Package 'c2z'

Search Cristin API

Description

Use search parameters for the Cristin API and return the results as a tibble. See CristinWrangler

Usage

Cristin(
  id = NULL,
  doi = NULL,
  title = NULL,
  contributor = NULL,
  issn = NULL,
  unit = NULL,
  institution = NULL,
  user = NULL,
  category = NULL,
  published_since = NULL,
  published_before = NULL,
  created_since = NULL,
  created_before = NULL,
  modified_since = NULL,
  modified_before = NULL,
  year_reported = NULL,
  project_code = NULL,
  funding_source = NULL,
  funding = NULL,
  lang = NULL,
  page = 1,
  per_page = 1000,
  max.results = NULL,
  no.results = FALSE,
  sort = NULL,
  filter = NULL,
  fields = "all",
  open.query = NULL,
  all.results = TRUE,
  force = FALSE,
  remove.duplicates = TRUE,
  silent = FALSE,
  base.url = "https://api.cristin.no/v2/results",
  custom.url = NULL,
  use.identifiers = TRUE,
  crossref.search = FALSE,
  autosearch = TRUE,
  zotero = NULL,
  zotero.import = TRUE,
  zotero.check = TRUE,
  nvi = FALSE,
  remove.na = TRUE,
  replace.na = "book",
  force.type = NULL,
  override = FALSE,
  polite = TRUE,
  log = list()
)

Arguments

id	The Cristin id of the result, Default: NULL
doi	DOI name (e.g. doi=10.1000/123456), Default: NULL
title	The title of the result, Default: NULL
contributor	Author's name or Cristin person id, Default: NULL
issn	The issn of the result, Default: NULL
unit	Id (e.g. unit=185.53.18.10), Default: NULL
institution	Id (one number, e.g. institution=185), name or acronym of the institution the contributors belong to, Default: NULL
user	A person's username in Cristin together with the institution id separated by colon (e.g., 'askeladd:185'), Default: NULL
category	Categories. See category codes, Default: NULL
published_since	Results published since and inclusive the given year, (yyyy), Default: NULL
published_before	Results published before and inclusive the given year, (yyyy), Default: NULL
created_since	Results created since and inclusive the given date, (yyyy-mm-dd), Default: NULL
created_before	Results created before and inclusive the given date, (yyyy-mm-dd), Default: NULL
modified_since	Results modified since and inclusive the given date, (yyyy-mm-dd), Default: NULL
modified_before	Results modified before and inclusive the given date, (yyyy-mm-dd), Default: NULL
year_reported	The year a result was reported, Default: NULL
project_code	Project code is the internal reference number used by funding source, Default: NULL
funding_source	Funding source code e.g: NFR, Default: NULL
funding	Funding source code e.g: NFR, and project_code together separated by colon (e.g., NFR:1234), Default: NULL
lang	Two letter language code, Default: NULL
page	Page number. See pagination, Default: 1
per_page	Number of items per page (1000 is max). See pagination, Default: 1000
max.results	Do you need a limit?, Default: NULL
no.results	Do you need only the number of results?, Default: FALSE
sort	Sorts on 'category' and/or 'year_published'. See search and sort. Default sort order is on 'cristin_result_id' in ascending order, Default: NULL
filter	Vector of cateogries to include in results. See category code, Default: NULL
fields	'fields = all' gives a list of result objects with all available fields. If this parameter is omitted, a list of result summaries with fewer fields will be returned, Default: all
open.query	Define your own query terms, Default: NULL
all.results	Find all results in query, Default: TRUE
force	Force is seldom wise, but sometimes..., Default: FALSE
remove.duplicates	Remove duplicates if TRUE, Default: TRUE
silent	c2z is noisy, tell it to be quiet, Default: FALSE
base.url	The base url for the Cristin API, Default: https://api.cristin.no/v2/results
custom.url	Define your own Cristin API url, Default: NULL
use.identifiers	Use if ISBN/DOI identifiers if enabled, Default: TRUE
crossref.search	Query Crossref database based on title, authors, and date if enabled, Default: FALSE
autosearch	Results could be automatically evaluated (based on some logic) or you could inspect them manually if set to FALSE, Default: TRUE
zotero	A list with information on the specified Zotero library (e.g., id, API key, collections, and items), Default: NULL
zotero.import	Use CristinWrangler to wrangle metadata into an acceptable format for Zotero, Default: TRUE
zotero.check	Check for Cristin references already stored in Zotero, Default: TRUE
nvi	Filter out non-NVI publications Default: FALSE
remove.na	Cristin contains many, more or less, obscure categories, and not all are (yet) supported. By default these are removed, however, if this option is set to FALSE unsupported categories are treated according to replace.na, Default: TRUE
replace.na	May the odds be in your favor and replace unsupported categories with a predefined itemType if remove.na is set to false, Default: 'book'
force.type	Force all items to a predefined itemType, Default: NULL
override	Put your faith in the algorithms and the identifiers (i.e., DOI/ISBN) and override what is reported in Cristin, Default: FALSE
polite	Please store you email in '.Renviron' to query Crossref, Default: TRUE
log	A list for storing log elements, Default: list()

