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citation.R
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# File src/library/utils/R/citation.R
# Part of the R package, https://www.R-project.org
#
# Copyright (C) 1995-2023 The R Core Team
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# A copy of the GNU General Public License is available at
# https://www.R-project.org/Licenses/
## What a silly name ...
.is_not_nonempty_text <-
function(x)
is.null(x) || anyNA(x) || all(grepl("^[[:space:]]*$", x))
person <-
function(given = NULL, family = NULL, middle = NULL,
email = NULL, role = NULL, comment = NULL,
first = NULL, last = NULL)
{
## Arrange all arguments in lists of equal length.
args <- list(given = given, family = family, middle = middle,
email = email, role = role, comment = comment,
first = first, last = last)
if(all(vapply(args, is.null, NA)))
return(.person())
args <- lapply(args, .listify)
args_length <- lengths(args)
if(!all(args_length_ok <- args_length %in% c(1L, max(args_length))))
warning(gettextf("Not all arguments are of the same length, the following need to be recycled: %s",
paste(names(args)[!args_length_ok],
collapse = ", ")),
domain = NA)
args <- lapply(args, function(x) rep_len(x, max(args_length)))
## <COMMENT Z>
## We could do this more elegantly, but let's just go through the
## list processing person by person. I'm just recycling the old
## person() code for this.
## </COMMENT>
person1 <-
function(given = NULL, family = NULL, middle = NULL,
email = NULL, role = NULL, comment = NULL,
first = NULL, last = NULL)
{
if(!.is_not_nonempty_text(first)) {
if(!.is_not_nonempty_text(given))
stop(gettextf("Use either %s or %s/%s but not both.",
sQuote("given"),
sQuote("first"), sQuote("middle")),
domain = NA)
warning(gettextf("It is recommended to use %s instead of %s.",
sQuote("given"), sQuote("first")),
domain = NA)
given <- first
}
if(!.is_not_nonempty_text(middle)) {
warning(gettextf("It is recommended to use %s instead of %s.",
sQuote("given"), sQuote("middle")),
domain = NA)
given <- c(given, unlist(strsplit(middle, "[[:space:]]+")))
}
if(!.is_not_nonempty_text(last)) {
if(!.is_not_nonempty_text(family))
stop(gettextf("Use either %s or %s but not both.",
sQuote("family"), sQuote("last")),
domain = NA)
warning(gettextf("It is recommended to use %s instead of %s.",
sQuote("family"), sQuote("last")),
domain = NA)
family <- last
}
## Canonicalize: set all empty arguments to NULL, and remove
## leading/trailing whitespace otherwise (which in turn coerces
## to character).
## In principle, all non-NULL arguments whould be character:
## maybe this should be checked for?
.canonicalize <- function(s)
if(.is_not_nonempty_text(s)) NULL else trimws(s)
given <- .canonicalize(given)
family <- .canonicalize(family)
email <- .canonicalize(email)
if(.is_not_nonempty_text(role) && !is.null(role))
warning(sprintf(ngettext(length(role),
"Invalid role specification: %s.",
"Invalid role specifications: %s."),
paste(sQuote(role), collapse = ", ")),
domain = NA)
role <- .canonicalize(role)
comment <- .canonicalize(comment)
## <FIXME>
## Use something along the lines of
## tools:::.valid_maintainer_field_regexp
## to validate given email addresses.
## </FIXME>
if(length(role))
role <- .canonicalize_person_role(role)
if(length(comment)) {
## Be nice and recognize ORCID identifiers given as URLs
## but perhaps without an ORCID name.
ind <- grepl(sprintf("^https?://orcid.org/%s$",
tools:::.ORCID_iD_regexp),
comment)
if(any(ind)) {
if(is.null(names(comment)))
names(comment) <- ifelse(ind, "ORCID", "")
else
names(comment)[ind] <- "ORCID"
}
}
rval <- list(given = given, family = family, role = role,
email = email, comment = comment)
## Canonicalize 0-length character arguments to NULL.
if(any(ind <- (lengths(rval) == 0L)))
rval[ind] <- vector("list", length = sum(ind))
## Give nothing if there is nothing.
if(all(vapply(rval, is.null, NA)))
NULL
else
rval
} ## end{ person1 }
force(person1)# {codetools}
rval <-
lapply(seq_along(args$given),
function(i)
with(args,
person1(given = given[[i]], family = family[[i]],
middle = middle[[i]], email = email[[i]],
role = role[[i]], comment = comment[[i]],
first = first[[i]], last = last[[i]])))
