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Work with 'bibentryExtra' objects

bibentryExtra.Rd

Objects from class "bibentryExtra" represent a collection of bibliographic references. This page documents functions to create such objects or convert other compatible objects to "bibentryExtra", as well as methods for subsetting and replacing parts of them.

Usage

bibentryExtra(bibtype = NULL, ...)

as.bibentryExtra(x, ...)

# S3 method for class 'bibentryExtra'
x[[i, j, drop = TRUE]]

# S3 method for class 'bibentryExtra'
x[[i]] <- value

# S3 method for class 'bibentryExtra'
x[i, j, drop = TRUE]

# S3 method for class 'bibentryExtra'
x$name <- value

Arguments

bibtype

a character string specifying the type of the bib entry. Can also be a character vector to create an object containing more than one entry, see bibentry.

x

for bibentryExtra, an object to be converted; otherwise an object from class "bibentryExtra".

i

the bib entry to extract or assign to, a character string (the key), a singe integer number (position), or a list of length 2. For the extractor, "[[", i can also be of length more than 1 (character or integer) when j is missing completely. See section ‘Details’ for complete details.

j

field(s) to extract, a character vector or missing, see section ‘Details’.

name

field to extract.

drop

if TRUE, each entry in the returned list will contain the attributes (e.g., "bibtype" and "key").

value

value(s) to use for replacement, a list. For "[<-", an object inheriting from "bibentry" (so, including "bibentryExtra"), containing exactly one bib item. Alternatively, a character vector or a list, see section ‘Details’.

...

for bibentryExtra, any arguments that bibentry accepts.

Details

bibentryExtra creates a "bibentryExtra" object. It has the same arguments as bibentry, see its help page for full details. The main difference is that for bibentryExtra, the bibentry type, is not restricted to have values from the list of standard Bibtex types (which is the case for bibtype).

bibentryExtra sets the "names" attribute to the keys of the bib entries in it. However, further changes in the names and/or the keys can make them different. If you want to keep the names always consistent with the keys, set names(bee) <- NULL. This will cause names to dynamically create collect the keys when called.

as.bibentryExtra is a generic function for conversion of objects to class "bibentryExtra", most notably from class "bibentry".

Details on the subsetting methods are given below. The main think that needs to be pointed out is that the bracket operators take as first argument the values of one or more keys, while for the dollar operators the argument is the name of a field (e.g., journal). This is convenient but can cause confusion, since usually $ and [[ are (mostly) equivalent. This can be avoided by using argument j, since in the (i,j) pair i is always a key (or keys) and j the names of fields.

The subsetting methods aim to provide convenient access to components of "bibentryExtra" objects. In comparison to the corresponding methods for "bibenry" objects, the methods for "bibentryExtra" provide some additional features. Most notably, some of them include argument j, see the details below. If you want similar access for "bibenry" objects, just convert them to "bibentryExtra" using as.bibentryExtra.

It is convenient to think of the "bibentryExtra" as a ragged array with ‘rows’ (the bib entries) and ‘columns’ (the fields in the items). This is a peculiar ragged array, where each bib item (row) may have a different collection of fields.

Additional functionality for the subscript operators that admit argument j is provided for "bibentryExtra" objects. We will say that argument j is missing completely if it is missing and there is no placeholder for it in the call. For example be[i] and be[i, drop = FALSE] are examples when j is missing completely. On the other hand, be[i, ] and be[i, , drop = FALSE] are examples when j is missing, but not completely.

When j is completely missing, the subscript operations for "bibentryExtra" objects work exactly as for bibentry objects (they don't have methods that use j). Alternatively, rather than use both i and j, one can set i to be a list of length 2, whose two components stand for i and j, respectively. The latter syntax can be used also for the methods that don't have j as an argument (but do have i).

The methods for the dollar operator

"$" extracts the specified field. "bibentryExtra" inherits the "bibentry" method for "$". The result is a list with one component for each bib entry.

Note that the result is a list for several reasons. First, some fields may have more than one element. Second, some values are likely to be NULL. Third, some fields may be compound objects, e.g. ‘Author’, which is from class "person". However, if the the returned list has one element, the enlosing list is removed (similarly to matrices with one row).

The "bibentryExtra" method for subset-assigment, "$<-", assigns a new value to the specified field. In most cases, value should be a list of the same length as x. Otherwise, it will be wrapped in a list If it is not a list, the result may be unexpected. For example, a character vector will replace the specified field in all bib entries.