Details

Please see #' https://oeysan.github.io/c2z/

Value

A list with (exported) items from Cristin

See Also

http_error, GET, RETRY tail, head slice

Examples

# Simple `Cristin` search by id
  example <- Cristin(id = "840998")

  # Print index using `ZoteroIndex`
  if (any(nrow(example$results))) {
    ZoteroIndex(example$results) |>
      dplyr::select(name) |>
      print(width = 80)
  }

---

Check for supported export formats from Cristin to Zotero

Description

Used to filter Cristin categories that are not supported

Usage

CristinSupported(
  data = NULL,
  zotero.check = TRUE,
  items = NULL,
  remove.na = TRUE,
  replace.na = "book",
  force.type = NULL,
  remove.duplicates = TRUE,
  silent = FALSE,
  log = list()
)

Arguments

data	Zotero-type matrix, Default: NULL
zotero.check	Should the function look for duplicates?, Default: TRUE
items	Items in library to check for
remove.na	Cristin contains many, more or less, obscure categories, and not all are (yet) supported. By default these are removed, however, if this option is set to FALSE unsupported categories are treated according to replace.na, Default: TRUE
replace.na	May the odds be in your favor and replace unsupported categories with a predefined itemType if remove.na is set to false, Default: 'book'
force.type	Force all items to a predefined itemType, Default: NULL
remove.duplicates	Remove duplicates if TRUE, Default: TRUE
silent	c2z is noisy, tell it to be quiet, Default: FALSE
log	A list for storing log elements, Default: list()

Details

Please see https://oeysan.github.io/c2z/

Value

Zotero supported items with unsupported categories as NA

See Also

tibble

Examples

# Supported Cristin items
print(CristinSupported(), n = 5)

---

Wrangle Cristin metadata into Zotero-type format

Description

The little engine that could, at least try, to wrangle metadata from Cristin into a Zotero-type matrix. References can be augmented, or replaced with metadata gathered through ISBN or DOI identifiers, and through Crossref queries if all other fails. Or, hope the best and place your misguided faith in the ability of researchers to correctly register their own publications.

Usage

CristinWrangler(
  data,
  meta = list(),
  use.identifiers = TRUE,
  crossref.search = FALSE,
  autosearch = TRUE,
  override = FALSE,
  silent = FALSE,
  polite = TRUE,
  prefer.semantic = TRUE,
  log = list()
)

Arguments

data	Tibble containing metadata from Cristin
meta	A list for storing data elements, Default: list()
use.identifiers	Use if ISBN/DOI identifiers if enabled, Default: TRUE
crossref.search	Query Crossref database based on title, authors, and date if enabled, Default: FALSE
autosearch	Results could be automatically evaluated (based on some logic) or you could inspect them manually if set to FALSE, Default: TRUE
override	Put your faith in the algorithms and the identifiers (i.e., DOI/ISBN) and override what is reported in Cristin, Default: FALSE
silent	Running silent, running deep, Default: FALSE
polite	Please store you email in '.Renviron' to query Crossref, Default: TRUE
prefer.semantic	Prefer metadata from Semantic Scholar, Default: TRUE
log	A list for storing log elements, Default: list()

