Nothing
R/exportDDI.R
In DDIwR: DDI with R
Defines functions
`exportDDI`
#' @name exportDDI
#' @title
#' Export to a DDI metadata file
#'
#' @description
#' Create a DDI Codebook version 2.5, XML file structure.
#'
#' @details
#' #' The information object can either be a data file (includign an R data
#' frame) or a list having two main list components:
#'
#' - **`fileDscr`**, if the data is provided in a subcomponent named
#' **`datafile`**
#'
#' - **`dataDscr`**, having as many components as the number of variables in the
#' (meta)data. For each variable, there should a mandatory subcomponent called
#' **`label`** (that contains the variable's label) and, if the variable is of a
#' categorical type, another subcomponent called **`labels`**.
#'
#' Additional informations about the variables can be specified as further
#' subcomponents, combining DDI specific data but also other information that
#' might not be covered by DDI:
#'
#' - **`measurement`** is the equivalent of the specific DDI attribute
#' **`nature`** of the **`var`** element, which accepts these values:
#' `"nominal"`, `"ordinal"`, `"interval"`, `"ratio"`, `"percent"`, and
#' `"other"`.
#'
#' - **`type`** is useful for multiple reasons. A first one, if the variable is
#' numerical, is to differentiate between `discrete` and `continuous` values of
#' the attribute **`intrvl`** from the same DDI element **`var`**. Another
#' reason is to help identifying pure string variables (containing text), when
#' the subcomponent **`type`** is equal to `"char"`. It is also used for the
#' subelement **`varFormat`** of the element **`var`**. Finally, another reason
#' is to differentiate between pure categorical (`"cat"`) and pure numerical
#' (`"num"`) variables, as well as mixed ones, among which `"numcat"` referring
#' to a numerical variable with very few values (such as the number of
#' children), for which it is possible to also produce a table of frequencies
#' along the numerical summaries. There are also categorical variables that can
#' be interpreted as numeric (`"catnum"`), such as a Likert type response scale
#' with 7 values, where numerical summaries are also routinely performed along
#' with the usual table of frequencies.
#'
#' - **`missing`** is an important subcomponent, indicating which of the values
#' in the variable are going to be treated as missing values, and it is going to
#' be exported as the attribute `missing` of the DDI subelement **`catgry`**.
#'
#' There are many more possible attributes and DDI elements to be added in the
#' information object, future versions of this function will likely expand.
#'
#' For the moment, only DDI codebook version 2.5 is exported, and DDI Lifecycle
#' is planned for future releases.
#'
#' Argument **`xmlang`** expects a two letter ISO country coding, for instance
#' `"en"` to indicate English, or `"ro"` to indicate Romanian etc.
#'
#' If the document is monolang, this argument is placed a single time for the
#' entire document, in the attributes of the `codeBook` element. For
#' multilingual documents, it is placed in the attributes of various other
#' (sub)elements, for instance `abstract` as an obvious one, or the study
#' title, name of the distributing institution, variable labels etc.
#'
#' The argument **`OS`** can be either:\cr
#' `"windows"` (default), or `"Windows"`, `"Win"`, `"win"`,\cr
#' `"MacOS"`, `"Darwin"`, `"Apple"`, `"Mac"`, `"mac"`,\cr
#' `"Linux"`, `"linux"`.
#'
#' The end of line separator changes only when the target OS is different from
#' the running OS.
#'
#' The argument **`indent`** controls how many spaces will be used in the XML
#' file, to indent the different subelements.
#'
#' A small number of required DDI specific elements and attributes have generic
#' default values but they may be specified using the three dots **`...`**
#' argument. For the current version, these are: `IDNo`, `titl`, `agency`, `URI`
#' (for the `holdings` element), `distrbtr`, `abstract` and `level` (for the
#' `otherMat` element).
#'
#' @return
#' An XML file containing a DDI version 2.5 metadata.
#'
#' @seealso
#' \url{https://ddialliance.org/Specification/DDI-Codebook/2.5/XMLSchema/field_level_documentation.html}
#'
#' @examples
#' codeBook <- list(dataDscr = list(
#' ID = list(
#' label = "Questionnaire ID",
#' type = "num",
#' measurement = "interval"
#' ),
#' V1 = list(
#' label = "Label for the first variable",
#' labels = c(
#' "No" = 0,
#' "Yes" = 1,
#' "Not applicable" = -97,
#' "Not answered" = -99),
#' na_values = c(-99, -97),
#' type = "cat",
#' measurement = "nominal"
#' ),
#' V2 = list(
#' label = "Label for the second variable",
#' labels = c(
#' "Very little" = 1,
#' "Little" = 2,
#' "So, so" = 3,
#' "Much" = 4,
#' "Very much" = 5,
#' "Don't know" = -98),
#' na_values = c(-98),
#' type = "cat",
#' measurement = "ordinal"
#' ),
#' V3 = list(
#' label = "Label for the third variable",
#' labels = c(
#' "First answer" = "A",
#' "Second answer" = "B",
#' "Don't know" = -98),
#' na_values = c(-98),
#' type = "cat",
#' measurement = "nominal"
#' ),
#' V4 = list(
#' label = "Number of children",
#' labels = c(
#' "Don't know" = -98,
#' "Not answered" = -99),
#' na_values = c(-99, -98),
#' type = "numcat",
#' measurement = "ratio"
#' ),
#' V5 = list(
#' label = "Political party reference",
#' type = "char",
#' txt = "When the respondent indicated his political party reference,
#' his/her open response was recoded on a scale of 1-99 with parties
#' with a left-wing orientation coded on the low end of the scale and
#' parties with a right-wing orientation coded on the high end of the
#' scale. Categories 90-99 were reserved miscellaneous responses."
#' )))
#'
#' \dontrun{
#' exportDDI(codeBook, file = "codebook.xml")
#'
#' # using a namespace
#' exportDDI(codeBook, file = "codebook.xml", xmlns = "ddi")
#' }
#'
#' @author Adrian Dusa
#'
#' @param codebook
#' A list object containing the metadata, or a path to a directory
#' where these objects are located, for batch processing
#'
#' @param file
#' either a character string naming a file or a connection open for
#' writing. "" indicates output to the console
#'
#' @param embed
#' Logical, embed the CSV datafile in the XML file, if present
#'
#' @param OS
#' The target operating system, for the eol - end of line character(s)
#'
#' @param indent Indent width, in number of spaces
#'
#' @param monolang Logical, monolang or multilingual document
#'
#' @param xmlang ISO two letter code for the language used in the DDI elements
#'
#' @param xmlns
#' Character, namespace for the XML file (ignored if already present
#' in the codebook object)
#'
#' @param ... Other arguments, mainly for internal use
#'
#' @export
`exportDDI` <- function(
codebook, file = "", embed = TRUE, OS = "", indent = 4,
monolang = FALSE, xmlang = "en", xmlns = "", ...