## <COMMENT Z>
## Should we check that for each person there is at least one
## non-NULL entry?
## </COMMENT>
## Yes!
.person(rval[!vapply(rval, is.null, NA)])
}
.person <-
function(x = list())
{
class(x) <- "person"
x
}
.canonicalize_person_role <-
function(role)
{
## Be nice. Given roles must either exactly match the role code,
## or be uniquely pmatchable modulo case against the role terms.
pos <- which(is.na(match(role, MARC_relator_db$code)))
if(length(pos)) {
ind <- pmatch(tolower(role[pos]),
tolower(MARC_relator_db$name),
0L)
role[pos[ind > 0L]] <- MARC_relator_db$code[ind]
if(any(ind <- (ind == 0L))) {
warning(sprintf(ngettext(length(pos[ind]),
"Invalid role specification: %s.",
"Invalid role specifications: %s."),
paste(sQuote(role[pos[ind]]), collapse = ", ")),
domain = NA)
role <- role[-pos[ind]]
}
}
role
}
`[[.person` <-
`[.person` <-
function(x, i)
{
rval <- unclass(x)[i]
class(rval) <- class(x)
return(rval)
}
print.person <-
function(x, ...)
{
if(length(x)) print(format(x, ...)) else cat("person()\n")
invisible(x)
}
`$.person` <-
function(x, name)
{
## <COMMENT Z>
## extract internal list elements, return list if length > 1, vector
## otherwise (to mirror the behaviur of the input format for
## person())
## </COMMENT>
name <- match.arg(name,
c("given", "family", "role", "email", "comment",
"first", "last", "middle")) # for now ...
## <COMMENT Z>
## Let's be nice and support first/middle/last for now.
## </COMMENT>
if(name %in% c("first", "last", "middle")) {
message(gettextf("It is recommended to use %s/%s instead of %s/%s/%s.",
sQuote("given"), sQuote("family"),
sQuote("first"), sQuote("middle"), sQuote("last")),
domain = NA)
oname <- name
name <- switch(name,
"first" = "given",
"middle" = "given",
"last" = "family"
)
} else {
oname <- name
}
rval <- lapply(unclass(x), function(p) p[[name]])
if(oname == "first") rval <- lapply(rval, head, 1L)
if(oname == "middle") {
rval <- lapply(rval, tail, -1L)
if(any(ind <- (lengths(rval) == 0L)))
rval[ind] <- vector("list", length = sum(ind))
}
if(length(rval) == 1L) rval <- rval[[1L]]
rval
}
`$<-.person` <-
function(x, name, value)
{
name <- match.arg(name, c("given", "family", "role", "email", "comment"))
x <- .listify(unclass(x))
value <- rep_len(value, length(x))
if(name == "role")
value <- lapply(value, .canonicalize_person_role)
for(i in seq_along(x)) {
x[[i]][[name]] <- if(.is_not_nonempty_text(value[[i]]))
NULL
else as.character(value[[i]])
}
class(x) <- "person"
x
}
c.person <-
function(..., recursive = FALSE)
{
args <- list(...)
if(!all(vapply(args, inherits, NA, "person")))
warning(gettextf("method is only applicable to %s objects",
sQuote("person")),
domain = NA)
args <- lapply(args, unclass)
rval <- do.call(c, args)
class(rval) <- "person"
rval
}
as.person <-
function(x)
UseMethod("as.person")
as.person.default <-
function(x)
{
if(inherits(x, "person")) return(x)
x <- trimws(as.character(x))
if(!length(x)) return(person())