Details

Please see https://oeysan.github.io/c2z/

Value

A Zotero-type matrix (tibble)

See Also

unnest, nest filter, across, reexports, bind, mutate, distinct RETRY tibble

Examples

# Simple `Cristin` search by id with import set as FALSE
  example <- Cristin(id = "840998", zotero.import = FALSE)

  if (any(nrow(example$results))) {
    # Use `ZoteroIndex` to print `CristinWrangler`
    CristinWrangler(example$results)$results |>
      ZoteroIndex() |>
      dplyr::select(name) |>
      print(width = 80)
  }

---

Wrangle CrossRef metadata into Zotero-type format

Description

Query CrossRef by DOI and fetch metadata

Usage

DoiCrossref(data, meta = list(), silent = TRUE, log = list())

Arguments

data	XML data from CrossRef containing metadata
meta	A list collecting all metadata used to create , Default: list()
silent	c2z is noisy, tell it to be quiet, Default: TRUE
log	A list for storing log elements, Default: list()

Details

Please see https://oeysan.github.io/c2z/

Value

A Zotero-type matrix (tibble)

Examples

# `DoiCrossref` is called from `ZoteroDoi` (if item found)
  example <- ZoteroDoi("10.1126/sciadv.abd1705")

  # Print index using `ZoteroIndex`
  if (!is.null(example$data)) {
    ZoteroIndex(example$data) |>
      dplyr::select(name) |>
      print(width = 80)

    # Display catalog
    example$data$libraryCatalog
  }

---

Wrangle DataCite metadata into Zotero-type format

Description

Query DataCite by DOI and fetch metadata

Usage

DoiDatacite(data, meta = list(), silent = TRUE, log = list())

Arguments

data	XML data from DataCite containing metadata
meta	A list collecting all metadata used to create , Default: list()
silent	c2z is noisy, tell it to be quiet, Default: TRUE
log	A list for storing log elements, Default: list()

Details

Please see https://oeysan.github.io/c2z/

Value

A Zotero-type matrix (tibble)

Examples

# `DoiDatacite` is called from `ZoteroDoi` (if item found)
  example <- ZoteroDoi("10.17605/OSF.IO/7HZ4P")

  # Use `ZoteroIndex` to print
  # Print index using `ZoteroIndex`
  if (any(nrow(example$data))) {
    ZoteroIndex(example$data) |>
      dplyr::select(name) |>
      print(width = 80)

    # Display catalog
    example$data$libraryCatalog
  }

---

Connect to Zotero API

Description

Wrapper to connect with the Zotero API and the main functions of *c2z*

Usage

Zotero(
  collection.names = NULL,
  collection.key = NULL,
  collection.path = NULL,
  item.key = NULL,
  library = FALSE,
  case.insensitive = TRUE,
  ancestor = FALSE,
  recursive = FALSE,
  create = FALSE,
  limit = 100,
  start = 0,
  search.collections = TRUE,
  get.collections = TRUE,
  get.items = TRUE,
  item.type = NULL,
  all.results = TRUE,
  max.results = NULL,
  collections = NULL,
  items = NULL,
  attachments = NULL,
  metadata = NULL,
  doi = NULL,
  isbn = NULL,
  export = FALSE,
  csl.type = NULL,
  csl.name = "style",
  format = "biblatex",
  save.data = FALSE,
  save.path = NULL,
  bib.name = "references",
  library.type = NULL,
  linkwrap = 1,
  style = "apa",
  locale = "en-US",
  copy = FALSE,
  copy.collections = TRUE,
  copy.items = TRUE,
  copy.extras = TRUE,
  remove.missing = TRUE,
  change.library = FALSE,
  copy.user = TRUE,
  copy.id = NULL,
  copy.api = NULL,
  post = FALSE,
  post.collections = TRUE,
  post.items = TRUE,
  post.attachments = TRUE,
  post.limit = 50,
  delete = FALSE,
  delete.collections = FALSE,
  delete.items = FALSE,
  delete.limit = 50,
  ragnarok = FALSE,
  user = TRUE,
  index = FALSE,
  id = NULL,
  token = NULL,
  token.api = NULL,
  api = NULL,
  force = FALSE,
  base.url = "https://api.zotero.org",
  silent = FALSE,
  zotero = NULL,
  log = list()
)