) {
# https://ddialliance.org/Specification/DDI-Codebook/2.5/XMLSchema/field_level_documentation.html
# validation procedure:
# https://ddialliance.org/Specification/DDI-Codebook/2.5/
# schema <- read_xml("path/to/ddi_2_5_1/schemas/codebook.xsd")
# doc <- read_xml("path/to/filetovalidate.xml")
# xml_validate(doc, schema)
`check_arg` <- function(x, vx, type = "c") {
valid <- !is.null(vx) && is.atomic(vx) && length(vx) == 1
if (valid & type == "c") { # character
valid <- is.character(vx) & !admisc::possibleNumeric(vx)
}
if (!valid) {
admisc::stopError(
sprintf(
"Argument '%s' should be a%s vector of length 1",
x,
ifelse(type == "c", " character", "")
)
)
}
}
`check_dots` <- function(x, default, type = "c") {
if (is.element(x, names(dots))) {
dotsx <- dots[[x]]
check_arg(x, dotsx, type = type)
return(dotsx)
}
return(default)
}
`generateUUID` <- function(x) {
toreturn <- rep(NA, x)
first <- sample(c(LETTERS, letters), x, replace = TRUE)
for (i in seq(x)) {
toreturn[i] <- paste(
c(
first[i],
sample(c(LETTERS, letters, 0:9), 15, replace = TRUE)
),
collapse = ""
)
}
return(toreturn)
# a safer way is to use unique() but it is highly unlikely this would be needed
# toreturn <- unique(toreturn)
# if (length(toreturn) == x) return(toreturn)
}
`repeatSpace` <- function(times) {
paste(rep(" ", times*indent), collapse = "")
}
`replaceChars` <- function(x) {
x <- replaceTicks(x)
x <- gsub(
"<", "<",
gsub(
">", ">",
gsub(
"&", "&",
x
)
)
)
tc <- admisc::tryCatchWEM({
# use case: StatConverter in Electron, the terminal that opens R
# probably doesn't have a suitable locale and it outputs an error
# this does the same thing (using hexadecimal code) and is better
# weird space character: gsub(rawToChar(as.raw(c(194, 160))), " ", x)
x <- gsub("\u00a0", " ", x)
})
return(x)
}
dots <- list(...)
IDNo <- check_dots("IDNo", "S0000", type = "any")
titl <- check_dots("titl", "Generic title")
agency <- check_dots("agency", "default")
URI <- check_dots("URI", "http://www.default.eu")
distrbtr <- check_dots("distrbtr", "Name of the distributing institution")
abstract <- check_dots("abstract", "Study abstract")
level <- check_dots("level", "0")
check_arg("xmlang", xmlang)
xmlang <- paste0(
ifelse(isTRUE(monolang), "", " "),
"xml:lang=\"", xmlang, "\""
)
ns <- codebook[["xmlns"]]
if (is.null(ns)) ns <- xmlns
check_arg("xmlns", ns, "c")
s0 <- repeatSpace(0)
s1 <- repeatSpace(1)
s2 <- repeatSpace(2)
s3 <- repeatSpace(3)
s4 <- repeatSpace(4)
s5 <- repeatSpace(5)
# `catText` <- function(x, ...) {
# cat(paste(
# repeatSpace(x),
# paste(
# unlist(list(...)),
# collapse = ""
# ),
# enter,
# sep = ""
# ))
# }
if (OS == "") {
OS <- Sys.info()[["sysname"]]
}
enter <- getEnter(OS = OS)
data <- codebook[["fileDscr"]][["datafile"]]
stdyDscr <- codebook[["stdyDscr"]]
dataDscr <- codebook[["dataDscr"]]
pN <- logical(length(dataDscr))
# uuid for all variables
uuid <- generateUUID(length(dataDscr))
prodDate <- as.character(Sys.time())
version <- as.character(packageVersion("DDIwR"))
varnames <- names(dataDscr)
if (!identical(file, "")) {
sink(file)
on.exit(sink())
}
cat(paste(
s0, "<?xml version=\"1.0\" encoding=\"UTF-8\"?>",
enter,
sep = ""
))
cat(paste(
s0, "<", ns, ifelse(identical(ns, ""), "", ":"), "codeBook version=\"2.5\"",
enter,
# Apparently, Nesstar interprets this ID as the Study Description ID
# "ID=\"", generateUUID(1), "\"",
# enter,
ifelse(isTRUE(monolang), paste0(xmlang, enter), ""),
"xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\"",
enter,
"xmlns:xsd=\"http://www.w3.org/2001/XMLSchema\"",
enter,
"xsi:schemaLocation=\"",
"ddi:codebook:2_5 https://ddialliance.org/Specification/DDI-Codebook/2.5/XMLSchema/codebook.xsd\"",
enter,
paste0("xmlns", ifelse(identical(ns, ""), "", ":"), ns, "=\"ddi:codebook:2_5\">"),
enter,
sep = ""
))
if (!identical(ns, "")) ns <- paste0(ns, ":")
if (isTRUE(monolang)) {
xmlang <- ""
}
# Document description
cat(paste(s1, "<", ns, "docDscr>", enter, sep = ""))
cat(paste(s2, "<", ns, "citation>", enter, sep = ""))
cat(paste(s3, "<", ns, "titlStmt>", enter, sep = ""))
cat(paste(
s4, "<", ns, "titl", xmlang, ">", titl, "</", ns, "titl>",
enter,
sep = ""
))
cat(paste(
s4, "<", ns, "IDNo agency=\"", agency,"\">", generateUUID(1), "</", ns, "IDNo>",
enter,
sep = ""
))
cat(paste(s3, "</", ns, "titlStmt>", enter, sep = ""))
cat(paste(s3, "<", ns, "prodStmt>", enter, sep = ""))
cat(paste(
s4, "<", ns, "prodDate date=\"", prodDate, "\">",
prodDate, "</", ns, "prodDate>",
enter,
sep = ""
))
cat(paste(
s4, "<", ns, "software version=\"", version,