## Need to split the strings into individual person components.
## We used to split at ',' and 'and', but of course these could be
## contained in roles or comments as well.
## Hence, try the following.
## A. Replace all comment, role and email substrings by all-z
## substrings of the same length.
## B. Tokenize the strings according to the split regexp matches in
## the corresponding z-ified strings.
## C. Extract the persons from the thus obtained tokens.
## Create strings consisting of a given character c with given
## numbers n of characters.
strings <- function(n, c = "z") {
vapply(Map(rep.int, rep.int(c, length(n)), n,
USE.NAMES = FALSE),
paste, "", collapse = "")
}
## Replace matches of pattern in x by all-z substrings of the same
## length.
zify <- function(pattern, x) {
if(!length(x)) return(character())
m <- gregexpr(pattern, x)
regmatches(x, m) <-
Map(strings, lapply(regmatches(x, m), nchar))
x
}
## Step A.
y <- zify("\\([^)]*\\)", x)
y <- zify("\\[[^]]*\\]", y)
y <- zify("<[^>]*>", y)
## Step B.
pattern <- "[[:space:]]?(,|,?[[:space:]]and)[[:space:]]+"
x <- do.call(c, regmatches(x, gregexpr(pattern, y), invert = TRUE))
x <- x[!vapply(x, .is_not_nonempty_text, NA)]
## don't expect Jr. to be a person
jr <- which(!is.na(match(x, c("Jr", "Jr.", "jr", "jr."))))
if(length(jr)) {
jr <- jr[jr > 1L]
x[jr - 1L] <- paste(x[jr - 1L], x[jr], sep = ", ")
x <- x[-jr]
}
if(!length(x)) return(person())
## Step C.
as_person1 <- function(x) {
comment <- if(grepl("\\(.*\\)", x))
sub(".*\\(([^)]*)\\).*", "\\1", x)
else NULL
x <- sub("[[:space:]]*\\([^)]*\\)", "", x)
email <- if(grepl("<.*>", x))
unlist(strsplit(gsub("[[:space:]]*", "",
sub(".*<([^>]*)>.*", "\\1", x)),
",", fixed = TRUE))
else NULL
x <- sub("[[:space:]]*<[^>]*>", "", x)
role <- if(grepl("\\[.*\\]", x))
unlist(strsplit(gsub("[[:space:]]*", "",
sub(".*\\[([^]]*)\\].*", "\\1", x)),
",", fixed = TRUE))
else NULL
x <- sub("[[:space:]]*\\[[^)]*\\]", "", x)
x <- unlist(strsplit(x, "[[:space:]]+"))
## try to correctly guess von/van/de, Jr., etc.
jr <- c("Jr", "Jr.")
von <- c("De", "Den", "Der", "La", "Le", "Ten", "Van", "Von")
family <- x[length(x)]
given <- x[-length(x)]
if(length(family) &&
!is.na(match(family, c(jr, tolower(jr))))) {
family <- paste(given[length(given)], family)
given <- given[-length(given)]
}
if((ng <- length(given)) &&
!is.na(match(gng <- given[ng], c(von, tolower(von))))) {
family <- paste(gng, family)
given <- given[-ng]
}
if((ng <- length(given)) &&
!is.na(match(gng <- given[ng], c(von, tolower(von))))) {
family <- paste(gng, family)
given <- given[-ng]
}
z <- person(given = given, family = family,
email = email, role = role, comment = comment)
return(z)
}
as.list(do.call(c, lapply(x, as_person1)))
}
personList <-
function(...)
{
z <- list(...)
if(!all(vapply(z, inherits, NA, "person")))
stop(gettextf("all arguments must be of class %s",
dQuote("person")),
domain = NA)
do.call(c, z)
}
as.personList <-
function(x)
UseMethod("as.personList")
as.personList.person <-
function(x)
x
as.personList.default <-
function(x)
{
if(inherits(x, "person")) return(x)
do.call(c, lapply(x, as.person))
}
format.person <-
function(x,
include = c("given", "family", "email", "role", "comment"),
braces =
list(given = "", family = "", email = c("<", ">"),
role = c("[", "]"), comment = c("(", ")")),
collapse =
list(given = " ", family = " ", email = ", ",
role = ", ", comment = ", "),
...,
style = c("text", "R")
)
{
if(!length(x)) return(character())
style <- match.arg(style)
if(style == "R") return(.format_person_as_R_code(x))
args <- c("given", "family", "email", "role", "comment")
include <- vapply(include, match.arg, "", args)
## process defaults
braces <- braces[args]
collapse <- collapse[args]
names(braces) <- names(collapse) <- args
if(is.null(braces$given)) braces$given <- ""
if(is.null(braces$family)) braces$family <- ""
if(is.null(braces$email)) braces$email <- c("<", ">")
if(is.null(braces$role)) braces$role <- c("[", "]")
if(is.null(braces$comment)) braces$comment <- c("(", ")")
braces <- lapply(braces, rep_len, 2L)
if(is.null(collapse$given)) collapse$given <- " "
if(is.null(collapse$family)) collapse$family <- " "
if(is.null(collapse$email)) collapse$email <- ", "
if(is.null(collapse$role)) collapse$role <- ", "
if(is.null(collapse$comment)) collapse$comment <- ", "
collapse <- lapply(collapse, rep_len, 1L)
## extract selected elements
x <- lapply(unclass(x), `[`, include)
braces <- braces[include]
collapse <- collapse[include]
if(any(include == "comment"))
x <- lapply(x,
function(e) {
e$comment <-
.expand_ORCID_identifier(e$comment)
e
})
paste_collapse <- function(x, collapse) {
if(is.na(collapse) || isFALSE(collapse)) {
x[1L]
} else {
paste(x, collapse = collapse)
}
}
## format 1 person
format_person1 <- function(p) {
rval <- lapply(seq_along(p),
function(i) {
if(is.null(p[[i]]))
NULL
else
paste0(braces[[i]][1L],
paste_collapse(p[[i]],
collapse[[i]]),
braces[[i]][2L])
})
paste(do.call(c, rval), collapse = " ")
}
vapply(x, format_person1, "")
}
as.character.person <-
function(x, ...)