Arguments

collection.names	Vector of collection names to create or search for, Default: NULL
collection.key	A specified collection key, Default: NULL
collection.path	Vector of nested collection keys, Default: NULL
item.key	A specified item key, Default: NULL
library	Use 'ZoteroLibrary' to fetch collections and items, Default: FALSE
case.insensitive	Disregard letter casing when searching for collections, Default: TRUE
ancestor	Trace the lineage of a collection (i.e., find the top-level collection), Default: FALSE
recursive	Find all nested collections, Default: FALSE
create	Create missing collections, Default: FALSE
limit	Number of results per query (max 100), Default: 100
start	Starting position of query (0 = first result), Default: 0
search.collections	Search all collections if collection.key fails, Default: TRUE
get.collections	Fetch collections, Default: TRUE
get.items	Fetch items, Default: TRUE
item.type	Items to search for (NULL = everything), Default: NULL
all.results	Find all results in query, Default: TRUE
max.results	Do you need a limit?, Default: NULL
collections	Predefined collections (as tibble), Default: NULL
items	Predefined metadata (as tibble), Default: NULL
attachments	Predefined attachments (as tibble), Default: NULL
metadata	Predefined metadata in Zotero-format, Default: NULL
doi	Use ZoteroDoi to fetch DOI metadata, Default: NULL
isbn	Use ZoteroIsbn to fetch ISBN metadata, Default: NULL
export	Use 'ZoteroExport' to export items, Default: FALSE
csl.type	Specify a CSL type to Official repository for Citation Style Language (CSL), Default: NULL
csl.name	Name of saved CSL file, Default: 'style'
format	Export format of Zotero items, Default: 'biblatex'
save.data	Save data (e.g., bibliography) to disk, Default: FALSE
save.path	Location to store data on disk, Default: NULL
bib.name	Name of exported bibliography, Default: 'references'
library.type	Commma-separated data from Zotero (i.e., data, bib, citation), Default: NULL
linkwrap	Set URL (e.g., DOI) as HTML link (1 = yes), Default: 1
style	Citation style to use for appended bibliography and/or citations, Default: apa
locale	Desired language format of bibliography, Default: 'en-US'
copy	Use 'ZoteroCopy' to delete collections and/or items, Default: FALSE
copy.collections	Try to copy specified collections, Default: TRUE
copy.items	Try to copy specified items?, Default: TRUE
copy.extras	Try to copy specified extras (i.e., attachments and notes)?, Default: TRUE
remove.missing	Deleted missing extras, Default: TRUE
change.library	Stage changing of library (e.g., from a group to a personal library), Default: FALSE
copy.user	New user type (The functions will use 'group' as prefix if FALSE), Default: TRUE
copy.id	New id, Default: NULL
copy.api	New API key. Set API to 'NA' if key is not needed, Default: NULL
post	Use 'ZoteroPost' to post collections and/or items, Default: FALSE
post.collections	Try to copy specified collections, Default: TRUE
post.items	Try to copy specified items?, Default: TRUE
post.attachments	Try to copy specified extras (i.e., attachments and notes)?, Default: TRUE
post.limit	Number of collections/items to post per request (max 50), Default: 50
delete	Use 'ZoteroDelete' to delete collections and/or items, Default: FALSE
delete.collections	Try to delete specified collections, Default: TRUE
delete.items	Try to delete specified items?, Default: TRUE
delete.limit	Number of collections/items to delete per request (max 50), Default: 50
ragnarok	Delete EVERYTHING in the specified library, Default: FALSE
user	User type (The functions will use 'group' as prefix if FALSE), Default: TRUE
index	Create an index of items, Default: FALSE
id	User or group ID, Default: NULL
token	Name of user or group token as defined in '.Renviron', Default: NULL
token.api	Name of API token as defined in '.Renviron', Default: NULL
api	API key to connect with the Zotero library. Set API to 'NA' if key is not needed. See Zotero API, Default: NULL
force	Force is seldom wise, but sometimes..., Default: FALSE
base.url	Base url of the Zotero API, Default: 'https://api.zotero.org'
silent	c2z is noisy, tell it to be quiet, Default: FALSE
zotero	A list with information on the specified Zotero library (e.g., id, API key, collections, and items), Default: NULL
log	A list for storing log elements, Default: list()