"\">R package DDIwR</", ns, "software>",
enter, sep = ""
))
cat(paste(s3, "</", ns, "prodStmt>", enter, sep = ""))
cat(paste(s2, "</", ns, "citation>", enter, sep = ""))
cat(paste(s1, "</", ns, "docDscr>", enter, sep = ""))
# Study description
if (is.null(stdyDscr)) {
cat(paste(s1, "<", ns, "stdyDscr>", enter, sep = ""))
cat(paste(s2, "<", ns, "citation>", enter, sep = ""))
cat(paste(s3, "<", ns, "titlStmt>", enter, sep = ""))
cat(paste(
s4, "<", ns, "titl", xmlang, ">", titl, "</", ns, "titl>",
enter,
sep = ""
))
cat(paste(
s4, "<", ns, "IDNo agency=\"", agency,"\">", IDNo, "</", ns, "IDNo>",
enter,
sep = ""
))
cat(paste(s3, "</", ns, "titlStmt>", enter, sep = ""))
cat(paste(s3, "<", ns, "distStmt>", enter, sep = ""))
cat(paste(
s4, "<", ns, "distrbtr", xmlang, ">", distrbtr,
"</", ns, "distrbtr>",
enter, sep = ""
))
cat(paste(s3, "</", ns, "distStmt>", enter, sep = ""))
cat(paste(
s3, "<", ns, "holdings URI=\"", URI,
"\">Description of the study holdings</", ns, "holdings>",
enter, sep = ""
))
cat(paste(s2, "</", ns, "citation>", enter, sep = ""))
cat(paste(s2, "<", ns, "stdyInfo>", enter, sep = ""))
cat(paste(
s3,
"<", ns, "abstract", xmlang, ">", abstract, "</", ns, "abstract>",
enter, sep = ""
))
cat(paste(s2, "</", ns, "stdyInfo>", enter, sep = ""))
cat(paste(s1, "</", ns, "stdyDscr>", enter, sep = ""))
}
else {
cat(paste(makeXML(stdyDscr, 1, indent, ns, enter), collapse = ""))
## when no xml namespace is needed, this works:
# stdyDscr <- as_xml_document(list(stdyDscr = stdyDscr))
# addns <- function(x) {
# if (!is.null(names(x))) {
# names(x) <- paste0(ns, names(x))
# if (is.list(x)) {
# x <- lapply(x, function(x) {
# addns(x)
# })
# }
# }
# return(x)
# }
# stdyDscr <- lapply(list(stdyDscr), addns)
# names(stdyDscr) <- paste0(ns, "stdyDscr")
# stdyDscr <- as_xml_document(stdyDscr) # error can not find namespace
# cat(as.character(stdyDscr))
}
fileDscrUUID <- generateUUID(1)
cat(paste(
s1, "<", ns, "fileDscr ID=\"", fileDscrUUID, "\">",
enter,
sep = ""
))
if (!is.null(data)) {
if (!is.data.frame(data)) {
admisc::stopError(
"The 'datafile' component should be a data frame."
)
}
else if (!identical(toupper(names(data)), toupper(names(dataDscr)))) {
admisc::stopError(
paste(
"Variables in the data do not match",
"the variables in the data description."
)
)
}
cat(paste(s2, "<", ns, "fileTxt>", enter, sep = ""))
if (!is.null(fileName <- codebook[["fileDscr"]][["fileName"]])) {
cat(paste(
s3,
"<", ns, "fileName>", fileName, "</", ns, "fileName>",
enter,
sep = ""
))
}
cat(paste(s3, "<", ns, "dimensns>", enter, sep = ""))
cat(paste(
s4,
"<", ns, "caseQnty>", nrow(data), "</", ns, "caseQnty>",
enter,
sep = ""
))
cat(paste(
s4,
"<", ns, "varQnty>", ncol(data), "</", ns, "varQnty>",
enter,
sep = ""
))
cat(paste(s3, "</", ns, "dimensns>", enter, sep = ""))
if (!is.null(fileType <- codebook[["fileDscr"]][["fileType"]])) {
cat(paste(
s3,
"<", ns, "fileType>", fileType, "</", ns, "fileType>",
enter,
sep = ""
))
}
cat(paste(s2, "</", ns, "fileTxt>", enter, sep = ""))
if (embed) {
cat(paste(s2, "<", ns, "notes level=\"file\" subject=\"CSV dataset\">", enter, sep = ""))
cat(paste(
s3, "<![CDATA[# start data #",
enter,
sep = ""
))
tt <- tempfile()
# sink()
suppressWarnings(
write.table(
undeclare(data, drop = TRUE),
file = tt,
sep = ",",
na = "",
# append = TRUE,
row.names = FALSE
)
)
# sink(file, append = TRUE)
cat(
paste(s3, readLines(tt), collapse = enter, sep = ""),
enter,
sep = ""
)
cat(paste(s3,
"# end data #]]>",
enter,
sep = ""
))
cat(paste(s2, "</", ns, "notes>", enter, sep = ""))
}
pN <- sapply(data[names(dataDscr)], function(x) {
admisc::possibleNumeric(unclass(x))
})
aN <- lapply(
subset(
data,
select = is.element(
names(data),
names(pN)[pN]
)
),
# data[, names(pN)[pN], drop = FALSE],
function(x) admisc::asNumeric(unclass(x))
)
}
cat(paste(s1, "</", ns, "fileDscr>", enter, sep = ""))
cat(paste(s1, "<", ns, "dataDscr>", enter, sep = ""))
for (i in seq(length(dataDscr))) {
dcml <- ""
if (!is.null(data) && pN[i]) {
dcml <- paste0(
" dcml=\"",
admisc::numdec(na.omit(aN[[varnames[i]]])),
"\""
)
}
nature <- ""
if (is.element("measurement", names(dataDscr[[i]]))) {
nature <- paste0(
" nature=\"",
gsub(
"categorical|quantitative|, ", "",
dataDscr[[i]]$measurement,
),
"\""
)
}
cat(paste0(
s2, "<", ns, "var ID=\"", uuid[i], "\"",
" name=\"", varnames[i], "\"",
" files=\"", fileDscrUUID, "\"",
dcml, nature, ">",
enter
))
if (!is.null(dataDscr[[i]][["label"]])) {
if (!is.na(dataDscr[[i]][["label"]])) {
cat(paste(