format(x, ...)
toBibtex.person <-
function(object, escape = FALSE, ...)
{
object <- vapply(object, function(p) {
br <- if(is.null(p$family)) c("{", "}") else c("", "")
s <- format(p, include = c("family", "given"),
braces = list(given = br, family = c("", ",")))
if(isTRUE(escape) &&
(Encoding(s <- enc2utf8(s)) == "UTF-8"))
tools::encoded_text_to_latex(s, "UTF-8")
else s
}, "")
paste(object[nzchar(object)], collapse = " and ")
}
.canonicalize_ORCID_identifier <-
function(x)
{
paste0("https://orcid.org/",
sub(tools:::.ORCID_iD_variants_regexp, "\\3", x))
}
.expand_ORCID_identifier <-
function(x)
{
if(any(ind <- ((names(x) == "ORCID") &
grepl(tools:::.ORCID_iD_variants_regexp, x))))
x[ind] <- paste0("<",
.canonicalize_ORCID_identifier(x[ind]),
">")
x
}
as.data.frame.person <- as.data.frame.vector
######################################################################
bibentry <-
function(bibtype, textVersion = NULL, header = NULL, footer = NULL, key = NULL,
...,
other = list(), mheader = NULL, mfooter = NULL)
{
BibTeX_names <- names(tools:::BibTeX_entry_field_db)
args <- c(list(...), other)
if(!length(args))
return(.bibentry(list(), mheader, mfooter))
if(any(vapply(names(args), .is_not_nonempty_text, NA)))
stop("all fields have to be named")
## arrange all arguments in lists of equal length
args <- c(list(bibtype = bibtype, textVersion = textVersion,
header = header, footer = footer, key = key), list(...))
args <- lapply(args, .listify)
other <- lapply(other, .listify)
max_length <- max(lengths(c(args, other)))
args_length <- lengths(args)
if(!all(args_length_ok <- args_length %in% c(1L, max_length)))
warning(gettextf("Not all arguments are of the same length, the following need to be recycled: %s",
paste(names(args)[!args_length_ok],
collapse = ", ")),
domain = NA)
args <- lapply(args, function(x) rep_len(x, max_length))
other_length <- lengths(other)
if(!all(other_length_ok <- other_length %in% c(1L, max_length)))
warning(gettextf("Not all arguments are of the same length, the following need to be recycled: %s",
paste(names(other)[!other_length_ok],
collapse = ", ")),
domain = NA)
other <- lapply(other, function(x) rep_len(x, max_length))
bibentry1 <-
function(bibtype, textVersion, header = NULL, footer = NULL, key = NULL, ..., other = list())
{
## process bibtype
bibtype <- as.character(bibtype)
stopifnot(length(bibtype) == 1L)
pos <- match(tolower(bibtype), tolower(BibTeX_names))
if(is.na(pos))
stop(gettextf("%s has to be one of %s",
sQuote("bibtype"),
paste(BibTeX_names, collapse = ", ")),
domain = NA)
bibtype <- BibTeX_names[pos]
## process fields
rval <- c(list(...), other)
rval <- rval[!vapply(rval, .is_not_nonempty_text, NA)]
fields <- tolower(names(rval))
names(rval) <- fields
attr(rval, "bibtype") <- bibtype
## check required fields
.bibentry_check_bibentry1(rval)
## canonicalize
pos <- fields %in% c("author", "editor")
if(any(pos)) {
for(i in which(pos)) rval[[i]] <- as.person(rval[[i]])
}
if(any(!pos)) {
for(i in which(!pos)) rval[[i]] <- as.character(rval[[i]])
}
## set attributes
attr(rval, "key") <-