Details

Please see https://oeysan.github.io/c2z/

Value

A list with information on the specified Zotero library (e.g., id, API key, collections, and items)

See Also

http_error, GET

Examples

# Create the default Zotero list
example <- Zotero(id = "9913421", api = "RqlAmlH5l1KPghfCseAq1sQ1")
# Print the interesting pars of an otherwise empty list
print(tail(example,5))

---

Add items to Zotero list

Description

Use identifiers or predefined data to add to the Zotero list

Usage

ZoteroAdd(zotero, metadata = NULL, doi = NULL, isbn = NULL, silent = FALSE)

Arguments

zotero	A list with information on the specified Zotero library (e.g., id, API key, collections, and items)
metadata	Predefined metadata in Zoter-format, Default: NULL
doi	Use ZoteroDoi to fetch DOI metadata, Default: NULL
isbn	Use ZoteroIsbn to fetch ISBN metadata, Default: NULL
silent	c2z is noisy, tell it to be quiet, Default: FALSE

Details

Please see https://oeysan.github.io/c2z/

Value

Will add data to the Zotero list

Examples

# Add items from `ZoteroIsbn` to the default Zotero list
  example <- ZoteroAdd(
    Zotero(
      id = "9913421",
      api = "RqlAmlH5l1KPghfCseAq1sQ1"
    ),
    isbn = "978-1529797138"
  )
  # Print index using `ZoteroIndex`
  if (any(nrow(example$items))) {
    ZoteroIndex(example$items) |>
      dplyr::select(name) |>
      print(width = 80)
  }

---

Check Zotero library for duplicates

Description

Remove references that are not modified since last added to Zotero

Usage

ZoteroCheck(
  data,
  id,
  id.type,
  created,
  last.modified,
  items,
  remove.duplicates = TRUE,
  silent = FALSE,
  log = list()
)

Arguments

data	Tibble containing metadata (from Cristin)
id	column containing identifier (e.g., cristin_result_id)
id.type	Type of metadata as found in the Zotero extra field ("e.g., Cristin)
created	column containing creation date in UNIX timestamp format (e.g., created)
last.modified	column containing modification date in UNIX timestamp format (e.g., last_modified)
items	Items in library to check for
remove.duplicates	Remove duplicates if TRUE, Default: TRUE
silent	c2z is noisy, tell it to be quiet, Default: FALSE
log	A list for storing log elements, Default: list()

Details

Please see https://oeysan.github.io/c2z/

Value

Returns non-duplicated data in a Zotero-type matrix (tibble)

See Also

arrange, coalesce, bind_rows, filter

Examples

# Simple `Cristin` search by id
  cristin.data <- Cristin(
    id = "840998",
    zotero.import = FALSE
  )

  # Simple `ZoteroCheck`
  example <- ZoteroCheck(
    data = cristin.data$result,
    id = "cristin_result_id",
    id.type = "Cristin",
    created = "created",
    last.modified = "last_modified",
    items = Zotero(
      user = FALSE,
      id = "4827927",
      api = "RqlAmlH5l1KPghfCseAq1sQ1",
      library = TRUE,
      silent = TRUE
    )$items
  )

---

Copy collections and items from a Zotero library

Description

Replace key identifiers with new ones while keeping existing structure and relationship between collections and items

Usage

ZoteroCopy(
  zotero,
  copy.collections = TRUE,
  copy.items = TRUE,
  copy.extras = TRUE,
  remove.missing = TRUE,
  change.library = FALSE,
  copy.user = TRUE,
  copy.id = NULL,
  copy.api = NULL,
  silent = FALSE
)