s3, "<", ns, "labl", xmlang, ">",
replaceChars(
dataDscr[[i]][["label"]]
),
"</", ns, "labl>",
enter,
sep = ""
))
}
}
na_values <- NULL
if (is.element("na_values", names(dataDscr[[i]]))) {
na_values <- dataDscr[[i]]$na_values
}
na_range <- NULL
if (is.element("na_range", names(dataDscr[[i]]))) {
na_range <- dataDscr[[i]]$na_range
}
if (length(na_range) > 0) {
cat(paste(s3, "<", ns, "invalrng>", enter, sep = ""))
if (any(is.element(na_range, c(-Inf, Inf)))) {
if (identical(na_range[1], -Inf)) {
cat(paste(
s4,
sprintf(
"<%srange UNITS=\"INT\" max=\"%s\"/>",
ns, na_range[2]
),
enter,
sep = ""
))
}
else {
cat(paste(
s4,
sprintf(
"<%srange UNITS=\"INT\" min=\"%s\"/>",
ns, na_range[1]
),
enter,
sep = ""
))
}
}
else {
cat(paste(
s4,
sprintf(
"<%srange UNITS=\"INT\" min=\"%s\" max=\"%s\"/>",
ns, na_range[1], na_range[2]
),
enter,
sep = ""
))
}
cat(paste(s3, "</", ns, "invalrng>", enter, sep = ""))
}
lbls <- dataDscr[[i]][["labels"]]
# if (!is.null(lbls)) {
# # non-ASCII also means non multibyte characters
# lbls <- setNames(
# admisc::trimstr(
# iconv(lbls, "UTF-8", "ASCII", sub = "")
# ),
# names(lbls)
# )
# }
type <- dataDscr[[i]]$type
# even if the data is not present, pN is FALSE for all variables
if (pN[i]) {
vals <- aN[[names(dataDscr)[i]]]
if (!is.null(lbls)) {
ismiss <- is.element(lbls, na_values)
if (length(na_range) > 0) {
ismiss <- ismiss | (lbls >= na_range[1] & lbls <= na_range[2])
}
vals[is.element(vals, lbls[ismiss])] <- NA
}
vals <- na.omit(vals)
# this is a test if a variable truly is numeric
# (not just categorical using numbers)
# if it has at least four(?) values different from the labels
printnum <- length(setdiff(vals, lbls)) > 4
if (!is.null(type)) {
# at least two non missing values are needed to calculate sd()
printnum <- printnum | (length(vals) > 2 & grepl("num", type))
}
if (printnum) { # numeric variable
cat(paste(
s3,
"<", ns, "sumStat type=\"min\">",
format(
min(vals, na.rm = TRUE),
scientific = FALSE
),
"</", ns, "sumStat>",
enter,
sep = ""
))
cat(paste(
s3,
"<", ns, "sumStat type=\"max\">",
format(
max(vals, na.rm = TRUE),
scientific = FALSE
),
"</", ns, "sumStat>",
enter,
sep = ""
))
cat(paste(
s3,
"<", ns, "sumStat type=\"mean\">",
format(
mean(vals, na.rm = TRUE),
scientific = FALSE
),
"</", ns, "sumStat>",
enter,
sep = ""
))
cat(paste(
s3,
"<", ns, "sumStat type=\"medn\">",
format(
median(vals, na.rm = TRUE),
scientific = FALSE
),
"</", ns, "sumStat>",
enter,
sep = ""
))
cat(paste(
s3,
"<", ns, "sumStat type=\"stdev\">",
format(
sd(vals, na.rm = TRUE),
scientific = FALSE
),
"</", ns, "sumStat>",
enter,
sep = ""
))
}
}
if (!is.null(lbls)) {
# what is the difference from data[[i]] ?
tbl <- table(data[[names(dataDscr)[i]]])
for (v in seq(length(lbls))) {
ismiss <- is.element(lbls[v], na_values)
if (length(na_range) > 0 & pN[i]) {
ismiss <- ismiss | (
lbls[v] >= na_range[1] & lbls[v] <= na_range[2]
)
}
cat(paste(
s3,
"<", ns, "catgry",
ifelse(ismiss, " missing=\"Y\"", ""), ">",
enter,
sep = ""
))
cat(paste(
s4,
"<", ns, "catValu>",
replaceChars(lbls[v]),
"</", ns, "catValu>",
enter,
sep = ""
))
cat(paste(
s4,
"<", ns, "labl", xmlang, ">",
replaceChars(names(lbls)[v]),
"</", ns, "labl>",
enter,
sep = ""
))
if (!is.null(data)) {
freq <- tbl[match(lbls[v], names(tbl))]
cat(paste(
s4,
"<", ns, "catStat type=\"freq\">",
ifelse(
is.na(freq),
0,
format(freq, scientific = FALSE)
),
"</", ns, "catStat>",
enter,
sep = ""
))
}
cat(paste(s3, "</", ns, "catgry>", enter, sep = ""))
}
}
if (any(grepl("type", names(dataDscr[[i]])))) {
varFormat <- dataDscr[[i]]$varFormat[1] # SPSS
cat(paste(
s3,
"<", ns, "varFormat type=\"",
ifelse(
grepl("char", dataDscr[[i]]$type),
"character",
"numeric"
),
"\" schema=\"other\" formatname=\"",
substr(varFormat, 1, 1),
"\">",
varFormat,
"</", ns, "varFormat>",
enter,
sep = ""
))
}
if (any(grepl("txt", names(dataDscr[[i]])))) {
cat(paste(s3, "<", ns, "txt>", enter, sep = ""))
cat(paste(
s0,
"<![CDATA[", dataDscr[[i]]$txt, "]]>",
enter,
sep = ""
))
cat(paste(s3, "</", ns, "txt>", enter, sep = ""))
}
cat(paste(s2, "</", ns, "var>", enter, sep = ""))
}
cat(paste(s1, "</", ns, "dataDscr>", enter, sep = ""))
cat(paste(
s1,
"<", ns, "otherMat level=\"", level, "\"></", ns, "otherMat>",
enter,
sep = ""
))
cat(paste(s0, "</", ns, "codeBook>", enter, sep = ""))
}
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Defines functions `exportDDI`
#' @name exportDDI
#' @title
#' Export to a DDI metadata file
#'
#' @description
#' Create a DDI Codebook version 2.5, XML file structure.
#'
#' @details
#' #' The information object can either be a data file (includign an R data
#' frame) or a list having two main list components:
#'
#' - **`fileDscr`**, if the data is provided in a subcomponent named
#' **`datafile`**
#'
#' - **`dataDscr`**, having as many components as the number of variables in the
#' (meta)data. For each variable, there should a mandatory subcomponent called
#' **`label`** (that contains the variable's label) and, if the variable is of a
#' categorical type, another subcomponent called **`labels`**.
#'
#' Additional informations about the variables can be specified as further
#' subcomponents, combining DDI specific data but also other information that
#' might not be covered by DDI:
#'
#' - **`measurement`** is the equivalent of the specific DDI attribute
#' **`nature`** of the **`var`** element, which accepts these values:
#' `"nominal"`, `"ordinal"`, `"interval"`, `"ratio"`, `"percent"`, and
#' `"other"`.
#'
#' - **`type`** is useful for multiple reasons. A first one, if the variable is
#' numerical, is to differentiate between `discrete` and `continuous` values of
#' the attribute **`intrvl`** from the same DDI element **`var`**. Another
#' reason is to help identifying pure string variables (containing text), when
#' the subcomponent **`type`** is equal to `"char"`. It is also used for the
#' subelement **`varFormat`** of the element **`var`**. Finally, another reason
#' is to differentiate between pure categorical (`"cat"`) and pure numerical
#' (`"num"`) variables, as well as mixed ones, among which `"numcat"` referring
#' to a numerical variable with very few values (such as the number of
#' children), for which it is possible to also produce a table of frequencies
#' along the numerical summaries. There are also categorical variables that can
#' be interpreted as numeric (`"catnum"`), such as a Likert type response scale
#' with 7 values, where numerical summaries are also routinely performed along
#' with the usual table of frequencies.
#'
#' - **`missing`** is an important subcomponent, indicating which of the values
#' in the variable are going to be treated as missing values, and it is going to
#' be exported as the attribute `missing` of the DDI subelement **`catgry`**.
#'
#' There are many more possible attributes and DDI elements to be added in the
#' information object, future versions of this function will likely expand.
#'
#' For the moment, only DDI codebook version 2.5 is exported, and DDI Lifecycle
#' is planned for future releases.
#'
#' Argument **`xmlang`** expects a two letter ISO country coding, for instance
#' `"en"` to indicate English, or `"ro"` to indicate Romanian etc.
#'
#' If the document is monolang, this argument is placed a single time for the
#' entire document, in the attributes of the `codeBook` element. For
#' multilingual documents, it is placed in the attributes of various other
#' (sub)elements, for instance `abstract` as an obvious one, or the study
#' title, name of the distributing institution, variable labels etc.
#'
#' The argument **`OS`** can be either:\cr
#' `"windows"` (default), or `"Windows"`, `"Win"`, `"win"`,\cr
#' `"MacOS"`, `"Darwin"`, `"Apple"`, `"Mac"`, `"mac"`,\cr
#' `"Linux"`, `"linux"`.
#'
#' The end of line separator changes only when the target OS is different from
#' the running OS.
#'
#' The argument **`indent`** controls how many spaces will be used in the XML
#' file, to indent the different subelements.
#'
#' A small number of required DDI specific elements and attributes have generic
#' default values but they may be specified using the three dots **`...`**
#' argument. For the current version, these are: `IDNo`, `titl`, `agency`, `URI`
#' (for the `holdings` element), `distrbtr`, `abstract` and `level` (for the
#' `otherMat` element).
#'
#' @return
#' An XML file containing a DDI version 2.5 metadata.
#'
#' @seealso
#' \url{https://ddialliance.org/Specification/DDI-Codebook/2.5/XMLSchema/field_level_documentation.html}
#'
#' @examples
#' codeBook <- list(dataDscr = list(
#' ID = list(
#' label = "Questionnaire ID",
#' type = "num",
#' measurement = "interval"
#' ),
#' V1 = list(
#' label = "Label for the first variable",
#' labels = c(
#' "No" = 0,
#' "Yes" = 1,
#' "Not applicable" = -97,
#' "Not answered" = -99),
#' na_values = c(-99, -97),
#' type = "cat",
#' measurement = "nominal"
#' ),
#' V2 = list(
#' label = "Label for the second variable",
#' labels = c(
#' "Very little" = 1,
#' "Little" = 2,
#' "So, so" = 3,
#' "Much" = 4,
#' "Very much" = 5,
#' "Don't know" = -98),
#' na_values = c(-98),
#' type = "cat",
#' measurement = "ordinal"
#' ),
#' V3 = list(
#' label = "Label for the third variable",
#' labels = c(
#' "First answer" = "A",
#' "Second answer" = "B",
#' "Don't know" = -98),
#' na_values = c(-98),
#' type = "cat",
#' measurement = "nominal"
#' ),
#' V4 = list(
#' label = "Number of children",
#' labels = c(
#' "Don't know" = -98,
#' "Not answered" = -99),
#' na_values = c(-99, -98),
#' type = "numcat",
#' measurement = "ratio"
#' ),
#' V5 = list(
#' label = "Political party reference",
#' type = "char",
#' txt = "When the respondent indicated his political party reference,
#' his/her open response was recoded on a scale of 1-99 with parties
#' with a left-wing orientation coded on the low end of the scale and
#' parties with a right-wing orientation coded on the high end of the
#' scale. Categories 90-99 were reserved miscellaneous responses."
#' )))
#'
#' \dontrun{
#' exportDDI(codeBook, file = "codebook.xml")
#'
#' # using a namespace
#' exportDDI(codeBook, file = "codebook.xml", xmlns = "ddi")
#' }
#'
#' @author Adrian Dusa
#'
#' @param codebook
#' A list object containing the metadata, or a path to a directory
#' where these objects are located, for batch processing
#'
#' @param file
#' either a character string naming a file or a connection open for
#' writing. "" indicates output to the console
#'
#' @param embed
#' Logical, embed the CSV datafile in the XML file, if present
#'
#' @param OS
#' The target operating system, for the eol - end of line character(s)
#'
#' @param indent Indent width, in number of spaces
#'
#' @param monolang Logical, monolang or multilingual document
#'
#' @param xmlang ISO two letter code for the language used in the DDI elements
#'
#' @param xmlns
#' Character, namespace for the XML file (ignored if already present
#' in the codebook object)
#'
#' @param ... Other arguments, mainly for internal use
#'
#' @export
`exportDDI` <- function(
codebook, file = "", embed = TRUE, OS = "", indent = 4,
monolang = FALSE, xmlang = "en", xmlns = "", ...