if(is.null(key)) NULL else as.character(key)
if(!is.null(textVersion))
attr(rval, "textVersion") <- as.character(textVersion)
if(!.is_not_nonempty_text(header))
attr(rval, "header") <- paste(header, collapse = "\n")
if(!.is_not_nonempty_text(footer))
attr(rval, "footer") <- paste(footer, collapse = "\n")
return(rval)
}
rval <- lapply(seq_along(args$bibtype),
function(i)
do.call(bibentry1,
c(lapply(args, `[[`, i),
list(other = lapply(other, `[[`, i)))))
.bibentry(rval, mheader, mfooter)
}
.bibentry <-
function(x = list(), mheader = NULL, mfooter = NULL)
{
class(x) <- "bibentry"
## add main header/footer for overall bibentry vector
if(!.is_not_nonempty_text(mheader))
attr(x, "mheader") <- paste(mheader, collapse = "\n")
if(!.is_not_nonempty_text(mfooter))
attr(x, "mfooter") <- paste(mfooter, collapse = "\n")
x
}
.bibentry_check_bibentry1 <-
function(x, force = FALSE)
{
fields <- names(x)
if(!force && !.is_not_nonempty_text(x$crossref)) return(NULL)
bibtype <- attr(x, "bibtype")
rfields <-
strsplit(tools:::BibTeX_entry_field_db[[bibtype]], "|",
fixed = TRUE)
if(length(rfields) > 0L) {
ok <- vapply(rfields, function(f) any(f %in% fields), NA)
if(any(!ok))
stop(sprintf(ngettext(sum(!ok),
"A bibentry of bibtype %s has to specify the field: %s",
"A bibentry of bibtype %s has to specify the fields: %s"),
sQuote(bibtype), paste(rfields[!ok], collapse = ", ")),
domain = NA)
}
}
bibentry_attribute_names <-
c("bibtype", "textVersion", "header", "footer", "key")
bibentry_list_attribute_names <-
c("mheader", "mfooter")
.bibentry_get_key <-
function(x)
{
if(!length(x)) return(character())
keys <- lapply(unclass(x), attr, "key")
keys[!lengths(keys)] <- ""
unlist(keys)
}
`[[.bibentry` <-
`[.bibentry` <-
function(x, i, drop = TRUE)
{
if(!length(x)) return(x)
cl <- class(x)
class(x) <- NULL
## For character subscripting, use keys if there are no names.
## Note that creating bibentries does not add the keys as names:
## assuming that both can independently be set, we would need to
## track whether names were auto-generated or not.
## (We could consider providing a names() getter which returns given
## names or keys as used for character subscripting, though).
if(is.character(i) && is.null(names(x)))
names(x) <- .bibentry_get_key(x)
y <- x[i]
if(!all(ok <- lengths(y) > 0L)) {
warning("subscript out of bounds")
y <- y[ok]
}
if(!drop)
attributes(y) <- attributes(x)[bibentry_list_attribute_names]
class(y) <- cl
y
}
bibentry_format_styles <-
c("text", "Bibtex", "citation", "html", "latex", "textVersion", "R")
.bibentry_match_format_style <-
function(style)
{
ind <- pmatch(tolower(style), tolower(bibentry_format_styles),
nomatch = 0L)
if(all(ind == 0L))
stop(gettextf("%s should be one of %s",
sQuote("style"),
paste(dQuote(bibentry_format_styles),
collapse = ", ")),
domain = NA)
bibentry_format_styles[ind]
}
format.bibentry <-
function(x, style = "text", .bibstyle = NULL,
bibtex = length(x) <= 1, # *NOT* using option("citation.bibtex.max") here
citMsg = missing(bibtex),
sort = FALSE,
macros = NULL,
...)
