
indexDatad <- which(stri_endswith_fixed(odkNames, whoNames[141]))
iv5Out[tolower(odk[ , indexData])=="yes" & odk[ , indexDatad]>=3, 141] <- "y"
iv5Out[tolower(odk[ , indexData])=="yes" & odk[ , indexDatad]< 3, 141] <- "n"
iv5Out[tolower(odk[ , indexData])=="no", 141] <- "n"
#143) Was (s)he unsconscious for at least 24 hours before death? unc 24+h
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"
#144) Was (s)he unsconscious for at least 6 hours before death? unc 6+h
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"
#149) Did the convulsions last for less than 10 minutes? conv <10m
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] <- "."
#150) Did the convulsions last for at least 10 minutes? conv 10+m
iv5Out[odk[ , indexData]=="yes" & odk[ , indexData_min]< 10, 150] <- "n"
iv5Out[odk[ , indexData]=="yes" & odk[ , indexData_min]>=10, 150] <- "y"
#161) Did the ulcer ooze pus for at least 2 weeks? sk ul 2+w
indexData <- which(stri_endswith_fixed(odkNames, whoNames[161]))
iv5Out[odk[ , indexData]>=14, 161] <- "y"
iv5Out[odk[ , indexData]< 14, 161] <- "n"
#163) Did (s)he have the skin rash for less than one week? sk ra <1w
indexData <- which(stri_endswith_fixed(odkNames, whoNames[163]))
iv5Out[odk[ , indexData]< 7, 163] <- "y"
iv5Out[odk[ , indexData]>=7, 163] <- "n"
#164) Did (s)he have the skin rash for at least one week? sk ra 1+w
iv5Out[odk[ , indexData]>=7, 164] <- "y"
iv5Out[odk[ , indexData]< 7, 164] <- "n"
#165) Did (s)he have a rash on the face? sk ra face
indexData <- which(stri_endswith_fixed(odkNames, whoNames[165]))
iv5Out[stri_endswith_fixed(tolower(odk[ , indexData]), "face"), 165] <- "y"
iv5Out[stri_endswith_fixed(tolower(odk[ , indexData]), negate = TRUE, "face"), 165] <- "n"
iv5Out[tolower(odk[ , indexData])=="", 165] <- "."
#166) Did (s)he have a rash on the trunk or abdomen? sk ra abd
indexData <- which(stri_endswith_fixed(odkNames, whoNames[166]))
iv5Out[stri_endswith_fixed(tolower(odk[ , indexData]), "abdomen|trunk"), 166] <- "y"
iv5Out[stri_endswith_fixed(tolower(odk[ , indexData]), negate = TRUE, "abdomen|trunk"), 166] <- "n"
iv5Out[tolower(odk[ , indexData])=="", 166] <- "."
#167) Did (s)he have a rash on the extremities? sk ra ext
indexData <- which(stri_endswith_fixed(odkNames, whoNames[167]))
iv5Out[stri_endswith_fixed(tolower(odk[ , indexData]), "extremities"), 167] <- "y"
iv5Out[stri_endswith_fixed(tolower(odk[ , indexData]), negate = TRUE, "extremities"), 167] <- "n"
iv5Out[tolower(odk[ , indexData])=="", 167] <- "."
#168) Did (s)he have a rash everywhere? sk ra all
indexData <- which(stri_endswith_fixed(odkNames, whoNames[168]))
iv5Out[stri_endswith_fixed(tolower(odk[ , indexData]), "everywhere"), 168] <- "y"
iv5Out[stri_endswith_fixed(tolower(odk[ , indexData]), negate = TRUE, "everywhere"), 168] <- "n"
iv5Out[tolower(odk[ , indexData])=="", 168] <- "."
#181) Did (s)he have puffiness of the face for at least one week before death? sw p f 1+w
indexData <- which(stri_endswith_fixed(odkNames, whoNames[181]))
iv5Out[odk[ , indexData]>=7, 181] <- "y"
iv5Out[odk[ , indexData]< 7, 181] <- "n"
#183) Did the swelling last for at least 3 days before death? sw lf 3+d
indexData <- which(stri_endswith_fixed(odkNames, whoNames[183]))
iv5Out[odk[ , indexData]>=3, 183] <- "y"
iv5Out[odk[ , indexData]< 3, 183] <- "n"
#193) Was only the right side of the body paralysed? par rs
indexData <- which(stri_endswith_fixed(odkNames, whoNames[193]))
iv5Out[tolower(odk[ , indexData])=="right_side", 193] <- "y"
iv5Out[tolower(odk[ , indexData])!="right_side", 193] <- "n"
iv5Out[tolower(odk[ , indexData])=="", 193] <- "."
#194) Was only the left side of the body paralysed? par ls
iv5Out[tolower(odk[ , indexData])=="left_side", 194] <- "y"
iv5Out[tolower(odk[ , indexData])!="left_side", 194] <- "n"
iv5Out[tolower(odk[ , indexData])=="", 194] <- "."
#195) Was only the lower part of the body paralysed? par lo
iv5Out[tolower(odk[ , indexData])=="lower_part_of_body", 195] <- "y"
iv5Out[tolower(odk[ , indexData])!="lower_part_of_body", 195] <- "n"
iv5Out[tolower(odk[ , indexData])=="", 195] <- "."
#196) Was only the upper part of the body paralysed? par up
iv5Out[tolower(odk[ , indexData])=="upper_part_of_body", 196] <- "y"
iv5Out[tolower(odk[ , indexData])!="upper_part_of_body", 196] <- "n"
iv5Out[tolower(odk[ , indexData])=="", 196] <- "."
#197) Was only one leg paralysed? par leg
iv5Out[tolower(odk[ , indexData])=="one_leg_only", 197] <- "y"
iv5Out[tolower(odk[ , indexData])!="one_leg_only", 197] <- "n"
iv5Out[tolower(odk[ , indexData])=="", 197] <- "."
#198) Was only one arm paralysed? par arm
iv5Out[tolower(odk[ , indexData])=="one_arm_only", 198] <- "y"
iv5Out[tolower(odk[ , indexData])!="one_arm_only", 198] <- "n"
iv5Out[tolower(odk[ , indexData])=="", 198] <- "."
#199) Was the entire body paralysed? par all
iv5Out[tolower(odk[ , indexData])=="whole_body", 199] <- "y"
iv5Out[tolower(odk[ , indexData])!="whole_body", 199] <- "n"
iv5Out[tolower(odk[ , indexData])=="", 199] <- "."
#201) Did (s)he have difficulty swallowing for at least one week before death? swa 1+w
indexData <- which(stri_endswith_fixed(odkNames, whoNames[201]))
iv5Out[odk[ , indexData]>=7, 201] <- "y"
iv5Out[odk[ , indexData]< 7, 201] <- "n"
#202) Did (s)he have difficulty with swallowing solids? swa sol
indexData <- which(stri_endswith_fixed(odkNames, whoNames[202]))
iv5Out[tolower(odk[ , indexData])=="solids", 202] <- "y"
iv5Out[tolower(odk[ , indexData])=="both", 202] <- "y"
iv5Out[tolower(odk[ , indexData])=="liquids", 202] <- "n"
#203) Did (s)he have difficulty with swallowing liquids? swa liq
iv5Out[tolower(odk[ , indexData])=="solids", 203] <- "n"
iv5Out[tolower(odk[ , indexData])=="both", 203] <- "y"
iv5Out[tolower(odk[ , indexData])=="liquids", 203] <- "y"
#206) Did (s)he have the yellow discolouration for at least 3 weeks before death? yell 3+w
indexData <- which(stri_endswith_fixed(odkNames, whoNames[206]))
iv5Out[odk[ , indexData]>=21, 206] <- "y"
iv5Out[odk[ , indexData]< 21, 206] <- "n"
#214) Did the baby stop suckling on the 2nd day of life or later? suck st d1
indexData <- which(stri_endswith_fixed(odkNames, whoNames[214]))
iv5Out[odk[ , indexData[1]]>=2, 214] <- "y"
iv5Out[odk[ , indexData[1]]< 2, 214] <- "n"
#224) Was the baby more than 3 days old when it started feeling cold to touch? cold 3+d
indexData <- which(stri_endswith_fixed(odkNames, whoNames[224]))
iv5Out[odk[ , indexData]> 3, 224] <- "y"
iv5Out[odk[ , indexData]<=3, 224] <- "n"
#239) Had her period been overdue for at least 4 weeks? men l 4+w
indexData <- which(stri_endswith_fixed(odkNames, whoNames[239]))
iv5Out[odk[ , indexData]>=4, 239] <- "y"
iv5Out[odk[ , indexData]< 4, 239] <- "n"
#243) Was she, or had she been, pregnant for less than 6 months when she died? d <6m pr
indexData <- which(stri_endswith_fixed(odkNames, whoNames[243]))
iv5Out[odk[ , indexData]< 6, 243] <- "y"
iv5Out[odk[ , indexData]>=6, 243] <- "n"
#252) Did she die during or after her first pregnancy? 1st pr.