) {
# https://ddialliance.org/Specification/DDI-Codebook/2.5/XMLSchema/field_level_documentation.html
# validation procedure:
# https://ddialliance.org/Specification/DDI-Codebook/2.5/
# schema <- read_xml("path/to/ddi_2_5_1/schemas/codebook.xsd")
# doc <- read_xml("path/to/filetovalidate.xml")
# xml_validate(doc, schema)
`check_arg` <- function(x, vx, type = "c") {
valid <- !is.null(vx) && is.atomic(vx) && length(vx) == 1
if (valid & type == "c") { # character
valid <- is.character(vx) & !admisc::possibleNumeric(vx)
}
if (!valid) {
admisc::stopError(
sprintf(
"Argument '%s' should be a%s vector of length 1",
x,
ifelse(type == "c", " character", "")
)
)
}
}
`check_dots` <- function(x, default, type = "c") {
if (is.element(x, names(dots))) {
dotsx <- dots[[x]]
check_arg(x, dotsx, type = type)
return(dotsx)
}
return(default)
}
`generateUUID` <- function(x) {
toreturn <- rep(NA, x)
first <- sample(c(LETTERS, letters), x, replace = TRUE)
for (i in seq(x)) {
toreturn[i] <- paste(
c(
first[i],
sample(c(LETTERS, letters, 0:9), 15, replace = TRUE)
),
collapse = ""
)
}
return(toreturn)
# a safer way is to use unique() but it is highly unlikely this would be needed
# toreturn <- unique(toreturn)
# if (length(toreturn) == x) return(toreturn)
}
`repeatSpace` <- function(times) {
paste(rep(" ", times*indent), collapse = "")
}
`replaceChars` <- function(x) {
x <- replaceTicks(x)
x <- gsub(
"<", "<",
gsub(
">", ">",
gsub(
"&", "&",
x
)
)
)
tc <- admisc::tryCatchWEM({
# use case: StatConverter in Electron, the terminal that opens R
# probably doesn't have a suitable locale and it outputs an error
# this does the same thing (using hexadecimal code) and is better
# weird space character: gsub(rawToChar(as.raw(c(194, 160))), " ", x)
x <- gsub("\u00a0", " ", x)
})
return(x)
}
dots <- list(...)
IDNo <- check_dots("IDNo", "S0000", type = "any")
titl <- check_dots("titl", "Generic title")
agency <- check_dots("agency", "default")
URI <- check_dots("URI", "http://www.default.eu")
distrbtr <- check_dots("distrbtr", "Name of the distributing institution")
abstract <- check_dots("abstract", "Study abstract")
level <- check_dots("level", "0")
check_arg("xmlang", xmlang)
xmlang <- paste0(
ifelse(isTRUE(monolang), "", " "),
"xml:lang=\"", xmlang, "\""
)
ns <- codebook[["xmlns"]]
if (is.null(ns)) ns <- xmlns
check_arg("xmlns", ns, "c")
s0 <- repeatSpace(0)
s1 <- repeatSpace(1)
s2 <- repeatSpace(2)
s3 <- repeatSpace(3)
s4 <- repeatSpace(4)
s5 <- repeatSpace(5)
# `catText` <- function(x, ...) {
# cat(paste(
# repeatSpace(x),
# paste(
# unlist(list(...)),
# collapse = ""
# ),
# enter,
# sep = ""
# ))
# }
if (OS == "") {
OS <- Sys.info()[["sysname"]]
}
enter <- getEnter(OS = OS)
data <- codebook[["fileDscr"]][["datafile"]]
stdyDscr <- codebook[["stdyDscr"]]
dataDscr <- codebook[["dataDscr"]]
pN <- logical(length(dataDscr))
# uuid for all variables
uuid <- generateUUID(length(dataDscr))
prodDate <- as.character(Sys.time())
version <- as.character(packageVersion("DDIwR"))
varnames <- names(dataDscr)
if (!identical(file, "")) {
sink(file)
on.exit(sink())
}
cat(paste(
s0, "<?xml version=\"1.0\" encoding=\"UTF-8\"?>",
enter,
sep = ""
))
cat(paste(
s0, "<", ns, ifelse(identical(ns, ""), "", ":"), "codeBook version=\"2.5\"",
enter,
# Apparently, Nesstar interprets this ID as the Study Description ID
# "ID=\"", generateUUID(1), "\"",
# enter,
ifelse(isTRUE(monolang), paste0(xmlang, enter), ""),
"xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\"",
enter,
"xmlns:xsd=\"http://www.w3.org/2001/XMLSchema\"",
enter,
"xsi:schemaLocation=\"",
"ddi:codebook:2_5 https://ddialliance.org/Specification/DDI-Codebook/2.5/XMLSchema/codebook.xsd\"",
enter,
paste0("xmlns", ifelse(identical(ns, ""), "", ":"), ns, "=\"ddi:codebook:2_5\">"),
enter,
sep = ""
))
if (!identical(ns, "")) ns <- paste0(ns, ":")
if (isTRUE(monolang)) {
xmlang <- ""
}
# Document description
cat(paste(s1, "<", ns, "docDscr>", enter, sep = ""))
cat(paste(s2, "<", ns, "citation>", enter, sep = ""))
cat(paste(s3, "<", ns, "titlStmt>", enter, sep = ""))
cat(paste(
s4, "<", ns, "titl", xmlang, ">", titl, "</", ns, "titl>",
enter,
sep = ""
))
cat(paste(
s4, "<", ns, "IDNo agency=\"", agency,"\">", generateUUID(1), "</", ns, "IDNo>",
enter,
sep = ""
))
cat(paste(s3, "</", ns, "titlStmt>", enter, sep = ""))
cat(paste(s3, "<", ns, "prodStmt>", enter, sep = ""))
cat(paste(
s4, "<", ns, "prodDate date=\"", prodDate, "\">",
prodDate, "</", ns, "prodDate>",