{
if(!length(x)) return(character())
style <- .bibentry_match_format_style(style)
if(sort) x <- sort(x, .bibstyle = .bibstyle)
x$.index <- as.list(seq_along(x))
format_via_Rd <- function(f) {
out <- file()
saveopt <- tools::Rd2txt_options(width = getOption("width"))
on.exit({tools::Rd2txt_options(saveopt); close(out)})
permissive <-
Sys.getenv("_R_UTILS_FORMAT_BIBENTRY_VIA_RD_PERMISSIVE_",
"TRUE")
permissive <- tools:::config_val_to_logical(permissive)
if(is.null(macros))
macros <- tools:::initialRdMacros()
else if(is.character(macros))
macros <- tools::loadRdMacros(macros,
tools:::initialRdMacros())
vapply(.bibentry_expand_crossrefs(x),
function(y) {
txt <- tools::toRd(y, style = .bibstyle)
## <FIXME>
## Ensure a closing </p> via a final empty line for
## now (PR #15692).
if(style == "html") txt <- paste(txt, "\n")
## </FIXME>
con <- textConnection(txt)
on.exit(close(con))
rd <- tools::parse_Rd(con,
fragment = TRUE,
permissive = permissive,
macros = macros)
rd <- tools:::processRdSexprs(rd,
"install",
macros = attr(rd, "macros"))
f(rd, fragment = TRUE, out = out,
outputEncoding = "UTF-8", ...)
paste(readLines(out, encoding = "UTF-8"),
collapse = "\n")
},
"")
}
format_as_citation <- function(x, msg) { # also (.., bibtex)
m <- attr(x, "mheader")
if(is.null(m) &&
is.null(unlist(x$header)) &&
!is.null(p <- attr(x, "package")))
m <- gettextf("To cite package %s in publications use:",
sQuote(p))
i <- !is.null(m)
c(paste(strwrap(m), collapse = "\n"),
unlist(lapply(x, function(y) {
h <- y$header
j <- !is.null(h)
s <- y$textVersion
if(is.null(s))
s <- format(y)
paste(c(if(j)
c(strwrap(h), ""),
if(i || j)
strwrap(s, prefix = " ") else strwrap(s),
if(bibtex) {
c(gettext("\nA BibTeX entry for LaTeX users is\n"),
paste0(" ", unclass(toBibtex(y))))
},
if(!is.null(y$footer))
c("", strwrap(y$footer))),
collapse = "\n")
})),
paste(strwrap(c(attr(x, "mfooter"),
if(!bibtex && msg)
{
prt <- sys.nframe() > 4L && sys.call(-4L)[[1L]] == quote(print.bibentry)
c(if(!is.null(attr(x, "mfooter"))) "",
paste0(
"To see these entries in BibTeX format, use '", if(prt) "print" else "format",
"(<citation>, bibtex=TRUE)', ",
if(prt)"'toBibtex(.)', or set 'options(citation.bibtex.max=999)'." else "or 'toBibtex(.)'."))
}
)), collapse = "\n")
)
}
out <-
switch(style,
"text" = format_via_Rd(tools::Rd2txt),
"html" = format_via_Rd(tools::Rd2HTML),
"latex" = format_via_Rd(tools::Rd2latex),
"Bibtex" = {
unlist(lapply(x,
function(y)
paste(toBibtex(y), collapse = "\n")))
},
"textVersion" = {
out <- lapply(unclass(x), attr, "textVersion")
out[!lengths(out)] <- ""
unlist(out)
},
"citation" = format_as_citation(.bibentry(x), msg = citMsg),
"R" = .format_bibentry_as_R_code(x, ...)
)
as.character(out)
}
.bibentry_expand_crossrefs <-
function(x, more = list())
{
y <- if(length(more))
do.call(c, c(list(x), more))
else
x
x <- unclass(x)
y <- unclass(y)
crossrefs <- lapply(x, `[[`, "crossref")
pc <- which(lengths(crossrefs) > 0L)
if(length(pc)) {
pk <- match(unlist(crossrefs[pc]), .bibentry_get_key(y))
## If an entry has a crossref we cannot resolve it might still
## be complete: we could warn about the bad crossref ...
ok <- !is.na(pk)
## Merge entries: note that InCollection and InProceedings need
## to remap title to booktitle as needed.
x[pc[ok]] <-
Map(function(u, v) {
add <- setdiff(names(v), names(u))
u[add] <- v[add]
if(!is.na(match(tolower(attr(u, "bibtype")),
c("incollection", "inproceedings"))) &&
is.null(u$booktitle))
u$booktitle <- v$title
u
},
x[pc[ok]],
y[pk[ok]])