Arguments

zotero	A list with information on the specified Zotero library (e.g., id, API key, collections, and items)
copy.collections	Try to copy specified collections, Default: TRUE
copy.items	Try to copy specified items?, Default: TRUE
copy.extras	Try to copy specified extras (i.e., attachments and notes)?, Default: TRUE
remove.missing	Deleted missing extras, Default: TRUE
change.library	Stage changing of library (e.g., from a group to a personal library), Default: FALSE
copy.user	New user type (The functions will use 'group' as prefix if FALSE), Default: TRUE
copy.id	New id, Default: NULL
copy.api	New API key, Default: NULL
silent	c2z is noisy, tell it to be quiet, Default: FALSE

Details

Please see https://oeysan.github.io/c2z/

Value

A list with information on the specified Zotero library (e.g., copied collections and items)

See Also

GET mutate, case_when, filter, select, across, arrange pmap all_of

Examples

# Fetching collections and items from default group
  zotero = Zotero(
    user = FALSE,
    id = "4827927",
    api = "RqlAmlH5l1KPghfCseAq1sQ1",
    library = TRUE
  )

  # Display collections
  if (any(nrow(zotero$collections))) {
    zotero$collections |>
      dplyr::select(key, version, parentCollection) |>
      print(width = 80)
  }

  # Display items
  if (any(nrow(zotero$items))) {
    zotero$items |>
      dplyr::select(key, version) |>
      print(width = 80)
  }

  # Copy items
  example <- ZoteroCopy(
    zotero,
  )

  # Display collections
  if (any(nrow(example$collections))) {
    example$collections |>
      dplyr::select(key, version, parentCollection) |>
      print(width = 80)
  }

  # Display items
  if (any(nrow(example$items))) {
    example$items |>
      dplyr::select(key, version) |>
      print(width = 80)
  }

---

Wrangle CRAN metadata into Zotero-type format

Description

Query CRAN by name and fetch metadata

Usage

ZoteroCran(id, meta = list(), silent = TRUE, log = list())

Arguments

id	name of R package
meta	A list collecting all metadata used to create , Default: list()
silent	c2z is noisy, tell it to be quiet, Default: TRUE
log	A list for storing log elements, Default: list()

Details

Please see https://oeysan.github.io/c2z/

Value

A Zotero-type matrix (tibble)

See Also

RETRY reexports

Examples

# Search cran for package `dplyr`
  example <- ZoteroCran(c("dplyr", "jsonlite", "httr"))

  # Print index using `ZoteroIndex`
  if (any(nrow(example$data))) {
  ZoteroIndex(example$data) |>
    dplyr::select(name) |>
    print(width = 80)
  }

---

Delete collections and items from a Zotero library

Description

Cleaning the Zotero library

Usage

ZoteroDelete(
  zotero,
  delete.collections = FALSE,
  delete.items = FALSE,
  delete.limit = 50,
  force = FALSE,
  ragnarok = FALSE,
  silent = FALSE
)

Arguments

zotero	A list with information on the specified Zotero library (e.g., id, API key, collections, and items)
delete.collections	Try to delete specified collections, Default: TRUE
delete.items	Try to delete specified items?, Default: TRUE
delete.limit	Number of collections/items to delete per request (max 50), Default: 50
force	Force is seldom wise, but sometimes..., Default: FALSE
ragnarok	Delete EVERYTHING in the specified library, Default: FALSE
silent	c2z is noisy, tell it to be quiet, Default: FALSE

Details

Please see https://oeysan.github.io/c2z/

Value

A list with information on the specified Zotero library (e.g., deleted collections and items)

See Also

add_headers, RETRY

Examples

# Delete everything in a group
  example <- ZoteroDelete(
    Zotero(
      user = FALSE,
      id = "4988497",
      api = "RqlAmlH5l1KPghfCseAq1sQ1"
    ),
    ragnarok = TRUE,
    force = TRUE
  )

---

Use DOI to acquire metadata

Description

Connects with doi.org to create metadata

Usage

ZoteroDoi(
  doi,
  meta = list(),
  prefer.semantic = FALSE,
  check.retraction = TRUE,
  silent = TRUE,
  log = list()
)

Arguments

doi	A digital object identifier
meta	A list collecting all metadata used to create , Default: list()
prefer.semantic	Prefer metadata from Semantic Scholar, Default: FALSE
check.retraction	Check if marked as retracted, Default: TRUE
silent	c2z is noisy, tell it to be quiet, Default: TRUE
log	A list for storing log elements, