| Title: | Read Data from JSTOR/DfR |
|---|---|
| Description: | Functions and helpers to import metadata, ngrams and full-texts delivered by Data for Research by JSTOR. |
| Authors: | Thomas Klebel [aut, cre] |
| Maintainer: | Thomas Klebel <[email protected]> |
| License: | GPL-3 |
| Version: | 0.3.11 |
| Built: | 2024-08-16 05:46:29 UTC |
| Source: | https://github.com/ropensci/jstor |
This function adds a column with the total count of pages. It calls
jst_get_total_pages() which does the main work.
jst_add_total_pages(meta_data, quietly = FALSE)jst_add_total_pages(meta_data, quietly = FALSE)
meta_data |
Data which was processed via |
quietly |
Should warnings from converting page ranges be suppressed? |
A tibble, as provided with in meta_data, with an additional
column on total number of pages.
This function takes data from jst_get_article() and
applies helper functions for cleaning the data.
jst_augment(meta_data, quietly = FALSE)jst_augment(meta_data, quietly = FALSE)
meta_data |
Data which was processed via |
quietly |
Should warnings from converting page ranges be suppressed? |
Data from DfR is inherently messy. For many examples see
vignette("known-quirks", package = "jstor"). jst_augment() is a
convenience function that tries to deal with a few common tasks to
clean the data.
For journal articles, it calls jst_clean_page() to convert first and last
page, jst_unify_journal_id() and jst_add_total_pages().
A cleaned tibble.
jst_clean_page() jst_unify_journal_id() jst_add_total_pages()
jst_get_total_pages()
This function tries to convert character vectors into integers. This function should not be called on page ranges.
jst_clean_page(page)jst_clean_page(page)
page |
A character vector for pages. |
An integer vector, cleaned and converted from the input vector.
jst_clean_page("2") # anything that is not a digit gets removed jst_clean_page("A2-") # a weird format from the American Journal of Sociology is convered correctly jst_clean_page("AJSv104p126") # this is done by searching for "p", and if it is found, extracting the # content after "p".jst_clean_page("2") # anything that is not a digit gets removed jst_clean_page("A2-") # a weird format from the American Journal of Sociology is convered correctly jst_clean_page("AJSv104p126") # this is done by searching for "p", and if it is found, extracting the # content after "p".
jst_combine_outputs() helps you to manage the multitude of files you might
receive after running jst_import() or jst_import_zip() with more than
one batch.
jst_combine_outputs( path, write_to_file = TRUE, out_path = NULL, overwrite = FALSE, clean_up = FALSE, warn = TRUE )jst_combine_outputs( path, write_to_file = TRUE, out_path = NULL, overwrite = FALSE, clean_up = FALSE, warn = TRUE )
path |
A path to a directory, containing .csv-files from
|
write_to_file |
Should combined data be written to a file? |
out_path |
A directory where to write the combined files. If no
directory is supplied and |
overwrite |
Should files be overwritten? |
clean_up |
Do you want to remove the original batch files? Use with caution. |
warn |
Should warnings be raised, if the file type cannot be determined? |
Splitting the output of jst_import() or jst_import_zip() might be done
for multiple reasons, but in the end you possibly want to combine all outputs
into one file/data.frame. This function makes a few assumptions in order to
combine files:
Files with similar names (except for trailing dashes with numbers) belong together and will be combined into one file.
The names of the combined files can be determined from the original files.
If you want to combine foo-1.csv and foo-2.csv, the combined file will
be combined_foo.csv.
The directory only contains files which were imported via
jst_import() or jst_import_zip(). If the directory contains other
.csv files, you should supply a character vector with paths to only those
files, which you want to import.
Either writes to disk, or returns a list with all combined files.