## Now check entries with crossrefs for completeness.
## Ignore bad entries with a warning.
status <- lapply(x[pc],
function(e)
tryCatch(.bibentry_check_bibentry1(e, TRUE),
error = identity))
bad <- which(vapply(status, inherits, NA, "error"))
if(length(bad)) {
for(b in bad) {
warning(gettextf("Dropping invalid entry %d:\n%s",
pc[b],
conditionMessage(status[[b]])))
}
x[pc[bad]] <- NULL
}
}
.bibentry(x)
}
print.bibentry <-
function(x, style = "text", .bibstyle = NULL,
bibtex = length(x) <= getOption("citation.bibtex.max", 1L), # using option() here
...)
{
style <- .bibentry_match_format_style(style)
n <- length(x)
if(!n) {
cat(switch((cl <- class(x)[[1L]]),
"bibentry" = "bibentry()",
sprintf("<0-length %s>", cl)), sep="", "\n")
} else if(style == "R") {
writeLines(format(x, "R", bibtex=bibtex, collapse = TRUE, ...))
} else {
y <- format(x, style, .bibstyle, bibtex=bibtex, citMsg = missing(bibtex), ...)
if(style == "citation") {
## Printing in citation style does extra headers/footers
## (which however may be empty), so it is handled
## differently.
## Old-style with extra empty lines before/after outer
## footer/header:
## n <- length(y)
## if(nzchar(header <- y[1L]))
## header <- c("", header, "")
## if(nzchar(footer <- y[n]))
## footer <- c("", footer, "")
## writeLines(c(header,
## paste(y[-c(1L, n)], collapse = "\n\n"),
## footer))
## New-style without:
writeLines(paste(y[nzchar(y)], collapse = "\n\n"))
## Which could be used for all print styles ...?
} else {
writeLines(paste(y, collapse = "\n\n"))
}
}
invisible(x)
}
.format_call_RR <-
function(cname, cargs)
{
## Format call with ragged right argument list (one arg per line).
cargs <- as.list(cargs)
n <- length(cargs)
lens <- lengths(cargs)
sums <- cumsum(lens)
starters <- c(sprintf("%s(", cname),
rep.int(strrep(" ", nchar(cname) + 1L), sums[n] - 1L))
trailers <- c(rep.int("", sums[n] - 1L), ")")
trailers[sums[-n]] <- ","
sprintf("%s%s%s", starters, unlist(cargs), trailers)
}
.format_bibentry_as_R_code <-
function(x, collapse = FALSE)
{
if(!length(x)) return("bibentry()")
x$.index <- NULL
## There are two subleties for constructing R calls giving a given
## bibentry object.
## * There can be mheader and mfooter entries.
## If there are, we put them into the first bibentry.
## * There could be field names which clash with the names of the
## bibentry() formals: these would need to be put as a list into
## the 'other' formal.
## The following make it into the attributes of an entry.
anames <- bibentry_attribute_names
## The following make it into the attributes of the object.
manames <- c("mheader", "mfooter")
## Format a single element (person or string, at least for now).
f <- function(e) {
if(inherits(e, "person"))
.format_person_as_R_code(e)
else
deparse(e)
}
g <- function(u, v) {
prefix <- sprintf("%s = ", u)
n <- length(v)
if(n > 1L)
prefix <- c(prefix,
rep.int(strrep(" ", nchar(prefix)), n - 1L))
sprintf("%s%s", prefix, v)
}
s <- lapply(unclass(x),
function(e) {
a <- Filter(length, attributes(e)[anames])
e <- e[!vapply(e, is.null, NA)]
ind <- !is.na(match(names(e),
c(anames, manames, "other")))
if(any(ind)) {
other <- paste(names(e[ind]),
sapply(e[ind], f),
sep = " = ")
other <- Map(g,
names(e[ind]),
sapply(e[ind], f))
other <- .format_call_RR("list", other)
e <- e[!ind]
} else {
other <- NULL
}
c(Map(g, names(a), sapply(a, deparse)),
Map(g, names(e), sapply(e, f)),
if(length(other)) list(g("other", other)))
})
if(!is.null(mheader <- attr(x, "mheader")))