enter,
sep = ""
))
cat(paste(
s4, "<", ns, "software version=\"", version,
"\">R package DDIwR</", ns, "software>",
enter, sep = ""
))
cat(paste(s3, "</", ns, "prodStmt>", enter, sep = ""))
cat(paste(s2, "</", ns, "citation>", enter, sep = ""))
cat(paste(s1, "</", ns, "docDscr>", enter, sep = ""))
# Study description
if (is.null(stdyDscr)) {
cat(paste(s1, "<", ns, "stdyDscr>", enter, sep = ""))
cat(paste(s2, "<", ns, "citation>", enter, sep = ""))
cat(paste(s3, "<", ns, "titlStmt>", enter, sep = ""))
cat(paste(
s4, "<", ns, "titl", xmlang, ">", titl, "</", ns, "titl>",
enter,
sep = ""
))
cat(paste(
s4, "<", ns, "IDNo agency=\"", agency,"\">", IDNo, "</", ns, "IDNo>",
enter,
sep = ""
))
cat(paste(s3, "</", ns, "titlStmt>", enter, sep = ""))
cat(paste(s3, "<", ns, "distStmt>", enter, sep = ""))
cat(paste(
s4, "<", ns, "distrbtr", xmlang, ">", distrbtr,
"</", ns, "distrbtr>",
enter, sep = ""
))
cat(paste(s3, "</", ns, "distStmt>", enter, sep = ""))
cat(paste(
s3, "<", ns, "holdings URI=\"", URI,
"\">Description of the study holdings</", ns, "holdings>",
enter, sep = ""
))
cat(paste(s2, "</", ns, "citation>", enter, sep = ""))
cat(paste(s2, "<", ns, "stdyInfo>", enter, sep = ""))
cat(paste(
s3,
"<", ns, "abstract", xmlang, ">", abstract, "</", ns, "abstract>",
enter, sep = ""
))
cat(paste(s2, "</", ns, "stdyInfo>", enter, sep = ""))
cat(paste(s1, "</", ns, "stdyDscr>", enter, sep = ""))
}
else {
cat(paste(makeXML(stdyDscr, 1, indent, ns, enter), collapse = ""))
## when no xml namespace is needed, this works:
# stdyDscr <- as_xml_document(list(stdyDscr = stdyDscr))
# addns <- function(x) {
# if (!is.null(names(x))) {
# names(x) <- paste0(ns, names(x))
# if (is.list(x)) {
# x <- lapply(x, function(x) {
# addns(x)
# })
# }
# }
# return(x)
# }
# stdyDscr <- lapply(list(stdyDscr), addns)
# names(stdyDscr) <- paste0(ns, "stdyDscr")
# stdyDscr <- as_xml_document(stdyDscr) # error can not find namespace
# cat(as.character(stdyDscr))
}
fileDscrUUID <- generateUUID(1)
cat(paste(
s1, "<", ns, "fileDscr ID=\"", fileDscrUUID, "\">",
enter,
sep = ""
))
if (!is.null(data)) {
if (!is.data.frame(data)) {
admisc::stopError(
"The 'datafile' component should be a data frame."
)
}
else if (!identical(toupper(names(data)), toupper(names(dataDscr)))) {
admisc::stopError(
paste(
"Variables in the data do not match",
"the variables in the data description."
)
)
}
cat(paste(s2, "<", ns, "fileTxt>", enter, sep = ""))
if (!is.null(fileName <- codebook[["fileDscr"]][["fileName"]])) {
cat(paste(
s3,
"<", ns, "fileName>", fileName, "</", ns, "fileName>",
enter,
sep = ""
))
}
cat(paste(s3, "<", ns, "dimensns>", enter, sep = ""))
cat(paste(
s4,
"<", ns, "caseQnty>", nrow(data), "</", ns, "caseQnty>",
enter,
sep = ""
))
cat(paste(
s4,
"<", ns, "varQnty>", ncol(data), "</", ns, "varQnty>",
enter,
sep = ""
))
cat(paste(s3, "</", ns, "dimensns>", enter, sep = ""))
if (!is.null(fileType <- codebook[["fileDscr"]][["fileType"]])) {
cat(paste(
s3,
"<", ns, "fileType>", fileType, "</", ns, "fileType>",
enter,
sep = ""
))
}
cat(paste(s2, "</", ns, "fileTxt>", enter, sep = ""))
if (embed) {
cat(paste(s2, "<", ns, "notes level=\"file\" subject=\"CSV dataset\">", enter, sep = ""))
cat(paste(
s3, "<![CDATA[# start data #",
enter,
sep = ""
))
tt <- tempfile()
# sink()
suppressWarnings(
write.table(
undeclare(data, drop = TRUE),
file = tt,
sep = ",",
na = "",
# append = TRUE,
row.names = FALSE
)
)
# sink(file, append = TRUE)
cat(
paste(s3, readLines(tt), collapse = enter, sep = ""),
enter,
sep = ""
)
cat(paste(s3,
"# end data #]]>",
enter,
sep = ""
))
cat(paste(s2, "</", ns, "notes>", enter, sep = ""))
}
pN <- sapply(data[names(dataDscr)], function(x) {
admisc::possibleNumeric(unclass(x))
})
aN <- lapply(
subset(
data,
select = is.element(
names(data),
names(pN)[pN]
)
),
# data[, names(pN)[pN], drop = FALSE],
function(x) admisc::asNumeric(unclass(x))
)
}
cat(paste(s1, "</", ns, "fileDscr>", enter, sep = ""))
cat(paste(s1, "<", ns, "dataDscr>", enter, sep = ""))
for (i in seq(length(dataDscr))) {
dcml <- ""
if (!is.null(data) && pN[i]) {
dcml <- paste0(
" dcml=\"",
admisc::numdec(na.omit(aN[[varnames[i]]])),
"\""
)
}
nature <- ""
if (is.element("measurement", names(dataDscr[[i]]))) {
nature <- paste0(
" nature=\"",
gsub(
"categorical|quantitative|, ", "",
dataDscr[[i]]$measurement,
),
"\""
)
}
cat(paste0(
s2, "<", ns, "var ID=\"", uuid[i], "\"",
" name=\"", varnames[i], "\"",
" files=\"", fileDscrUUID, "\"",