To change the values of the keys, specify field "key". Again, remember that you get a list of all keys, unless there is only one bib entry in x. So, value should be a list of the same length.

The double bracket extractor method

The method for "[[" accepts, unusually, two indices, i and j, reflecting the above interpretation.

i is typically a character string or a positive integer number identifying the bib item to extract, while j is a character vector specifying the required fields of that bib item. The result is a list. If drop is FALSE, then the attributes of this list are set to those of the bib item (e.g., bibtype and key).

If j is missing, all fields of the item are included in the result. However it depends on how j is missing. If it is missing as in x[[i, ]] or x[[i, , drop = FALSE]], the result is as above and includes all entries in bib item i.

Alternatively, i can be a list of length 2 and j omitted. This is equivalent to a call with i = i[[1]] and j = i[[2]].

If there is no redundant comma in the call, as in x[[i]] or x[[i, drop = FALSE]], then i must be a single index value (positive integer number or character string). The result is a "bibentryExtra" object. This case is compatible with the method for "bibentry" objects, which does not have argument j. Note though that for the "bibentry" method i can be of length more than 1.

The double bracket assignment method

The assignment version of "[[" does not have argument j, so the two-element list form for i is used when fields are needed, see above.

If value inherits from "bibentry" (in particular, it can be a "bibentryExtra" object), then i must be a single character string or a positive integer specifying the bibitem to replace with value. Notice that the new item may have a different key.

Otherwise, value should be a named list and i a list of length 2. In this case, i[[1]] should be a character string of a positive integer identifyng the bib item on which replacement will take place, while i[[2]] is a character vector specifying the fields to replace. As a special case, i[[2]] can be the character string "*", which specifies that all elements of value should be used.

Usually value has names and these are interpreted as names of fields. In this case, the fields specified by i[[2]] are replaced by the corresponding fields in value.

If value has no names and i[[2]] is not equal to "*" (see above), value must have the same length as i[[2]] and its names are set to i[[2]].

The single bracket extractor method

For "[", i is an index vector specifying which bib entries to extract. If j is missing completely, the bib entries are extracted and returned as a "bibentryExtra" object.

If j is used, it is a character vector specifying which fields to keep. For example, this could be a list of all standard bibtex fields. Only fields from this list are kept. Note that this may leave some bib entries invalid (i.e., missing compulsory fields).

Note that in any case the returned object has class "bibentryExtra".

Value

for as.bibentryExtra and bibentryExtra, a "bibentryExtra" object;

for "$", a list containing the requested fields with one list component for each key. If only one key was specified, the outer list is dropped;

for "[[", typically a list, but if argument x is missing completely, the result is a "bibentryExtra" object, as described in section ‘The double bracket extractor method’;

for "[", a "bibentryExtra" object;

for the assignment operators ("[[<-", "[<-" and "$<-"), the modified object x.

for names, always a character vector. If attribute names is NULL, the keys are put in a character vector and returned.

Author

Georgi N. Boshnakov

Note

This is somewhat experimental but incompatible changes are unlikely.

See also

the vignette,

readBib for importing bibtex files,

readBibentry for importing from R source files containing bibentry expressions,

charToBib for converting character vectors containing bibentry expressions.

Examples

## example bib from ?bibentry
bref <- c(
    bibentry(
        bibtype = "Manual",
        title = "boot: Bootstrap R (S-PLUS) Functions",
        author = c(
            person("Angelo", "Canty", role = "aut",
                   comment = "S original"),
            person(c("Brian", "D."), "Ripley", role = c("aut", "trl", "cre"),
                   comment = "R port, author of parallel support",
                   email = "ripley@stats.ox.ac.uk")
        ),
        year = "2012",
        note = "R package version 1.3-4",
        url = "https://CRAN.R-project.org/package=boot",
        key = "boot-package"
    ),
 
    bibentry(
        bibtype = "Book",
        title = "Bootstrap Methods and Their Applications",
        author = as.person("Anthony C. Davison [aut], David V. Hinkley [aut]"),
        year = "1997",
        publisher = "Cambridge University Press",
        address = "Cambridge",
        isbn = "0-521-57391-2",
        url = "http://statwww.epfl.ch/davison/BMA/",
        key = "boot-book"
    )
  )

brefExtra <- as.bibentryExtra(bref)

## error: j is present, so i must have length 1:
## brefExtra[[1:2, "title"]]

## the returned list doesn't have attributes:
                                  brefExtra[[1, c("title", "author")]] # drop = TRUE by default
#> $title
#> [1] "boot: Bootstrap R (S-PLUS) Functions"
#> 
#> $author
#> [1] "Angelo Canty [aut] (S original)"                                                             
#> [2] "Brian D. Ripley <ripley@stats.ox.ac.uk> [aut, trl, cre] (R port, author of parallel support)"
#> 

## now it does:
brefExtra[[1, "title", drop = FALSE]]
#> $title
#> [1] "boot: Bootstrap R (S-PLUS) Functions"
#> 
#> attr(,"bibtype")
#> [1] "Manual"
#> attr(,"key")
#> [1] "boot-package"
brefExtra[["boot-package", "title", drop = FALSE]]
#> $title
#> [1] "boot: Bootstrap R (S-PLUS) Functions"
#> 
#> attr(,"bibtype")
#> [1] "Manual"
#> attr(,"key")
#> [1] "boot-package"

brefExtra[["boot-book", ]]
#> $title
#> [1] "Bootstrap Methods and Their Applications"
#> 
#> $author
#> [1] "Anthony C. Davison [aut]" "David V. Hinkley [aut]"  
#> 
#> $year
#> [1] "1997"
#> 
#> $publisher
#> [1] "Cambridge University Press"
#> 
#> $address
#> [1] "Cambridge"
#> 
#> $isbn
#> [1] "0-521-57391-2"
#> 
#> $url
#> [1] "http://statwww.epfl.ch/davison/BMA/"
#> 
#> attr(,"bibtype")
#> [1] "Book"
#> attr(,"key")
#> [1] "boot-book"
brefExtra[["boot-book"]]
#> Davison AC, Hinkley DV (1997). _Bootstrap Methods and Their
#> Applications_. Cambridge University Press, Cambridge. ISBN
#> 0-521-57391-2, <http://statwww.epfl.ch/davison/BMA/>.


## assignment "[[<-"
b2 <- brefExtra
b2
#> Canty A, Ripley BD (2012). _boot: Bootstrap R (S-PLUS) Functions_. R
#> package version 1.3-4, <https://CRAN.R-project.org/package=boot>.
#> 
#> Davison AC, Hinkley DV (1997). _Bootstrap Methods and Their
#> Applications_. Cambridge University Press, Cambridge. ISBN
#> 0-521-57391-2, <http://statwww.epfl.ch/davison/BMA/>.

## use all elements of 'value'
b2[[list(1, "*")]] <- list(title = "New title", note = "a new note")

## replace title
b2[[list(1, "title")]] <- list(title = "New title A")
b2
#> Canty A, Ripley BD (2012). _New title A_. a new note,
#> <https://CRAN.R-project.org/package=boot>.
#> 
#> Davison AC, Hinkley DV (1997). _Bootstrap Methods and Their
#> Applications_. Cambridge University Press, Cambridge. ISBN
#> 0-521-57391-2, <http://statwww.epfl.ch/davison/BMA/>.

## no change,'year' is not in 'value'
b2[[list(1, "year")]] <- list(title = "New title A2") 
b2
#> Canty A, Ripley BD (2012). _New title A_. a new note,
#> <https://CRAN.R-project.org/package=boot>.
#> 
#> Davison AC, Hinkley DV (1997). _Bootstrap Methods and Their
#> Applications_. Cambridge University Press, Cambridge. ISBN
#> 0-521-57391-2, <http://statwww.epfl.ch/davison/BMA/>.

## remove 'year'
b2[[list(1, "year")]] <- list(title = "New title A", year = NULL) ## removes 'year'
b2
#> Canty A, Ripley BD (????). _New title A_. a new note,
#> <https://CRAN.R-project.org/package=boot>.
#> 
#> Davison AC, Hinkley DV (1997). _Bootstrap Methods and Their
#> Applications_. Cambridge University Press, Cambridge. ISBN
#> 0-521-57391-2, <http://statwww.epfl.ch/davison/BMA/>.

## a bibentry 'value'
b2[[2]] <- bibentry(bibtype = "Misc", title = "Dummy title",
                    author = "A A Dummy", organization = "none")
b2
#> Canty A, Ripley BD (????). _New title A_. a new note,
#> <https://CRAN.R-project.org/package=boot>.
#> 
#> Dummy AA (????). “Dummy title.”