# WHO question is "How many births, including stillbirths, did she/the mother have before this baby?"
indexData <- which(stri_endswith_fixed(odkNames, whoNames[252]))
iv5Out[odk[ , indexData]==0, 252] <- "y"
iv5Out[odk[ , indexData]> 0, 252] <- "n"
#253) Did she have four or more pregnancies before this one? 4+ pr
iv5Out[odk[ , indexData]>=4, 253] <- "y"
iv5Out[odk[ , indexData]< 4, 253] <- "n"
#266) Did her labour last longer than 24 hours? lab 24+h
indexData <- which(stri_endswith_fixed(odkNames, whoNames[266]))
iv5Out[odk[ , indexData]> 24, 266] <- "y"
iv5Out[odk[ , indexData]<=24, 266] <- "n"
#271) Did the mother deliver at a health facility or clinic? del hfac
indexData <- which(stri_endswith_fixed(odkNames, whoNames[271]))
iv5Out[tolower(odk[ , indexData])=="hospital", 271] <- "y"
iv5Out[tolower(odk[ , indexData])=="other_health_facility", 271] <- "y"
iv5Out[tolower(odk[ , indexData])=="home", 271] <- "n"
iv5Out[tolower(odk[ , indexData])=="on_route_to_hospital_or_facility", 271] <- "n"
iv5Out[tolower(odk[ , indexData])=="other", 271] <- "n"
#272) Did the mother deliver at home? del home
iv5Out[tolower(odk[ , indexData])=="hospital", 272] <- "n"
iv5Out[tolower(odk[ , indexData])=="other_health_facility", 272] <- "n"
iv5Out[tolower(odk[ , indexData])=="home", 272] <- "y"
iv5Out[tolower(odk[ , indexData])=="on_route_to_hospital_or_facility", 272] <- "n"
iv5Out[tolower(odk[ , indexData])=="other", 272] <- "n"
#273) Did the mother deliver elsewhere (not at a health facility nor at home)? del else
iv5Out[tolower(odk[ , indexData])=="hospital", 273] <- "n"
iv5Out[tolower(odk[ , indexData])=="other_health_facility", 273] <- "n"
iv5Out[tolower(odk[ , indexData])=="home", 273] <- "n"
iv5Out[tolower(odk[ , indexData])=="on_route_to_hospital_or_facility", 273] <- "y"
iv5Out[tolower(odk[ , indexData])=="other", 273] <- "y"
#281) If the child was part of a multiple birth, was it born first? mult fir
indexData <- which(stri_endswith_fixed(odkNames, whoNames[281]))
iv5Out[tolower(odk[ , indexData])=="first", 281] <- "y"
iv5Out[tolower(odk[ , indexData])=="second_or_later", 281] <- "n"
#283) Did the child's mother die during or shortly after the delivery? moth d del
indexData <- which(stri_endswith_fixed(odkNames, whoNames[283]))
iv5Out[tolower(odk[ , indexData])=="after_delivery", 283] <- "y"
iv5Out[tolower(odk[ , indexData])=="during_delivery" , 283] <- "y"
#284) Did the child's mother die in the baby's first year of life? moth d y1
indexDataM <- which(stri_endswith_fixed(odkNames, whoNames[284]))
indexDataD <- which(stri_endswith_fixed(odkNames, "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"
#285) Was the baby born in a health facility or clinic? born fac
indexData <- which(stri_endswith_fixed(odkNames, whoNames[285]))
iv5Out[tolower(odk[ , indexData])=="hospital", 285] <- "y"
iv5Out[tolower(odk[ , indexData])=="other_health_facility", 285] <- "y"
iv5Out[tolower(odk[ , indexData])=="home", 285] <- "n"
iv5Out[tolower(odk[ , indexData])=="other", 285] <- "n"
iv5Out[tolower(odk[ , indexData])=="on_route_to_hospital_or_facility", 285] <- "n"
#286) Was the baby born at home? born home
iv5Out[tolower(odk[ , indexData])=="hospital", 286] <- "n"
iv5Out[tolower(odk[ , indexData])=="other_health_facility", 286] <- "n"
iv5Out[tolower(odk[ , indexData])=="home", 286] <- "y"
iv5Out[tolower(odk[ , indexData])=="other", 286] <- "n"
iv5Out[tolower(odk[ , indexData])=="on_route_to_hospital_or_facility", 286] <- "n"
#287) Was the baby born somewhere else (e.g. on the way to a clinic)? born on way
iv5Out[tolower(odk[ , indexData])=="hospital", 287] <- "n"
iv5Out[tolower(odk[ , indexData])=="other_health_facility", 287] <- "n"
iv5Out[tolower(odk[ , indexData])=="home", 287] <- "n"
iv5Out[tolower(odk[ , indexData])=="other", 287] <- "y"
iv5Out[tolower(odk[ , indexData])=="on_route_to_hospital_or_facility", 287] <- "y"
#293) Was the baby born during the ninth month (at least 37 weeks) of pregnancy? gest 9m
indexData <- which(stri_endswith_fixed(odkNames, whoNames[293]))
iv5Out[odk[ , indexData]>=9 & odk[ , indexData]< 88, 293] <- "y"
iv5Out[odk[ , indexData]< 9, 293] <- "n"
iv5Out[odk[ , indexData]==88, 293] <- "."
#294) Was the baby born during the eighth month (34 to 37 weeks) of pregnancy? gest 8m
iv5Out[odk[ , indexData]> 8 & odk[ , indexData]< 88, 294] <- "n"
iv5Out[odk[ , indexData]==8, 294] <- "y"
iv5Out[odk[ , indexData]< 8, 294] <- "n"
#295) Was the baby born before the eighth month (less than 34 weeks) of pregnancy? gest 7m
iv5Out[odk[ , indexData]>=8 & odk[ , indexData]< 88, 295] <- "n"
iv5Out[odk[ , indexData]< 8, 295] <- "y"
#304) Did labour and delivery take more than 24 hours? lab 24+h
indexData <- which(stri_endswith_fixed(odkNames, whoNames[304]))
iv5Out[odk[ , indexData]> 24, 304] <- "y"
iv5Out[odk[ , indexData]<=24, 304] <- "n"
#307) Was the liquor a green or brown colour when the waters broke? liq gr-br
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"
#313) Was this baby born from the mother's first pregnancy? born 1st pr
indexData <- which(stri_endswith_fixed(odkNames, whoNames[313]))
iv5Out[odk[ , indexData]==0, 313] <- "y"
iv5Out[odk[ , indexData]> 0, 313] <- "n"
#314) Did the baby's mother have four or more births before this one? born 4+ pr
iv5Out[odk[ , indexData]>=4, 314] <- "y"
iv5Out[odk[ , indexData]< 4, 314] <- "n"
#331) Did (s)he use non-smoking tobacco? tobac ns
indexData <- which(stri_endswith_fixed(odkNames, whoNames[331]))
iv5Out[tolower(odk[ , indexData])=="chewing_tobacco", 331] <- "y"
iv5Out[tolower(odk[ , indexData])=="cigarettes", 331] <- "n"
iv5Out[tolower(odk[ , indexData])=="pipe", 331] <- "n"
iv5Out[tolower(odk[ , indexData])=="local_form_of_tobacco", 331] <- "n"
iv5Out[tolower(odk[ , indexData])=="other", 331] <- "n"
#332) Did (s)he smoke at least 10 cigarettes daily? cigs >10
indexData <- which(stri_endswith_fixed(odkNames, whoNames[332]))
iv5Out[odk[ , indexData]>=10, 332] <- "y"
iv5Out[odk[ , indexData]< 10, 332] <- "n"
# check for NAs
if (numNA > 0) {
warning("Found unexpected input values (coded as missing)", call. = FALSE)
cat("Unexpected values found in: ", sep = "\n")
cat(paste(indexNA), sep = ", ")
cat("\n")
}
# check for NAs
numNA <- colSums(is.na(iv5Out))
indexNA <- which(numNA > 0)
if (length(indexNA) > 0) {
warning("NA's included in output", call. = FALSE)
cat(
paste("odk2openVA produced NA's in the following columns",
" (this may cause errors with openVA)",
sep = ""),
sep = "\n"
)
cat(
paste(iv5Names[indexNA], ## subtract 1 since ID is omitted
" Probably associated with WHO column containing: ",
whoNames[indexNA], ## subtract 1 since ID is omitted
sep = ""),
sep = "\n"
)
}
# Add ID as first column
indexID <- which(stri_endswith_fixed(odkNames, tolower(id_col)))
if (length(indexID)) {
iv5Out <- cbind(as.character(odk[, indexID]), iv5Out)
} else {
message("Did not find id_col, so assigning row numbers for IDs.",
call. = FALSE)
iv5Out <- cbind(as.character(1:nrow(iv5Out)), iv5Out)
}
# Attach column names
colnames(iv5Out) <- c("ID", iv5Names)
# That's all folks!
return(as.data.frame(iv5Out, stringsAsFactors = FALSE))
}
Try the CrossVA package in your browser
Any scripts or data that you put into this service are public.
CrossVA documentation built on Aug. 11, 2021, 1:06 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
#' Map VA records (version 1.4.1) to InterVA5 and InSilico (with option data.type = "WHO2016").
#'
#' \code{odk2openVA} transforms data collected with the 2016 WHO VA instrument
#' (version 1.4.1) to serve as the input to the InterVA5 and InSilicoVA
#' alogrithms for coding cause of death.
#'
#' @param odk A dataframe, obtained from reading an ODK Briefcase
#' export of records collected with the WHO questionnaire.
#'
#' @param id_col A character string of the column name (in odk) with the
#' unique ID for each death.
#'
#' @examples
#' \dontrun{
#' record_f_name <- system.file("sample", "who141_odk_export.csv", package = "CrossVA")
#' records <- read.csv(record_f_name, stringsAsFactors = FALSE)
#' output <- odk2openVA_v141(records)
#' }
#'
#' @importFrom stringi stri_endswith_fixed
#'
#' @export
#'
odk2openVA_v141 <- function (odk, id_col = "meta.instanceID") {
## Input Data
odkNames <- tolower(names(odk))
## Output Variables
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", "Id10185",
"Id10186", "Id10187", "Id10188", "Id10189", "Id10190", "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)
# check for missing indicators
tmpMat <- matrix(sapply(whoNames, stri_endswith_fixed, str = odkNames), nrow = length(odkNames))
indexData <- apply(tmpMat, 2, which)
warnZeroMatch <- which(sapply(indexData, length) == 0)
if (length(warnZeroMatch) > 0) {
cat(
paste("Expecting indicator(s) with name(s): ",
whoNames[unique(warnZeroMatch)],
sep = ""),
sep = "\n"
)
stop("Problem with data: please add above columns to your data frame")
}
numNA <- 0 # used for tracking columns with NAs
indexNA <- NULL
flagNonNumeric <- function(x) {
return(tryCatch(as.numeric(x),
error = function(c) -9999,
warning = function(c) -9999)
)
}
# function for creating simple Y/N indicators
qYesNo <- c(20:40, 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, 142:143, 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]
cat(
paste("Duplicate column names containing:",
tmpNames[unlist(dups)],
sep = " "),
sep = "\n"
)
stop("Problem with data: please remove or rename one of the duplicate columns.")
}
iv5Out[ , qYesNo] <- as.matrix(odk[ , indexData])
iv5Out[iv5Out=="yes" | iv5Out=="Yes" | iv5Out=="YES"] <- "y"
iv5Out[iv5Out=="no" | iv5Out=="No" | iv5Out=="NO"] <- "n"
iv5Out[iv5Out=="dk" | iv5Out=="DK" | iv5Out=="Doesn't Know"] <- "."
iv5Out[iv5Out=="Doesn't know" | iv5Out=="doesn't know"] <- "."
iv5Out[iv5Out=="does not know" | iv5Out=="Does Not Know" | iv5Out=="Does not know"] <- "."
iv5Out[iv5Out=="ref" | iv5Out=="Ref" | iv5Out=="REF"] <- "."
iv5Out[iv5Out==""] <- "."
iv5Out[is.na(iv5Out)] <- "."
# Step through iv5 indicators to create new values
#1) Did s(he) die during the wet season? d wet & 2) Did s(he) die during the dry season? d dry
indexData <- which(stri_endswith_fixed(odkNames, whoNames[1]))
iv5Out[tolower(odk[ , indexData])=="wet" | tolower(odk[ , indexData])=="wet season", 1] <- "y" ## wet season
iv5Out[tolower(odk[ , indexData])=="dry" | tolower(odk[ , indexData])=="dry season", 1] <- "n"
iv5Out[tolower(odk[ , indexData])=="wet" | tolower(odk[ , indexData])=="wet season", 2] <- "n" ## dry season
iv5Out[tolower(odk[ , indexData])=="dry" | tolower(odk[ , indexData])=="dry season", 2] <- "y"
#3) Was he male? male & ##4) Was he female? female
indexData_sex <- which(stri_endswith_fixed(odkNames, whoNames[3]))
iv5Out[tolower(odk[ , indexData_sex])=="male", 3] <- "y"
iv5Out[tolower(odk[ , indexData_sex])=="female", 3] <- "n"
iv5Out[tolower(odk[ , indexData_sex])=="male", 4] <- "n"
iv5Out[tolower(odk[ , indexData_sex])=="female", 4] <- "y"
# age
indexData1y <- which(stri_endswith_fixed(odkNames, "ageinyears"))
nonNumeric <- lapply(odk[ , indexData1y], flagNonNumeric)
nonNumeric <- unlist(nonNumeric)
containsNA <- ifelse(
sum(nonNumeric < 0, na.rm = TRUE) > 0,
1, 0)
numNA <- numNA + containsNA
if (containsNA > 0) indexNA <- c(indexNA, odkNames[indexData1y])
nonNumeric[nonNumeric < 0] <- NA
odk[is.na(nonNumeric), indexData1y] <- NA
odk[, indexData1y] <- as.numeric(odk[, indexData1y])
indexData1m <- which(stri_endswith_fixed(odkNames, "ageinmonths"))
nonNumeric <- lapply(odk[ , indexData1m], flagNonNumeric)
nonNumeric <- unlist(nonNumeric)
containsNA <- ifelse(
sum(nonNumeric < 0, na.rm = TRUE) > 0,
1, 0)
numNA <- numNA + containsNA
if (containsNA > 0) indexNA <- c(indexNA, odkNames[indexData1m])
nonNumeric[nonNumeric < 0] <- NA
odk[is.na(nonNumeric), indexData1m] <- NA
odk[, indexData1m] <- as.numeric(odk[, indexData1m])
indexData1d <- which(stri_endswith_fixed(odkNames, "ageindays"))
nonNumeric <- lapply(odk[ , indexData1d], flagNonNumeric)
nonNumeric <- unlist(nonNumeric)
containsNA <- ifelse(
sum(nonNumeric < 0, na.rm = TRUE) > 0,
1, 0)
numNA <- numNA + containsNA
if (containsNA > 0) indexNA <- c(indexNA, odkNames[indexData1d])
nonNumeric[nonNumeric < 0] <- NA
odk[is.na(nonNumeric), indexData1d] <- NA
odk[, indexData1d] <- as.numeric(odk[, indexData1d])
indexData2 <- which(stri_endswith_fixed(odkNames, "age_group"))
indexData3 <- which(stri_endswith_fixed(odkNames, "age_adult"))
nonNumeric <- lapply(odk[ , indexData3], flagNonNumeric)
nonNumeric <- unlist(nonNumeric)
containsNA <- ifelse(
sum(nonNumeric < 0, na.rm = TRUE) > 0,
1, 0)
numNA <- numNA + containsNA
if (containsNA > 0) indexNA <- c(indexNA, odkNames[indexData3])
nonNumeric[nonNumeric < 0] <- NA
odk[is.na(nonNumeric), indexData3] <- NA
odk[, indexData3] <- as.numeric(odk[, indexData3])
indexData4 <- which(stri_endswith_fixed(odkNames, "age_child_unit"))
indexData4d <- which(stri_endswith_fixed(odkNames, "age_child_days"))
nonNumeric <- lapply(odk[ , indexData4d], flagNonNumeric)
nonNumeric <- unlist(nonNumeric)
containsNA <- ifelse(
sum(nonNumeric < 0, na.rm = TRUE) > 0,
1, 0)
numNA <- numNA + containsNA
if (containsNA > 0) indexNA <- c(indexNA, odkNames[indexData4d])
nonNumeric[nonNumeric < 0] <- NA
odk[is.na(nonNumeric), indexData4d] <- NA
odk[, indexData4d] <- as.numeric(odk[, indexData4d])
indexData4m <- which(stri_endswith_fixed(odkNames, "age_child_months"))
nonNumeric <- lapply(odk[ , indexData4m], flagNonNumeric)
nonNumeric <- unlist(nonNumeric)
containsNA <- ifelse(
sum(nonNumeric < 0, na.rm = TRUE) > 0,
1, 0)
numNA <- numNA + containsNA
if (containsNA > 0) indexNA <- c(indexNA, odkNames[indexData4m])
nonNumeric[nonNumeric < 0] <- NA
odk[is.na(nonNumeric), indexData4m] <- NA
odk[, indexData4m] <- as.numeric(odk[, indexData4m])
indexData4y <- which(stri_endswith_fixed(odkNames, "age_child_years"))
nonNumeric <- lapply(odk[ , indexData4y], flagNonNumeric)
nonNumeric <- unlist(nonNumeric)
containsNA <- ifelse(
sum(nonNumeric < 0, na.rm = TRUE) > 0,
1, 0)
numNA <- numNA + containsNA
if (containsNA > 0) indexNA <- c(indexNA, odkNames[indexData4y])
nonNumeric[nonNumeric < 0] <- NA
odk[is.na(nonNumeric), indexData4y] <- NA
odk[, indexData4y] <- as.numeric(odk[, indexData4y])
indexData5d <- which(stri_endswith_fixed(odkNames, "age_neonate_days"))
nonNumeric <- lapply(odk[ , indexData5d], flagNonNumeric)
nonNumeric <- unlist(nonNumeric)
containsNA <- ifelse(
sum(nonNumeric < 0, na.rm = TRUE) > 0,
1, 0)
numNA <- numNA + containsNA
if (containsNA > 0) indexNA <- c(indexNA, odkNames[indexData5d])
nonNumeric[nonNumeric < 0] <- NA
odk[is.na(nonNumeric), indexData5d] <- NA
odk[, indexData5d] <- as.numeric(odk[, indexData5d])
indexData5h <- which(stri_endswith_fixed(odkNames, "age_neonate_hours"))
nonNumeric <- lapply(odk[ , indexData5h], flagNonNumeric)
nonNumeric <- unlist(nonNumeric)
containsNA <- ifelse(
sum(nonNumeric < 0, na.rm = TRUE) > 0,
1, 0)
numNA <- numNA + containsNA
if (containsNA > 0) indexNA <- c(indexNA, odkNames[indexData5h])
nonNumeric[nonNumeric < 0] <- NA
odk[is.na(nonNumeric), indexData5h] <- NA
odk[, indexData5h] <- as.numeric(odk[, indexData5h])
indexData5m <- which(stri_endswith_fixed(odkNames, "age_neonate_minutes"))
nonNumeric <- lapply(odk[ , indexData5m], flagNonNumeric)
nonNumeric <- unlist(nonNumeric)
containsNA <- ifelse(
sum(nonNumeric < 0, na.rm = TRUE) > 0,
1, 0)
numNA <- numNA + containsNA
if (containsNA > 0) indexNA <- c(indexNA, odkNames[indexData5m])
nonNumeric[nonNumeric < 0] <- NA
odk[is.na(nonNumeric), indexData5m] <- NA
odk[, indexData5m] <- as.numeric(odk[, indexData5m])
indexData_isNeonatal <- which(stri_endswith_fixed(odkNames, "isneonatal"))
indexData_isChild <- which(stri_endswith_fixed(odkNames, "ischild"))
indexData_isAdult <- which(stri_endswith_fixed(odkNames, "isadult"))
#5) Was s(he) aged 65 years or more at death? 65+
iv5Out[odk[ , indexData1y]>=65, 5] <- "y"
iv5Out[is.na(odk[ , indexData1y]) & odk[ , indexData2]=="adult" &
odk[ , indexData3]>=65, 5] <- "y"
#6) Was s(he) aged 50 to 64 years at death? 50 to 64
iv5Out[odk[ , indexData1y]< 65 & odk[ , indexData1y]>=50, 6] <- "y"
iv5Out[is.na(odk[ , indexData1y]) & odk[ ,indexData2]=="adult" &
odk[ ,indexData3]< 65 & odk[ ,indexData3]>=50, 6] <- "y"
#7) Was s(he) aged 15 to 49 years at death? 15-49
iv5Out[odk[ , indexData1y]< 50 & odk[ , indexData1y]>=15, 7] <- "y"
iv5Out[is.na(odk[ , indexData1y]) & odk[ , indexData2]=="adult" &
odk[ , indexData3]< 50 & odk[ , indexData3]>=15, 7] <- "y"
#8) Was s(he) aged 5-14 years at death? 5-14 (adult or child)
iv5Out[odk[ , indexData1y]< 15 & odk[ , indexData1y]>= 5, 8] <- "y"
iv5Out[is.na(odk[ , indexData1y]) & odk[ , indexData2]=="adult" &
odk[ , indexData3]< 15 & odk[ , indexData3]>=5, 8] <- "y"
iv5Out[is.na(odk[ , indexData1y]) & odk[ , indexData2]=="child" &
odk[ , indexData4]=="days" & odk[ , indexData4d]< 15*365.25 &
odk[ , indexData4d]>=5*365.25, 8] <- "y"
iv5Out[is.na(odk[ , indexData1y]) & odk[ , indexData2]=="child" &
odk[ , indexData4]=="months" & odk[ , indexData4m]< 15*12 &
odk[ , indexData4m]>=5*12, 8] <- "y"
iv5Out[is.na(odk[ , indexData1y]) & odk[ , indexData2]=="child" &
odk[ , indexData4]=="years" & odk[ , indexData4y]< 15 &
odk[ , indexData4y]>=5, 8] <- "y"
#9) Was s(he) aged 1 to 4 years at death? 1 to 4 (child)
iv5Out[odk[ , indexData1y]< 5 & odk[ , indexData1y]>=1, 9] <- "y"
iv5Out[is.na(odk[ , indexData1y]) & odk[ , indexData2]=="child" &
odk[ , indexData4]=="days" & odk[ , indexData4d]< 5*365.25 &
odk[ , indexData4d]>=1*365.25, 9] <- "y"
iv5Out[is.na(odk[ , indexData1y]) & odk[ , indexData2]=="child" &
odk[ , indexData4]=="months" & odk[ , indexData4m]< 5*12 &
odk[ , indexData4m]>=1*12, 9] <- "y"
iv5Out[is.na(odk[ , indexData1y]) & odk[ , indexData2]=="child" &
odk[ , indexData4]=="years" & odk[ , indexData4y]< 5 &
odk[ , indexData4y]>=1, 9] <- "y"
#10) Was s(he) aged 1 to 11 months at death? 1-11 months (child or neonate?)
iv5Out[odk[ , indexData1d]< 365.25 & odk[ , indexData1d]>=28, 10] <- "y"
iv5Out[is.na(odk[ , indexData1d]) & odk[ , indexData2]=="child" &
odk[ , indexData4]=="days" & odk[ , indexData4d]< 365.25 &
odk[ , indexData4d]>=28, 10] <- "y"
#11) Was s(he) aged < 1 month (28 days) at death? 0 - 27 days (neonate)
iv5Out[odk[ , indexData1d]< 28, 11] <- "y"
iv5Out[is.na(odk[ , indexData1d]) & odk[ , indexData2]=="neonate", 11] <- "y"
#12) Was s(he) a live baby who died within 24 hours of birth? day0 iv5Names[12]
iv5Out[odk[ , indexData1d]< 1, 12] <- "y"
ageDays <- odk[ , indexData5d]
ageHours <- odk[ , indexData5h]/24;
ageHours[is.na(ageHours)] <- 0
ageMinutes <- odk[ , indexData5m]/(24*12)
ageMinutes[is.na(ageMinutes)] <- 0
ageNeonate <- ageDays + ageHours + ageMinutes
iv5Out[odk[ , indexData2]=="neonate" & !is.na(odk[ , indexData5d]) &
ageNeonate< 1, 12] <- "y"
#13) Was s(he) a baby who died between 24 and 48 hours of birth? day1 iv5Names[13]
iv5Out[odk[ , indexData2]=="neonate" & !is.na(odk[ , indexData5d]) &
ageNeonate< 2 & ageNeonate>=1, 13] <- "y"
#14) Was s(he) a baby who died more than 48 hours from birth, but within the first week? day2-6 iv5Names[14]
iv5Out[odk[ , indexData2]=="neonate" & !is.na(odk[ , indexData5d]) &
ageNeonate< 7 & ageNeonate>=2, 14] <- "y"
#15) Was s(he) a baby who died after the first week, but within the first month? wk2-4 iv5Names[15]
iv5Out[odk[ , indexData2]=="neonate" & !is.na(odk[ , indexData5d]) &
ageNeonate< 28 & ageNeonate>=7, 15] <- "y"
# Finish coding age (5-15) -- if only only one age has "y", recode all others to "n"
## e.g., if age 65 == "y", then age 50-64 == "n" and age 15-49 == "n" etc.
indexData6 <-iv5Out[ , 5:11] != "y" ## identify elements in age columns that do not equal "y"
##indexData7 <- rowSums(iv5Out[ , 5:15] == "y") ## identify with rows/records only have 1 "y" for all age columns
indexData7 <- rowSums(iv5Out[ , 5:11] == "y", na.rm = TRUE) ## identify with rows/records only have 1 "y" for all age columns
## Now recode all "n"
iv5Out[indexData7 == 1, 5:11][ indexData6[indexData7 == 1, ] ] <- "n"
## Extend "n" to neonates sub-categories (if not a neonate)
indexData8 <- iv5Out[ , 11] == "n"
iv5Out[indexData8, 12:15] <- "n"
#16) Was she a woman aged 12-19 years at death? f-19
iv5Out[ , 16] <- ifelse(odk[ , indexData_sex]=="female" &
odk[ , indexData1y]< 20 &
odk[ , indexData1y]>= 12, "y", ".")
iv5Out[odk[ , indexData_sex]=="female" & odk[ , indexData1y]< 12, 16] <- "n"
iv5Out[odk[ , indexData_sex]=="female" & odk[ , indexData1y]> 19, 16] <- "n"
iv5Out[odk[ , indexData_sex]=="female" & is.na(odk[ , indexData1y]) &
odk[ , indexData2]=="adult" & odk[ , indexData3]< 20 &
odk[ , indexData3]>=12, 16] <- "y"
iv5Out[odk[ , indexData_sex]=="female" & is.na(odk[ , indexData1y]) &
odk[ , indexData2]=="adult" & odk[ , indexData3]< 12, 16] <- "n"
iv5Out[odk[ , indexData_sex]=="female" & is.na(odk[ , indexData1y]) &
odk[ , indexData2]=="adult" & odk[ , indexData3]> 19, 16] <- "n"
iv5Out[odk[ , indexData2]=="neonate", 16] <- "n"
iv5Out[odk[ , indexData_isNeonatal] == 1, 16] <- "n"
iv5Out[odk[ , indexData_isChild] == 1 & odk[ , indexData1y] < 12, 16] <- "n"
iv5Out[odk[ , indexData_isChild] == 1 & odk[ , indexData4y] < 12, 16] <- "n"
iv5Out[odk[ , indexData_isChild] == 1 &
odk[ , indexData4m] < 12*12, 16] <- "n"
iv5Out[odk[ , indexData_isChild] == 1 &
odk[ , indexData4d] < 12*365.25, 16] <- "n"
iv5Out[odk[ , indexData_sex]=="male", 16] <- "n"
#17) Was she a woman aged 20-34 years at death? f20-34
iv5Out[ , 17] <- ifelse(odk[ , indexData_sex]=="female" &
odk[ , indexData1y]< 35 &
odk[ , indexData1y]>= 20, "y", ".")
iv5Out[odk[ , indexData_sex]=="female" & odk[ , indexData1y]< 20, 17] <- "n"
iv5Out[odk[ , indexData_sex]=="female" & odk[ , indexData1y]> 34, 17] <- "n"
iv5Out[odk[ , indexData_sex]=="female" & is.na(odk[ , indexData1y]) &
odk[ , indexData2]=="adult" & odk[ , indexData3]< 35 &
odk[ , indexData3]>=20, 17] <- "y"
iv5Out[odk[ , indexData_sex]=="female" & is.na(odk[ , indexData1y]) &
odk[ , indexData2]=="adult" & odk[ , indexData3]< 20, 17] <- "n"
iv5Out[odk[ , indexData_sex]=="female" & is.na(odk[ , indexData1y]) &
odk[ , indexData2]=="adult" & odk[ , indexData3]> 34, 17] <- "n"
iv5Out[odk[ , indexData2]=="neonate", 17] <- "n"
iv5Out[odk[ , indexData_isNeonatal] == 1, 17] <- "n"
iv5Out[odk[ , indexData_isChild] == 1, 17] <- "n"
iv5Out[odk[ , indexData_sex]=="male", 17] <- "n"
#18) Was she a woman aged 35 to 49 years at death? f35-49
iv5Out[ , 18] <- ifelse(odk[ , indexData_sex]=="female" &
odk[ , indexData1y]< 50 &
odk[ , indexData1y]>= 35, "y", ".")
iv5Out[odk[ , indexData_sex]=="female" & odk[ , indexData1y]< 35, 18] <- "n"
iv5Out[odk[ , indexData_sex]=="female" & odk[ , indexData1y]> 49, 18] <- "n"
iv5Out[odk[ , indexData_sex]=="female" & is.na(odk[ , indexData1y]) &
odk[ , indexData2]=="adult" & odk[ , indexData3]< 50 &
odk[ , indexData3]>=35, 18] <- "y"
iv5Out[odk[ , indexData_sex]=="female" & is.na(odk[ , indexData1y]) &
odk[ , indexData2]=="adult" & odk[ , indexData3]< 35, 18] <- "n"
iv5Out[odk[ , indexData_sex]=="female" & is.na(odk[ , indexData1y]) &
odk[ , indexData2]=="adult" & odk[ , indexData3]> 49, 18] <- "n"
iv5Out[odk[ , indexData2]=="neonate", 18] <- "n"
iv5Out[odk[ , indexData_isNeonatal] == 1, 18] <- "n"
iv5Out[odk[ , indexData_isChild] == 1, 18] <- "n"
iv5Out[odk[ , indexData_sex]=="male", 18] <- "n"
#19) Was she married at the time of death? married
indexData <- which(stri_endswith_fixed(odkNames, whoNames[19]))
## table(odk[ , indexData])
iv5Out[odk[ , indexData_sex]=="female" & tolower(odk[ , indexData])=="married", 19] <- "y"
iv5Out[odk[ , indexData_sex]=="female" & tolower(odk[ , indexData])=="single", 19] <- "n"
iv5Out[odk[ , indexData_sex]=="female" & tolower(odk[ , indexData])=="partner", 19] <- "n"
iv5Out[odk[ , indexData_sex]=="female" & tolower(odk[ , indexData])=="divorced", 19] <- "n"
iv5Out[odk[ , indexData_sex]=="female" & tolower(odk[ , indexData])=="widowed", 19] <- "n"
iv5Out[odk[ , indexData_sex]=="female" & tolower(odk[ , indexData])=="too_young_to_be_married", 19] <- "n"
iv5Out[odk[ , indexData_sex]=="female" & tolower(odk[ , indexData])=="child", 19] <- "n"
iv5Out[odk[ , indexData_sex]=="male", 19] <- "n"
#41) Was it more than 5 minutes after birth before the baby first cried? cry 5+m
indexData <- which(stri_endswith_fixed(odkNames, whoNames[41]))
iv5Out[odk[ , indexData]> 5, 41] <- "y"
iv5Out[odk[ , indexData]<=5, 41] <- "n"
#43) Did the baby stop crying more than a day before (s)he died? cry st 1+d
indexData <- which(stri_endswith_fixed(odkNames, whoNames[43]))
iv5Out[odk[ , indexData]> 24, 43] <- "y"
iv5Out[odk[ , indexData]<=24, 43] <- "n"
#52) Did the final illness last less than 3 weeks? ill <3w.
indexDatad <- which(stri_endswith_fixed(odkNames, "id10120"))
indexDataw <- which(stri_endswith_fixed(odkNames, "id10122")) ## should this be "years"?
indexDatam <- which(stri_endswith_fixed(odkNames, "id10121"))
iv5Out[odk[ , indexDatad]< 21, 52] <- "y"
iv5Out[odk[ , indexDatad]>=21, 52] <- "n"
iv5Out[odk[ , indexDataw]< 3, 52] <- "y"
iv5Out[odk[ , indexDataw]>=3, 52] <- "n"
#iv5Out[odk[ , indexDatam]< 1, 52] <- "y"
iv5Out[odk[ , indexDatam]>=1, 52] <- "n"
#53) Did the final illness last at least 3 weeks? ill 3+w
iv5Out[odk[ , indexDatad]>=21, 53] <- "y"
iv5Out[odk[ , indexDatad]< 21, 53] <- "n"
iv5Out[odk[ , indexDataw]>= 3, 53] <- "y"
iv5Out[odk[ , indexDataw]< 3, 53] <- "n"
iv5Out[odk[ , indexDatam]>= 1, 53] <- "y"
#iv5Out[odk[ , indexDatam]< 1, 53] <- "y"
#75) Did the fever last less than a week before death? fev <1w
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]=="no", 75] <- "n"
#76) Did the fever last at least one week, but less than 2 weeks before death? fev 1-2w
iv5Out[odk[ , indexData]=="yes" & odk[ , indexData_days]< 7, 76] <- "n"
iv5Out[odk[ , indexData]=="yes" & odk[ , indexData_days]>= 7 & odk[ , indexData_days]< 14, 76] <- "y"
iv5Out[odk[ , indexData]=="yes" & odk[ , indexData_days]>=14, 76] <- "n"
iv5Out[odk[ , indexData]=="no", 76] <- "n"
#77) Did the fever last at least 2 weeks before death? fev 2+w
iv5Out[odk[ , indexData]=="yes" & odk[ , indexData_days]>= 14, 77] <- "y"
iv5Out[odk[ , indexData]=="yes" & odk[ , indexData_days]< 14, 77] <- "n"
iv5Out[odk[ , indexData]=="no", 77] <- "n"
#78) Did the fever continue until death
iv5Out[odk[ , indexData]=="no", 78] <- "n"
#79) Was the fever severe? fev sev
indexData_sev <- which(stri_endswith_fixed(odkNames, whoNames[79]))
iv5Out[odk[ , indexData]=="yes" & tolower(odk[ , indexData_sev])=="severe", 79] <- "y"
iv5Out[odk[ , indexData]=="yes" & tolower(odk[ , indexData_sev])=="mild", 79] <- "n"
iv5Out[odk[ , indexData]=="yes" & tolower(odk[ , indexData_sev])=="moderate", 79] <- "n"
iv5Out[odk[ , indexData]=="no", 79] <- "n"
#80) Was the fever continuous? fev cont
indexData_cont <- which(stri_endswith_fixed(odkNames, whoNames[80]))
iv5Out[odk[ , indexData]=="yes" & tolower(odk[ , indexData_cont])=="continuous", 80] <- "y"
iv5Out[odk[ , indexData]=="yes" & tolower(odk[ , indexData_cont])=="nightly", 80] <- "n"
iv5Out[odk[ , indexData]=="yes" & tolower(odk[ , indexData_cont])=="on_and_off", 80] <- "n"
iv5Out[odk[ , indexData]=="no", 80] <- "n"
#83) Did the cough last less than 3 weeks before death? cou <3w
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"
#84) Did the cough last at least 3 weeks before death? cou 3+w
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"
#90) Did the difficult breathing last for at least 3 days before death? dif br 3d
indexDatad <- which(stri_endswith_fixed(odkNames, whoNames[90]))
indexDatam <- which(stri_endswith_fixed(odkNames, "id10162"))
indexDatay <- which(stri_endswith_fixed(odkNames, "id10163"))
## indexDatad; odkNames[indexDatad]. #
iv5Out[odk[ , indexDatad]>=3, 90] <- "y"
iv5Out[odk[ , indexDatad]< 3, 90] <- "n"
iv5Out[odk[ , indexDatam]>=1, 90] <- "y"
iv5Out[odk[ , indexDatay]>=1, 90] <- "y"
#91) Was the difficult breathing continuous during this period? dif br con
indexData <- which(stri_endswith_fixed(odkNames, whoNames[91]))
iv5Out[tolower(odk[ , indexData])=="continuous", 91] <- "y"
iv5Out[tolower(odk[ , indexData])=="on_and_off", 91] <- "n"
#93) Did the fast breathing last for less than two weeks before death? br fs <2w
indexData <- which(stri_endswith_fixed(odkNames, whoNames[93]))
iv5Out[odk[ , indexData[1]]< 14, 93] <- "y"
iv5Out[odk[ , indexData[1]]>=14, 93] <- "n"
#94) Did the fast breathing last for at least 2 weeks before death? br fs 2+w
iv5Out[odk[ , indexData[1]]>=14, 94] <- "y"
iv5Out[odk[ , indexData[1]]< 14, 94] <- "n"
#96) Did the breathlessness last for less than 2 weeks before death? brl <2w
indexData <- which(stri_endswith_fixed(odkNames, whoNames[96]))
iv5Out[odk[ , indexData[1]]< 14, 96] <- "y"
iv5Out[odk[ , indexData[1]]>=14, 96] <- "n"
#97) Did the breathlessness last for at least 2 weeks before death? brl 2+w
iv5Out[odk[ , indexData[1]]>=14, 97] <- "y"
iv5Out[odk[ , indexData[1]]< 14, 97] <- "n"
#101) Did his/her breathing sound like wheezing or grunting? whz grun
indexData <- which(stri_endswith_fixed(odkNames, whoNames[101]))
iv5Out[stri_endswith_fixed(tolower(odk[ , indexData]), "grunting"), 101] <- "y"
iv5Out[stri_endswith_fixed(tolower(odk[ , indexData]), "stridor"), 101] <- "y"
iv5Out[stri_endswith_fixed(tolower(odk[ , indexData]), "wheezing"), 101] <- "y"
iv5Out[stri_endswith_fixed(tolower(odk[ , indexData]), "no"), 101] <- "n"
#104) Did (s)he experience chest pain at least 3 days before death? chp 3d
indexData <- which(stri_endswith_fixed(odkNames, whoNames[104]))
iv5Out[odk[ , indexData]>=3, 104] <- "y"
iv5Out[odk[ , indexData]< 3, 104] <- "n"
#105) Did the chest pain last for at least 30 minutes? chp 30m
indexDatam <- which(stri_endswith_fixed(odkNames, whoNames[105]))
indexDatah <- which(stri_endswith_fixed(odkNames, "id10179"))
iv5Out[odk[ , indexDatam]>=30, 105] <- "y"
iv5Out[odk[ , indexDatah]>=.5, 105] <- "y"
iv5Out[odk[ , indexDatam]< 30, 105] <- "n"
iv5Out[odk[ , indexDatah]< .5, 105] <- "n"
#107) Did (s)he have diarrhoea for less than 2 weeks before death? drr <2w
indexData <- which(stri_endswith_fixed(odkNames, whoNames[107]))
iv5Out[odk[ , indexData]< 14, 107] <- "y"
iv5Out[odk[ , indexData]>=14, 107] <- "n"
#108) Did (s)he have diarrhoea for at least 2 weeks but less than 4 weeks before death? drr 2-4w
iv5Out[odk[ , indexData]< 28 & odk[ , indexData]>=14, 108] <- "y"
iv5Out[odk[ , indexData]< 14, 108] <- "n"
iv5Out[odk[ , indexData]>=28, 108] <- "n"
#109) Did (s)he have diarrhoea for at least 4 weeks before death? drr 4+w
iv5Out[odk[ , indexData]>=28, 109] <- "y"
iv5Out[odk[ , indexData]< 28, 109] <- "n"
#110) Did the baby or child have at least 4 stools on the day that loose liquid stools were most frequent? 4+ stls
indexData <- which(stri_endswith_fixed(odkNames, whoNames[110]))
iv5Out[odk[ , indexData]>= 4 & odk[ , indexData]< 999, 110] <- "y"
iv5Out[odk[ , indexData]< 4, 110] <- "n"
#111) Did the frequent loose or liquid stools start at least 3 days before death? drr 3d
indexData <- which(stri_endswith_fixed(odkNames, whoNames[111]))
iv5Out[odk[ , indexData]>= 3 & odk[ , indexData]< 999, 111] <- "y"
iv5Out[odk[ , indexData]< 3, 111] <- "n"
#117) Did (s)he vomit for at least 3 days before death? vom 3d
indexData <- which(stri_endswith_fixed(odkNames, whoNames[117]))
iv5Out[odk[ , indexData]>= 3 & odk[ , indexData]< 999, 117] <- "y"
iv5Out[odk[ , indexData]< 3, 117] <- "n"
#123) Did (s)he have severe abdominal pain for less than 2 weeks before death? abd p <2w
## indexData <- which(stri_endswith_fixed(odkNames, whoNames[122]))
indexFilter <- which(stri_endswith_fixed(odkNames, "id10194"))
indexData <- which(stri_endswith_fixed(odkNames, "id10195"))
indexDatad <- which(stri_endswith_fixed(odkNames, "id10197"))
indexDatah <- which(stri_endswith_fixed(odkNames, "id10196"))
indexDataw <- which(stri_endswith_fixed(odkNames, "id10197b"))
indexDatam <- which(stri_endswith_fixed(odkNames, "id10198"))
iv5Out[tolower(odk[ , indexData])=="yes" & odk[ , indexDatad]< 14, 123] <- "y"
iv5Out[tolower(odk[ , indexData])=="yes" & odk[ , indexDatad]>=14, 123] <- "n"
iv5Out[tolower(odk[ , indexData])=="yes" & odk[ , indexDatah]< (24*14), 123] <- "y"
iv5Out[tolower(odk[ , indexData])=="yes" & odk[ , indexDatah]>=(24*14), 123] <- "n"
iv5Out[tolower(odk[ , indexData])=="yes" & odk[ , indexDataw]< 2, 123] <- "y"
iv5Out[tolower(odk[ , indexData])=="yes" & odk[ , indexDataw]>=2, 123] <- "n"
iv5Out[tolower(odk[ , indexData])=="yes" & odk[ , indexDatam]< 1, 123] <- "y"
iv5Out[tolower(odk[ , indexData])=="no", 123] <- "n"
iv5Out[tolower(odk[ , indexFilter])=="no", 123] <- "n"
#124) Did (s)he have severe abdominal pain for at least 2 weeks before death? abd p 2+w
iv5Out[tolower(odk[ , indexData])=="yes" & odk[ , indexDatad]>=14, 124] <- "y"
iv5Out[tolower(odk[ , indexData])=="yes" & odk[ , indexDatad]< 14, 124] <- "n"
iv5Out[tolower(odk[ , indexData])=="yes" & odk[ , indexDatah]>=(24*14), 124] <- "y"
iv5Out[tolower(odk[ , indexData])=="yes" & odk[ , indexDatah]< (24*14), 124] <- "n"
iv5Out[tolower(odk[ , indexData])=="yes" & odk[ , indexDataw]>=2, 124] <- "y"
iv5Out[tolower(odk[ , indexData])=="yes" & odk[ , indexDataw]< 2, 124] <- "n"
iv5Out[tolower(odk[ , indexData])=="yes" & odk[ , indexDatam]>=1, 124] <- "y"
iv5Out[tolower(odk[ , indexData])=="no", 124] <- "n"
iv5Out[tolower(odk[ , indexFilter])=="no", 124] <- "n"
#125) Was the pain in the upper abdomen? abd p up
indexData <- which(stri_endswith_fixed(odkNames, whoNames[125]))
iv5Out[tolower(odk[ , indexData])=="upper_abdomen", 125] <- "y"
iv5Out[tolower(odk[ , indexData])=="upper_lower_abdomen", 125] <- "y"
iv5Out[tolower(odk[ , indexData])=="lower_abdomen", 125] <- "n"
#126) Was the pain in the lower abdomen? abd p lo
iv5Out[tolower(odk[ , indexData])=="upper_abdomen", 126] <- "n"
iv5Out[tolower(odk[ , indexData])=="upper_lower_abdomen", 126] <- "y"
iv5Out[tolower(odk[ , indexData])=="lower_abdomen", 126] <- "y"
#128) Did (s)he have a more than usually protruding abdomen for less than 2 weeks before death? abd pr <2w
indexData <- which(stri_endswith_fixed(odkNames, "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"
#129) Did (s)he have a more than usually protruding abdomen for at least 2 weeks before death? abd pr 2+w
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"
#130) Did (s)he develop the protruding abdomen rapidly? abd pr rap
indexData <- which(stri_endswith_fixed(odkNames, whoNames[130]))
iv5Out[tolower(odk[ , indexData])=="rapidly", 130] <- "y"
iv5Out[tolower(odk[ , indexData])=="slowly", 130] <- "n"
#132) Did (s)he have a mass in the abdomen for less than 2 weeks before death? ab ms <2w
indexData <- which(stri_endswith_fixed(odkNames, "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"
#133) Did (s)he have a mass in the abdomen for at least 2 weeks before death? ab ms 2+w
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"
#136) Did (s)he have a stiff neck for less than one week before death? st n <1w
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"
#137) Did (s)he have a stiff neck for at least one week before death? st n 1+w
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"
#139) Did (s)he have a painful neck for at least one week before death? pa n 1+w
indexData <- which(stri_endswith_fixed(odkNames, "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"
#141) Did (s)he have mental confusion for at least 3 months before death? menc 3+m
indexData <- which(stri_endswith_fixed(odkNames, whoNames[140]))
indexDatad <- which(stri_endswith_fixed(odkNames, whoNames[141]))
iv5Out[tolower(odk[ , indexData])=="yes" & odk[ , indexDatad]>=3, 141] <- "y"
iv5Out[tolower(odk[ , indexData])=="yes" & odk[ , indexDatad]< 3, 141] <- "n"
iv5Out[tolower(odk[ , indexData])=="no", 141] <- "n"
#143) Was (s)he unsconscious for at least 24 hours before death? unc 24+h
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"
#144) Was (s)he unsconscious for at least 6 hours before death? unc 6+h
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"
#149) Did the convulsions last for less than 10 minutes? conv <10m
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] <- "."