# set up a temporary directory tmp <- tempdir() # find multiple files file_list <- rep(jst_example("article_with_references.xml"), 2) # convert and write to file jst_import(file_list, "article", out_path = tmp, .f = jst_get_article, n_batches = 2, show_progress = FALSE) # combine outputs jst_combine_outputs(tmp) list.files(tmp, "csv") ## Not run: # Trying to combine the files again raises an error. jst_combine_outputs(tmp) ## End(Not run) # this doesn't jst_combine_outputs(tmp, overwrite = TRUE) # we can remove the original files too jst_combine_outputs(tmp, overwrite = TRUE, clean_up = TRUE) list.files(tmp, "csv")# set up a temporary directory tmp <- tempdir() # find multiple files file_list <- rep(jst_example("article_with_references.xml"), 2) # convert and write to file jst_import(file_list, "article", out_path = tmp, .f = jst_get_article, n_batches = 2, show_progress = FALSE) # combine outputs jst_combine_outputs(tmp) list.files(tmp, "csv") ## Not run: # Trying to combine the files again raises an error. jst_combine_outputs(tmp) ## End(Not run) # this doesn't jst_combine_outputs(tmp, overwrite = TRUE) # we can remove the original files too jst_combine_outputs(tmp, overwrite = TRUE, clean_up = TRUE) list.files(tmp, "csv")
Define which parts of a zip file should be converted via which functions.
jst_define_import(...)jst_define_import(...)
... |
Named arguments with bare function names. |
The function accepts the following names: article, book, report, pamphlet, ngram1, ngram2, ngram3. The corresponding files from a .zip-archive will be imported via the supplied functions.
A specification of imports which is necessary for
jst_import_zip().
# articles will be imported via `jst_get_article()` and `jst_get_authors()` jst_define_import(article = c(jst_get_article, jst_get_authors)) # define a specification for importing article metadata and unigrams (ngram1) jst_define_import(article = jst_get_article, ngram1 = jst_get_ngram) # import all four types with one function each jst_define_import(article = jst_get_article, book = jst_get_book, report = jst_get_book, pamphlet = jst_get_article) # import all four types with multiple functions jst_define_import(article = c(jst_get_article, jst_get_authors, jst_get_references), book = c(jst_get_book, jst_get_chapters), report = jst_get_book, pamphlet = jst_get_article) # if you want to import chapters with authors, you can use an anonymous # function chapters_w_authors <- function(x) jst_get_chapters(x, authors = TRUE) jst_define_import(book = chapters_w_authors) ## Not run: # define imports imports <- jst_define_import(article = c(jst_get_article, jst_get_authors)) # convert the files to .csv jst_import_zip("my_archive.zip", out_file = "my_out_file", import_spec = imports) ## End(Not run)# articles will be imported via `jst_get_article()` and `jst_get_authors()` jst_define_import(article = c(jst_get_article, jst_get_authors)) # define a specification for importing article metadata and unigrams (ngram1) jst_define_import(article = jst_get_article, ngram1 = jst_get_ngram) # import all four types with one function each jst_define_import(article = jst_get_article, book = jst_get_book, report = jst_get_book, pamphlet = jst_get_article) # import all four types with multiple functions jst_define_import(article = c(jst_get_article, jst_get_authors, jst_get_references), book = c(jst_get_book, jst_get_chapters), report = jst_get_book, pamphlet = jst_get_article) # if you want to import chapters with authors, you can use an anonymous # function chapters_w_authors <- function(x) jst_get_chapters(x, authors = TRUE) jst_define_import(book = chapters_w_authors) ## Not run: # define imports imports <- jst_define_import(article = c(jst_get_article, jst_get_authors)) # convert the files to .csv jst_import_zip("my_archive.zip", out_file = "my_out_file", import_spec = imports) ## End(Not run)
jstor includes several sample files for demonstration purposes. This helper makes them easy to access.
jst_example(path = NULL)jst_example(path = NULL)
path |
Name of the example file. If |
The code for this function was adapted from the package readr.
Either a character vector with the names of example files (if
jst_example() is called without supplying an argument), or a character
vector indicating the path to the example file.
jst_example() jst_example("article_with_references.xml")jst_example() jst_example("article_with_references.xml")
jst_get_article() extracts meta-data from JSTOR-XML files for journal
articles.
jst_get_article(file_path)jst_get_article(file_path)
file_path |
A |
A tibble containing the extracted meta-data with the following
columns:
file_name (chr): The file_name of the original .xml-file. Can be used for joining with other parts (authors, references, footnotes, full-texts).
journal_doi (chr): A registered identifier for the journal.
journal_jcode (chr): A identifier for the journal like "amerjsoci" for the "American Journal of Sociology".
journal_pub_id (chr): Similar to journal_jcode. Most of the time either one is present.
journal_title (chr): The title of the journal.
article_doi (chr): A registered unique identifier for the article.
article_jcode (chr): A unique identifier for the article (not a DOI).
article_pub_id (chr): Infrequent, either part of the DOI or the article_jcode.
article_type (chr): The type of article (research-article, book-review, etc.).
article_title (chr): The title of the article.
volume (chr): The volume the article was published in.
issue (chr): The issue the article was published in.
language (chr): The language of the article.
pub_day (chr): Publication day, if specified.
pub_month (chr): Publication month, if specified.
pub_year (int): Year of publication.
first_page (int): Page number for the first page of the article.
last_page (int): Page number for the last page of the article.
page_range (chr): The range of pages for the article.
A note about publication dates: always the first entry is being extracted, which should correspond to the oldest date, in case there is more than one date.
jst_get_article(jst_example("article_with_references.xml"))jst_get_article(jst_example("article_with_references.xml"))
jst_get_authors() extracts information about authors from JSTOR-XML files.
jst_get_authors(file_path)jst_get_authors(file_path)
file_path |
A |
The function returns a tibble with the following six columns:
prefix: in case there was a prefix to the name, like "Dr.".
given_name: The author's given name, like "Albert".
surname: The author's surname like "Einstein".
string_name: In some cases data the name is not available in separate
fields, but just as a complete string: "Albert Einstein".
suffix: a suffix to the name, like "Jr.".
author_number: The authors are enumerated in the order they appear in the data.
A tibble containing the extracted authors. All empty fields are
NA_character.
jst_get_authors(jst_example("article_with_references.xml"))jst_get_authors(jst_example("article_with_references.xml"))
jst_get_book() extracts meta-data from JSTOR-XML files for book chapters.
jst_get_book(file_path)jst_get_book(file_path)
file_path |
A |
A tibble containing the extracted meta-data with the following
columns:
file_name (chr): The filename of the original .xml-file. Can be used for joining with other data for the same file.
discipline (chr): The discipline from the discipline names used on JSTOR.
book_id (chr): The book id of type "jstor", which is not a registered DOI.
book_title (chr): The title of the book.
book_subtitle (chr): The subtitle of the book.
pub_day (int): Publication day, if specified.
pub_month (int): Publication month, if specified.
pub_year (int): Year of publication.
isbn (chr): One or more entries for the book's ISBN. If two or more,
separated by "; ".
publisher_name (chr): The name of the publisher.
publisher_loc (chr): The location of the publisher.
n_pages (int): The number of pages.
language (chr): The language of the book.
A note about publication dates: always the first entry is being extracted, which should correspond to the oldest date, in case there is more than one date.
jst_get_book(jst_example("book.xml"))jst_get_book(jst_example("book.xml"))
jst_get_chapters() extracts meta-data from JSTOR-XML files for book
chapters.
jst_get_chapters(file_path, authors = FALSE)jst_get_chapters(file_path, authors = FALSE)
file_path |
The path to a |
authors |
Extracting the authors is an expensive operation which makes
the function ~3 times slower, depending on the number of chapters and
the number of authors. Defaults to |
Currently, jst_get_chapters() is quite a lot slower than most of the other
functions. It is roughly 10 times slower than jst_get_book, depending on
the number of chapters to extract.
A tibble containing the extracted meta-data with the following
columns:
book_id (chr): The book id of type "jstor", which is not a registered DOI.
file_name (chr): The filename of the original .xml-file. Can be used for joining with other data for the same file.
part_id (chr): The id of the part.
part_label (chr): A label for the part, if specified.
part_title (chr): The title of the part.
part_subtitle (chr): The subtitle of the part, if specified.
authors (list): A list-column with information on the authors. Can be
unnested with tidyr::unnest(). See the examples and jst_get_authors().
abstract (chr): The abstract to the part.
part_first_page (chr): The page where the part begins.