dcml, nature, ">",
enter
))
if (!is.null(dataDscr[[i]][["label"]])) {
if (!is.na(dataDscr[[i]][["label"]])) {
cat(paste(
s3, "<", ns, "labl", xmlang, ">",
replaceChars(
dataDscr[[i]][["label"]]
),
"</", ns, "labl>",
enter,
sep = ""
))
}
}
na_values <- NULL
if (is.element("na_values", names(dataDscr[[i]]))) {
na_values <- dataDscr[[i]]$na_values
}
na_range <- NULL
if (is.element("na_range", names(dataDscr[[i]]))) {
na_range <- dataDscr[[i]]$na_range
}
if (length(na_range) > 0) {
cat(paste(s3, "<", ns, "invalrng>", enter, sep = ""))
if (any(is.element(na_range, c(-Inf, Inf)))) {
if (identical(na_range[1], -Inf)) {
cat(paste(
s4,
sprintf(
"<%srange UNITS=\"INT\" max=\"%s\"/>",
ns, na_range[2]
),
enter,
sep = ""
))
}
else {
cat(paste(
s4,
sprintf(
"<%srange UNITS=\"INT\" min=\"%s\"/>",
ns, na_range[1]
),
enter,
sep = ""
))
}
}
else {
cat(paste(
s4,
sprintf(
"<%srange UNITS=\"INT\" min=\"%s\" max=\"%s\"/>",
ns, na_range[1], na_range[2]
),
enter,
sep = ""
))
}
cat(paste(s3, "</", ns, "invalrng>", enter, sep = ""))
}
lbls <- dataDscr[[i]][["labels"]]
# if (!is.null(lbls)) {
# # non-ASCII also means non multibyte characters
# lbls <- setNames(
# admisc::trimstr(
# iconv(lbls, "UTF-8", "ASCII", sub = "")
# ),
# names(lbls)
# )
# }
type <- dataDscr[[i]]$type
# even if the data is not present, pN is FALSE for all variables
if (pN[i]) {
vals <- aN[[names(dataDscr)[i]]]
if (!is.null(lbls)) {
ismiss <- is.element(lbls, na_values)
if (length(na_range) > 0) {
ismiss <- ismiss | (lbls >= na_range[1] & lbls <= na_range[2])
}
vals[is.element(vals, lbls[ismiss])] <- NA
}
vals <- na.omit(vals)
# this is a test if a variable truly is numeric
# (not just categorical using numbers)
# if it has at least four(?) values different from the labels
printnum <- length(setdiff(vals, lbls)) > 4
if (!is.null(type)) {
# at least two non missing values are needed to calculate sd()
printnum <- printnum | (length(vals) > 2 & grepl("num", type))
}
if (printnum) { # numeric variable
cat(paste(
s3,
"<", ns, "sumStat type=\"min\">",
format(
min(vals, na.rm = TRUE),
scientific = FALSE
),
"</", ns, "sumStat>",
enter,
sep = ""
))
cat(paste(
s3,
"<", ns, "sumStat type=\"max\">",
format(
max(vals, na.rm = TRUE),
scientific = FALSE
),
"</", ns, "sumStat>",
enter,
sep = ""
))
cat(paste(
s3,
"<", ns, "sumStat type=\"mean\">",
format(
mean(vals, na.rm = TRUE),
scientific = FALSE
),
"</", ns, "sumStat>",
enter,
sep = ""
))
cat(paste(
s3,
"<", ns, "sumStat type=\"medn\">",
format(
median(vals, na.rm = TRUE),
scientific = FALSE
),
"</", ns, "sumStat>",
enter,
sep = ""
))
cat(paste(
s3,
"<", ns, "sumStat type=\"stdev\">",
format(
sd(vals, na.rm = TRUE),
scientific = FALSE
),
"</", ns, "sumStat>",
enter,
sep = ""
))
}
}
if (!is.null(lbls)) {
# what is the difference from data[[i]] ?
tbl <- table(data[[names(dataDscr)[i]]])
for (v in seq(length(lbls))) {
ismiss <- is.element(lbls[v], na_values)
if (length(na_range) > 0 & pN[i]) {
ismiss <- ismiss | (
lbls[v] >= na_range[1] & lbls[v] <= na_range[2]
)
}
cat(paste(
s3,
"<", ns, "catgry",
ifelse(ismiss, " missing=\"Y\"", ""), ">",
enter,
sep = ""
))
cat(paste(
s4,
"<", ns, "catValu>",
replaceChars(lbls[v]),
"</", ns, "catValu>",
enter,
sep = ""
))
cat(paste(
s4,
"<", ns, "labl", xmlang, ">",
replaceChars(names(lbls)[v]),
"</", ns, "labl>",
enter,
sep = ""
))
if (!is.null(data)) {
freq <- tbl[match(lbls[v], names(tbl))]
cat(paste(
s4,
"<", ns, "catStat type=\"freq\">",
ifelse(
is.na(freq),
0,
format(freq, scientific = FALSE)
),
"</", ns, "catStat>",
enter,
sep = ""
))
}
cat(paste(s3, "</", ns, "catgry>", enter, sep = ""))
}
}
if (any(grepl("type", names(dataDscr[[i]])))) {
varFormat <- dataDscr[[i]]$varFormat[1] # SPSS
cat(paste(
s3,
"<", ns, "varFormat type=\"",
ifelse(
grepl("char", dataDscr[[i]]$type),
"character",
"numeric"
),
"\" schema=\"other\" formatname=\"",
substr(varFormat, 1, 1),
"\">",
varFormat,
"</", ns, "varFormat>",
enter,
sep = ""
))
}
if (any(grepl("txt", names(dataDscr[[i]])))) {
cat(paste(s3, "<", ns, "txt>", enter, sep = ""))
cat(paste(
s0,
"<![CDATA[", dataDscr[[i]]$txt, "]]>",
enter,
sep = ""
))
cat(paste(s3, "</", ns, "txt>", enter, sep = ""))
}
cat(paste(s2, "</", ns, "var>", enter, sep = ""))
}
cat(paste(s1, "</", ns, "dataDscr>", enter, sep = ""))
cat(paste(
s1,
"<", ns, "otherMat level=\"", level, "\"></", ns, "otherMat>",
enter,
sep = ""
))
cat(paste(s0, "</", ns, "codeBook>", enter, sep = ""))
}
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