#150) Did the convulsions last for at least 10 minutes? conv 10+m
iv5Out[odk[ , indexData]=="yes" & odk[ , indexData_min]< 10, 150] <- "n"
iv5Out[odk[ , indexData]=="yes" & odk[ , indexData_min]>=10, 150] <- "y"
#161) Did the ulcer ooze pus for at least 2 weeks? sk ul 2+w
indexData <- which(stri_endswith_fixed(odkNames, whoNames[161]))
iv5Out[odk[ , indexData]>=14, 161] <- "y"
iv5Out[odk[ , indexData]< 14, 161] <- "n"
#163) Did (s)he have the skin rash for less than one week? sk ra <1w
indexData <- which(stri_endswith_fixed(odkNames, whoNames[163]))
iv5Out[odk[ , indexData]< 7, 163] <- "y"
iv5Out[odk[ , indexData]>=7, 163] <- "n"
#164) Did (s)he have the skin rash for at least one week? sk ra 1+w
iv5Out[odk[ , indexData]>=7, 164] <- "y"
iv5Out[odk[ , indexData]< 7, 164] <- "n"
#165) Did (s)he have a rash on the face? sk ra face
indexData <- which(stri_endswith_fixed(odkNames, whoNames[165]))
iv5Out[stri_endswith_fixed(tolower(odk[ , indexData]), "face"), 165] <- "y"
iv5Out[stri_endswith_fixed(tolower(odk[ , indexData]), negate = TRUE, "face"), 165] <- "n"
iv5Out[tolower(odk[ , indexData])=="", 165] <- "."
#166) Did (s)he have a rash on the trunk or abdomen? sk ra abd
indexData <- which(stri_endswith_fixed(odkNames, whoNames[166]))
iv5Out[stri_endswith_fixed(tolower(odk[ , indexData]), "abdomen|trunk"), 166] <- "y"
iv5Out[stri_endswith_fixed(tolower(odk[ , indexData]), negate = TRUE, "abdomen|trunk"), 166] <- "n"
iv5Out[tolower(odk[ , indexData])=="", 166] <- "."
#167) Did (s)he have a rash on the extremities? sk ra ext
indexData <- which(stri_endswith_fixed(odkNames, whoNames[167]))
iv5Out[stri_endswith_fixed(tolower(odk[ , indexData]), "extremities"), 167] <- "y"
iv5Out[stri_endswith_fixed(tolower(odk[ , indexData]), negate = TRUE, "extremities"), 167] <- "n"
iv5Out[tolower(odk[ , indexData])=="", 167] <- "."
#168) Did (s)he have a rash everywhere? sk ra all
indexData <- which(stri_endswith_fixed(odkNames, whoNames[168]))
iv5Out[stri_endswith_fixed(tolower(odk[ , indexData]), "everywhere"), 168] <- "y"
iv5Out[stri_endswith_fixed(tolower(odk[ , indexData]), negate = TRUE, "everywhere"), 168] <- "n"
iv5Out[tolower(odk[ , indexData])=="", 168] <- "."
#181) Did (s)he have puffiness of the face for at least one week before death? sw p f 1+w
indexData <- which(stri_endswith_fixed(odkNames, whoNames[181]))
iv5Out[odk[ , indexData]>=7, 181] <- "y"
iv5Out[odk[ , indexData]< 7, 181] <- "n"
#183) Did the swelling last for at least 3 days before death? sw lf 3+d
indexData <- which(stri_endswith_fixed(odkNames, whoNames[183]))
iv5Out[odk[ , indexData]>=3, 183] <- "y"
iv5Out[odk[ , indexData]< 3, 183] <- "n"
#193) Was only the right side of the body paralysed? par rs
indexData <- which(stri_endswith_fixed(odkNames, whoNames[193]))
iv5Out[tolower(odk[ , indexData])=="right_side", 193] <- "y"
iv5Out[tolower(odk[ , indexData])!="right_side", 193] <- "n"
iv5Out[tolower(odk[ , indexData])=="", 193] <- "."
#194) Was only the left side of the body paralysed? par ls
iv5Out[tolower(odk[ , indexData])=="left_side", 194] <- "y"
iv5Out[tolower(odk[ , indexData])!="left_side", 194] <- "n"
iv5Out[tolower(odk[ , indexData])=="", 194] <- "."
#195) Was only the lower part of the body paralysed? par lo
iv5Out[tolower(odk[ , indexData])=="lower_part_of_body", 195] <- "y"
iv5Out[tolower(odk[ , indexData])!="lower_part_of_body", 195] <- "n"
iv5Out[tolower(odk[ , indexData])=="", 195] <- "."
#196) Was only the upper part of the body paralysed? par up
iv5Out[tolower(odk[ , indexData])=="upper_part_of_body", 196] <- "y"
iv5Out[tolower(odk[ , indexData])!="upper_part_of_body", 196] <- "n"
iv5Out[tolower(odk[ , indexData])=="", 196] <- "."
#197) Was only one leg paralysed? par leg
iv5Out[tolower(odk[ , indexData])=="one_leg_only", 197] <- "y"
iv5Out[tolower(odk[ , indexData])!="one_leg_only", 197] <- "n"
iv5Out[tolower(odk[ , indexData])=="", 197] <- "."
#198) Was only one arm paralysed? par arm
iv5Out[tolower(odk[ , indexData])=="one_arm_only", 198] <- "y"
iv5Out[tolower(odk[ , indexData])!="one_arm_only", 198] <- "n"
iv5Out[tolower(odk[ , indexData])=="", 198] <- "."
#199) Was the entire body paralysed? par all
iv5Out[tolower(odk[ , indexData])=="whole_body", 199] <- "y"
iv5Out[tolower(odk[ , indexData])!="whole_body", 199] <- "n"
iv5Out[tolower(odk[ , indexData])=="", 199] <- "."
#201) Did (s)he have difficulty swallowing for at least one week before death? swa 1+w
indexData <- which(stri_endswith_fixed(odkNames, whoNames[201]))
iv5Out[odk[ , indexData]>=7, 201] <- "y"
iv5Out[odk[ , indexData]< 7, 201] <- "n"
#202) Did (s)he have difficulty with swallowing solids? swa sol
indexData <- which(stri_endswith_fixed(odkNames, whoNames[202]))
iv5Out[tolower(odk[ , indexData])=="solids", 202] <- "y"
iv5Out[tolower(odk[ , indexData])=="both", 202] <- "y"
iv5Out[tolower(odk[ , indexData])=="liquids", 202] <- "n"
#203) Did (s)he have difficulty with swallowing liquids? swa liq
iv5Out[tolower(odk[ , indexData])=="solids", 203] <- "n"
iv5Out[tolower(odk[ , indexData])=="both", 203] <- "y"
iv5Out[tolower(odk[ , indexData])=="liquids", 203] <- "y"
#206) Did (s)he have the yellow discolouration for at least 3 weeks before death? yell 3+w
indexData <- which(stri_endswith_fixed(odkNames, whoNames[206]))
iv5Out[odk[ , indexData]>=21, 206] <- "y"
iv5Out[odk[ , indexData]< 21, 206] <- "n"
#214) Did the baby stop suckling on the 2nd day of life or later? suck st d1
indexData <- which(stri_endswith_fixed(odkNames, whoNames[214]))
iv5Out[odk[ , indexData[1]]>=2, 214] <- "y"
iv5Out[odk[ , indexData[1]]< 2, 214] <- "n"
#224) Was the baby more than 3 days old when it started feeling cold to touch? cold 3+d
indexData <- which(stri_endswith_fixed(odkNames, whoNames[224]))
iv5Out[odk[ , indexData]> 3, 224] <- "y"
iv5Out[odk[ , indexData]<=3, 224] <- "n"
#239) Had her period been overdue for at least 4 weeks? men l 4+w
indexData <- which(stri_endswith_fixed(odkNames, whoNames[239]))
iv5Out[odk[ , indexData]>=4, 239] <- "y"
iv5Out[odk[ , indexData]< 4, 239] <- "n"
#243) Was she, or had she been, pregnant for less than 6 months when she died? d <6m pr
indexData <- which(stri_endswith_fixed(odkNames, whoNames[243]))
iv5Out[odk[ , indexData]< 6, 243] <- "y"
iv5Out[odk[ , indexData]>=6, 243] <- "n"
#252) Did she die during or after her first pregnancy? 1st pr.
# WHO question is "How many births, including stillbirths, did she/the mother have before this baby?"
indexData <- which(stri_endswith_fixed(odkNames, whoNames[252]))
iv5Out[odk[ , indexData]==0, 252] <- "y"
iv5Out[odk[ , indexData]> 0, 252] <- "n"
#253) Did she have four or more pregnancies before this one? 4+ pr
iv5Out[odk[ , indexData]>=4, 253] <- "y"
iv5Out[odk[ , indexData]< 4, 253] <- "n"
#266) Did her labour last longer than 24 hours? lab 24+h
indexData <- which(stri_endswith_fixed(odkNames, whoNames[266]))
iv5Out[odk[ , indexData]> 24, 266] <- "y"
iv5Out[odk[ , indexData]<=24, 266] <- "n"
#271) Did the mother deliver at a health facility or clinic? del hfac
indexData <- which(stri_endswith_fixed(odkNames, whoNames[271]))
iv5Out[tolower(odk[ , indexData])=="hospital", 271] <- "y"
iv5Out[tolower(odk[ , indexData])=="other_health_facility", 271] <- "y"
iv5Out[tolower(odk[ , indexData])=="home", 271] <- "n"
iv5Out[tolower(odk[ , indexData])=="on_route_to_hospital_or_facility", 271] <- "n"
iv5Out[tolower(odk[ , indexData])=="other", 271] <- "n"
#272) Did the mother deliver at home? del home
iv5Out[tolower(odk[ , indexData])=="hospital", 272] <- "n"
iv5Out[tolower(odk[ , indexData])=="other_health_facility", 272] <- "n"
iv5Out[tolower(odk[ , indexData])=="home", 272] <- "y"
iv5Out[tolower(odk[ , indexData])=="on_route_to_hospital_or_facility", 272] <- "n"
iv5Out[tolower(odk[ , indexData])=="other", 272] <- "n"
#273) Did the mother deliver elsewhere (not at a health facility nor at home)? del else
iv5Out[tolower(odk[ , indexData])=="hospital", 273] <- "n"
iv5Out[tolower(odk[ , indexData])=="other_health_facility", 273] <- "n"
iv5Out[tolower(odk[ , indexData])=="home", 273] <- "n"
iv5Out[tolower(odk[ , indexData])=="on_route_to_hospital_or_facility", 273] <- "y"
iv5Out[tolower(odk[ , indexData])=="other", 273] <- "y"
#281) If the child was part of a multiple birth, was it born first? mult fir
indexData <- which(stri_endswith_fixed(odkNames, whoNames[281]))
iv5Out[tolower(odk[ , indexData])=="first", 281] <- "y"
iv5Out[tolower(odk[ , indexData])=="second_or_later", 281] <- "n"
#283) Did the child's mother die during or shortly after the delivery? moth d del
indexData <- which(stri_endswith_fixed(odkNames, whoNames[283]))
iv5Out[tolower(odk[ , indexData])=="after_delivery", 283] <- "y"
iv5Out[tolower(odk[ , indexData])=="during_delivery" , 283] <- "y"
#284) Did the child's mother die in the baby's first year of life? moth d y1
indexDataM <- which(stri_endswith_fixed(odkNames, whoNames[284]))
indexDataD <- which(stri_endswith_fixed(odkNames, "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"
#285) Was the baby born in a health facility or clinic? born fac
indexData <- which(stri_endswith_fixed(odkNames, whoNames[285]))
iv5Out[tolower(odk[ , indexData])=="hospital", 285] <- "y"
iv5Out[tolower(odk[ , indexData])=="other_health_facility", 285] <- "y"
iv5Out[tolower(odk[ , indexData])=="home", 285] <- "n"
iv5Out[tolower(odk[ , indexData])=="other", 285] <- "n"
iv5Out[tolower(odk[ , indexData])=="on_route_to_hospital_or_facility", 285] <- "n"
#286) Was the baby born at home? born home
iv5Out[tolower(odk[ , indexData])=="hospital", 286] <- "n"
iv5Out[tolower(odk[ , indexData])=="other_health_facility", 286] <- "n"
iv5Out[tolower(odk[ , indexData])=="home", 286] <- "y"
iv5Out[tolower(odk[ , indexData])=="other", 286] <- "n"
iv5Out[tolower(odk[ , indexData])=="on_route_to_hospital_or_facility", 286] <- "n"
#287) Was the baby born somewhere else (e.g. on the way to a clinic)? born on way
iv5Out[tolower(odk[ , indexData])=="hospital", 287] <- "n"
iv5Out[tolower(odk[ , indexData])=="other_health_facility", 287] <- "n"
iv5Out[tolower(odk[ , indexData])=="home", 287] <- "n"
iv5Out[tolower(odk[ , indexData])=="other", 287] <- "y"
iv5Out[tolower(odk[ , indexData])=="on_route_to_hospital_or_facility", 287] <- "y"
#293) Was the baby born during the ninth month (at least 37 weeks) of pregnancy? gest 9m
indexData <- which(stri_endswith_fixed(odkNames, whoNames[293]))
iv5Out[odk[ , indexData]>=9 & odk[ , indexData]< 88, 293] <- "y"
iv5Out[odk[ , indexData]< 9, 293] <- "n"
iv5Out[odk[ , indexData]==88, 293] <- "."
#294) Was the baby born during the eighth month (34 to 37 weeks) of pregnancy? gest 8m
iv5Out[odk[ , indexData]> 8 & odk[ , indexData]< 88, 294] <- "n"
iv5Out[odk[ , indexData]==8, 294] <- "y"
iv5Out[odk[ , indexData]< 8, 294] <- "n"
#295) Was the baby born before the eighth month (less than 34 weeks) of pregnancy? gest 7m
iv5Out[odk[ , indexData]>=8 & odk[ , indexData]< 88, 295] <- "n"
iv5Out[odk[ , indexData]< 8, 295] <- "y"
#304) Did labour and delivery take more than 24 hours? lab 24+h
indexData <- which(stri_endswith_fixed(odkNames, whoNames[304]))
iv5Out[odk[ , indexData]> 24, 304] <- "y"
iv5Out[odk[ , indexData]<=24, 304] <- "n"
#307) Was the liquor a green or brown colour when the waters broke? liq gr-br
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"
#313) Was this baby born from the mother's first pregnancy? born 1st pr
indexData <- which(stri_endswith_fixed(odkNames, whoNames[313]))
iv5Out[odk[ , indexData]==0, 313] <- "y"
iv5Out[odk[ , indexData]> 0, 313] <- "n"
#314) Did the baby's mother have four or more births before this one? born 4+ pr
iv5Out[odk[ , indexData]>=4, 314] <- "y"
iv5Out[odk[ , indexData]< 4, 314] <- "n"
#331) Did (s)he use non-smoking tobacco? tobac ns
indexData <- which(stri_endswith_fixed(odkNames, whoNames[331]))
iv5Out[tolower(odk[ , indexData])=="chewing_tobacco", 331] <- "y"
iv5Out[tolower(odk[ , indexData])=="cigarettes", 331] <- "n"
iv5Out[tolower(odk[ , indexData])=="pipe", 331] <- "n"
iv5Out[tolower(odk[ , indexData])=="local_form_of_tobacco", 331] <- "n"
iv5Out[tolower(odk[ , indexData])=="other", 331] <- "n"
#332) Did (s)he smoke at least 10 cigarettes daily? cigs >10
indexData <- which(stri_endswith_fixed(odkNames, whoNames[332]))
iv5Out[odk[ , indexData]>=10, 332] <- "y"
iv5Out[odk[ , indexData]< 10, 332] <- "n"
# check for NAs
if (numNA > 0) {
warning("Found unexpected input values (coded as missing)", call. = FALSE)
cat("Unexpected values found in: ", sep = "\n")
cat(paste(indexNA), sep = ", ")
cat("\n")
}
# check for NAs
numNA <- colSums(is.na(iv5Out))
indexNA <- which(numNA > 0)
if (length(indexNA) > 0) {
warning("NA's included in output", call. = FALSE)
cat(
paste("odk2openVA produced NA's in the following columns",
" (this may cause errors with openVA)",
sep = ""),
sep = "\n"
)
cat(
paste(iv5Names[indexNA], ## subtract 1 since ID is omitted
" Probably associated with WHO column containing: ",
whoNames[indexNA], ## subtract 1 since ID is omitted
sep = ""),
sep = "\n"
)
}
# Add ID as first column
indexID <- which(stri_endswith_fixed(odkNames, tolower(id_col)))
if (length(indexID)) {
iv5Out <- cbind(as.character(odk[, indexID]), iv5Out)
} else {
message("Did not find id_col, so assigning row numbers for IDs.",
call. = FALSE)
iv5Out <- cbind(as.character(1:nrow(iv5Out)), iv5Out)
}
# Attach column names
colnames(iv5Out) <- c("ID", iv5Names)
# That's all folks!
return(as.data.frame(iv5Out, stringsAsFactors = FALSE))
}
Try the CrossVA package in your browser
Any scripts or data that you put into this service are public.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.