# extract parts without authors jst_get_chapters(jst_example("book.xml")) # import authors too parts <- jst_get_chapters(jst_example("book.xml"), authors = TRUE) parts tidyr::unnest(parts)# extract parts without authors jst_get_chapters(jst_example("book.xml")) # import authors too parts <- jst_get_chapters(jst_example("book.xml"), authors = TRUE) parts tidyr::unnest(parts)
This helper simply extracts the basename of a path and removes the extension,
e.g. foo/bar.txt is shortened to bar.
jst_get_file_name(file_path)jst_get_file_name(file_path)
file_path |
A path to a file |
A character vector, containing the basename of the file without an extension.
This function extracts the content of fn-group from journal-articles.
jst_get_footnotes(file_path)jst_get_footnotes(file_path)
file_path |
The path to the |
The fn-group usually contains footnotes corresponding to the article.
However, since footnotes are currently not fully supported by DfR,
there is no comprehensive documentation on the different variants. jstor
therefore extracts the content of fn-group exactly as it appears in the
data. Because of this, there might be other content present than footnotes.
In order to get all available information on citation data, you might need to
combine jst_get_footnotes() with jst_get_references().
A tibble containing the content from fn-group (usually the
footnotes). If there were no footnotes, NA_character is returned for the
column footnotes.
jst_get_footnotes(jst_example("article_with_footnotes.xml"))jst_get_footnotes(jst_example("article_with_footnotes.xml"))
This function imports the full_text contents of a JSTOR-article.
jst_get_full_text(filename)jst_get_full_text(filename)
filename |
The path to the file. |
A tibble, containing the file-path as id, the full content of
the file, and the encoding which was used to read it.
Download most recent or display cached version of data on journals.
jst_get_journal_overview(most_recent = FALSE, quiet = FALSE)jst_get_journal_overview(most_recent = FALSE, quiet = FALSE)
most_recent |
Should the most recent version be downloaded from DfR? (Currently disabled due to changes on the JSTOR-servers). |
quiet |
Should status messages about the download be printed? |
When analysing your sample of articles from DfR, it might be helpful to have
some context about the journals in your sample. This function provides a
tibble with various information like the full name of the journal, the
short version of the name (sometimes referred to as JCODE), dates on where
the first
and last (available) issues were published, etc.
The data on journals might change. Therefore this function provides two sources of data: a cached version which gets updated with every release, and the ability to pull the most recent version directly from DfR (this had to be temporarily disabled.)
The cached version was updated on 2020-04-03.
A tibble with various information about journals.
# use the function without arguments to get a tibble from disk jst_get_journal_overview() ## Not run: # download the most recent version from DfR jst_get_journal_overview(most_recent = TRUE) ## End(Not run)# use the function without arguments to get a tibble from disk jst_get_journal_overview() ## Not run: # download the most recent version from DfR jst_get_journal_overview(most_recent = TRUE) ## End(Not run)
Read in data on ngrams via readr::read_tsv().
jst_get_ngram(file)jst_get_ngram(file)
file |
A path to a file or a zip location from |
This function is mainly useful when it is used in together with jst_import_zip, where you can use it to specify reading in ngram data.
A tibble::tibble() with two columns:
ngram: the ngram term (unigram, bigram, trigram)
n: an integer for the number of times the term occurred in the original file
This function extracts the content of ref-list from the xml-file.
jst_get_references(file_path, parse_refs = FALSE)jst_get_references(file_path, parse_refs = FALSE)
file_path |
The path to the |
parse_refs |
Should references be parsed, if available? |
This content may contain references or endnotes, depending on how the article
used citations. Since references are currently not fully supported by DfR,
there is no comprehensive documentation on the different variants. jstor
therefore extracts the content of ref-list exactly as it appears in the
data. Because of this, there might be other content present than references.
In order to get all available information on citation data, you might need to
combine jst_get_references() with jst_get_footnotes().
For newer xml-files, there would be the option to extract single elements
like authors, title or date of the source, but this is not yet implemented.
In general, the implementation is not as fast as jst_get_article() -
articles with many references slow the process down.
A tibble with the following columns:
file_name: the identifier for the article the references come from.
ref_title: the title of the references sections.
ref_authors: a string of authors. Several authors are separated with ;.
ref_editors: a string of editors, if available.
ref_collab: a field that may contain information on the authors, if authors
are not available.
ref_item_title: the title of the cited entry. For books this is often
empty, with the title being in ref_source.
ref_year: a year, often the article's publication year, but not always.
ref_source: the source of the cited entry. For books often the title of the
book, for articles the publisher of the journal.
ref_volume: the volume of the journal article.
ref_first_page: the first page of the article/chapter.
ref_last_page: the last page of the article/chapter.
ref_publisher: For books the publisher, for articles often missing.
ref_publication_type: Known types: book, journal, web, other.
ref_unparsed: The full references entry in unparsed form.
jst_get_references(jst_example("article_with_references.xml")) # import parsed references jst_get_references( jst_example("parsed_references.xml"), parse_refs = TRUE )jst_get_references(jst_example("article_with_references.xml")) # import parsed references jst_get_references( jst_example("parsed_references.xml"), parse_refs = TRUE )
This function is a simple helper to calculate the total number of pages of an article.
jst_get_total_pages(first_page, last_page, page_range, quietly = FALSE)jst_get_total_pages(first_page, last_page, page_range, quietly = FALSE)
first_page |
The first page of an article (numeric). |
last_page |
The last page of an article (numeric). |
page_range |
The page range of an article (character). |
quietly |
Sometimes page ranges contain roman numerals like |
This function deals with four cases:
if all three arguments are missing, NA is returned.
if page_range is supplied, the number of pages is calculated from it.
if only the first page is supplied, NA is returned.
if first and last page are supplied, the number of pages is calculated as
last_page - first_page + 1.
The algorithm to parse page ranges works as follows: A typical page range is
1-10, 200 where the article starts at page 1, ends at page 10, and has an
erratum at page 200. For this case, the range is calculated as
range + single_page, as in(10 - 1 + 1) + 1 = 11. Sometimes multiple
ranges are given: 1-10, 11-20. For those cases all ranges are summed:
(10 - 1 + 1) + (20 - 11 + 1) = 20. Another specification for multiple
ranges is 1-10+11-20, which is treated similarly.
A vector with the calculated total pages.
# calculate pages from first and last page first_pages <- sample(30:50, 10) last_pages <- first_pages + sample(5:20, 10) page_ranges <- rep(NA_character_, 10) jst_get_total_pages(first_pages, last_pages, page_ranges) # get pages from page range jst_get_total_pages(NA_real_, NA_real_, "51 - 70") jst_get_total_pages(NA_real_, NA_real_, "51 - 70, 350") jst_get_total_pages(NA_real_, NA_real_, "350, 51 - 70") jst_get_total_pages(NA_real_, NA_real_, "51 - 70, 80-100") jst_get_total_pages(NA_real_, NA_real_, "51-70+350")# calculate pages from first and last page first_pages <- sample(30:50, 10) last_pages <- first_pages + sample(5:20, 10) page_ranges <- rep(NA_character_, 10) jst_get_total_pages(first_pages, last_pages, page_ranges) # get pages from page range jst_get_total_pages(NA_real_, NA_real_, "51 - 70") jst_get_total_pages(NA_real_, NA_real_, "51 - 70, 350") jst_get_total_pages(NA_real_, NA_real_, "350, 51 - 70") jst_get_total_pages(NA_real_, NA_real_, "51 - 70, 80-100") jst_get_total_pages(NA_real_, NA_real_, "51-70+350")
This function applies an import function to a list of xml-files
or a .zip-archive in case of jst_import_zip and saves
the output in batches of .csv-files to disk.
jst_import( in_paths, out_file, out_path = NULL, .f, col_names = TRUE, n_batches = NULL, files_per_batch = NULL, show_progress = TRUE ) jst_import_zip( zip_archive, import_spec, out_file, out_path = NULL, col_names = TRUE, n_batches = NULL, files_per_batch = NULL, show_progress = TRUE, rows = NULL )jst_import( in_paths, out_file, out_path = NULL, .f, col_names = TRUE, n_batches = NULL, files_per_batch = NULL, show_progress = TRUE ) jst_import_zip( zip_archive, import_spec, out_file, out_path = NULL, col_names = TRUE, n_batches = NULL, files_per_batch = NULL, show_progress = TRUE, rows = NULL )
in_paths |
A character vector to the |
out_file |
Name of files to export to. Each batch gets appended by an increasing number. |
out_path |
Path to export files to (combined with filename). |
.f |
Function to use for import. Can be one of |
col_names |
Should column names be written to file? Defaults to |
n_batches |
Number of batches, defaults to 1. |
files_per_batch |
Number of files for each batch. Can be used instead of n_batches, but not in conjunction. |
show_progress |
Displays a progress bar for each batch, if the session is interactive. |
zip_archive |
A path to a .zip-archive from DfR |
import_spec |
A specification from jst_define_import for which parts of a .zip-archive should be imported via which functions. |
rows |
Mainly used for testing, to decrease the number of files which are imported (i.e. 1:100). |
Along the way, we wrap three functions, which make the process of converting many files easier:
When using one of the find_* functions, there should usually be no errors.
To avoid the whole computation to fail in the unlikely event that an error
occurs, we use safely() which let's us
continue the process, and catch the error along the way.
If you have many files to import, you might benefit from executing the
function in parallel. We use futures for this to give you maximum
flexibility. By default the code is executed sequentially. If you want to
run it in parallel, simply call future::plan() with
future::multisession() as an argument before
running jst_import or jst_import_zip.
After importing all files, they are written to disk with
readr::write_csv().
Since you might run out of memory when importing a large quantity of files,
you can split up the files to import into batches. Each batch is being
treated separately, therefore for each batch multiple processes from
future::multisession() are spawned, if you added this plan.
For this reason, it is not recommended to have very small batches,
as there is an overhead for starting and ending the processes. On the other
hand, the batches should not be too large, to not exceed memory limitations.
A value of 10000 to 20000 for files_per_batch should work fine on most
machines. If the session is interactive and show_progress is TRUE, a
progress bar is displayed for each batch.
Writes .csv-files to disk.
## Not run: # read from file list -------- # find all files meta_files <- list.files(pattern = "xml", full.names = TRUE) # import them via `jst_get_article` jst_import(meta_files, out_file = "imported_metadata", .f = jst_get_article, files_per_batch = 25000) # do the same, but in parallel library(future) plan(multiprocess) jst_import(meta_files, out_file = "imported_metadata", .f = jst_get_article, files_per_batch = 25000) # read from zip archive ------ # define imports imports <- jst_define_import(article = c(jst_get_article, jst_get_authors)) # convert the files to .csv jst_import_zip("my_archive.zip", out_file = "my_out_file", import_spec = imports) ## End(Not run)## Not run: # read from file list -------- # find all files meta_files <- list.files(pattern = "xml", full.names = TRUE) # import them via `jst_get_article` jst_import(meta_files, out_file = "imported_metadata", .f = jst_get_article, files_per_batch = 25000) # do the same, but in parallel library(future) plan(multiprocess) jst_import(meta_files, out_file = "imported_metadata", .f = jst_get_article, files_per_batch = 25000) # read from zip archive ------ # define imports imports <- jst_define_import(article = c(jst_get_article, jst_get_authors)) # convert the files to .csv jst_import_zip("my_archive.zip", out_file = "my_out_file", import_spec = imports) ## End(Not run)
This function gives you a quick preview about what a .zip-file from DfR contains.
jst_preview_zip(zip_archive)jst_preview_zip(zip_archive)
zip_archive |
A path to a .zip-file from DfR |
The function returns a tibble with three columns:
type: metadata or some form of ngram
meta_type: which type of metadata (book_chapter, journal article, ...)
n: a count for each category
jst_preview_zip(jst_example("pseudo_dfr.zip"))jst_preview_zip(jst_example("pseudo_dfr.zip"))
jst_re_import() lets you re-import a file which was exported via
jst_import() or jst_import_zip().
jst_re_import(file, warn = TRUE)jst_re_import(file, warn = TRUE)
file |
A path to a .csv file. |
warn |
Should warnings be emitted, if the type of file cannot be determined? |
When attempting to re-import, a heuristic is applied. If the file has column
names which match the names from any of the find_* functions, the file
is read with the corresponding specifications. If no column names are
recognized, files are recognized based on the number of columns. Since both
references and footnotes have only two columns, the first line is inspected
for either "Referenc...|Bilbio...|Endnote..." or "Footnote...".
In case there is still no match, the file is read with
readr::read_csv() with guess_max = 5000 and a warning is raised.
A tibble, with the columns determined based on heuristics applied
to the input file.
This function helps in defining a subset of ngram files which should be imported, since importing all ngrams at once can be very expensive (in terms of cpu and memory).
jst_subset_ngrams(zip_archives, ngram_type, selection, by = file_name)jst_subset_ngrams(zip_archives, ngram_type, selection, by = file_name)
zip_archives |
A character vector of one or multiple zip-files. |
ngram_type |
One of |
selection |
A data.frame with the articles/books which are to be selected. |
by |
A column name for matching. |
A list of zip-locations which can be read via jst_get_ngram().
# create sample output tmp <- tempdir() jst_import_zip(jst_example("pseudo_dfr.zip"), import_spec = jst_define_import(book = jst_get_book), out_file = "test", out_path = tmp) # re-import as our selection for which we would like to import ngrams selection <- jst_re_import(file.path(tmp, "test_book_chapter_jst_get_book-1.csv")) # get location of file zip_loc <- jst_subset_ngrams(jst_example("pseudo_dfr.zip"), "ngram1", selection) # import ngram jst_get_ngram(zip_loc[[1]]) unlink(tmp)# create sample output tmp <- tempdir() jst_import_zip(jst_example("pseudo_dfr.zip"), import_spec = jst_define_import(book = jst_get_book), out_file = "test", out_path = tmp) # re-import as our selection for which we would like to import ngrams selection <- jst_re_import(file.path(tmp, "test_book_chapter_jst_get_book-1.csv")) # get location of file zip_loc <- jst_subset_ngrams(jst_example("pseudo_dfr.zip"), "ngram1", selection) # import ngram jst_get_ngram(zip_loc[[1]]) unlink(tmp)
This function is a simple wrapper to unify journal ids.
jst_unify_journal_id(meta_data, remove_cols = TRUE)jst_unify_journal_id(meta_data, remove_cols = TRUE)
meta_data |
Data which was processed via |
remove_cols |
Should the original columns be removed after unifying? |
Date on journal ids can be found in three columns:
journal_pub_id, journal_jcode and journal_doi. From my experience,
most of the time the relevant dat ais present in journal_pub_id or
journal_jcode, with journal_jcode being to most common identifier.
This function takes the value from journal_pub_id, and if it is missing,
that from journal_jcode. journal_doi is currently disregarded.
A modified tibble.
A modified tibble.
article <- jst_get_article(jst_example("article_with_references.xml")) jst_unify_journal_id(article) # per default, original columns with data on the journal are removed library(dplyr) jst_unify_journal_id(article) %>% select(contains("journal")) %>% names() # you can keep them by setting `remove_cols` to `FALSE` jst_unify_journal_id(article, remove_cols = FALSE) %>% select(contains("journal")) %>% names()article <- jst_get_article(jst_example("article_with_references.xml")) jst_unify_journal_id(article) # per default, original columns with data on the journal are removed library(dplyr) jst_unify_journal_id(article) %>% select(contains("journal")) %>% names() # you can keep them by setting `remove_cols` to `FALSE` jst_unify_journal_id(article, remove_cols = FALSE) %>% select(contains("journal")) %>% names()
The tool Data for Research (DfR) by JSTOR is a
valuable source for citation analysis and text mining. jstor
provides functions and suggests workflows for importing
datasets from DfR.
Please refer to the vignettes for information on how to use the package:
browseVignettes("jstor")
If you encounter any issues or have ideas for new features, please file an issue at https://github.com/ropensci/jstor/issues.
Thomas Klebel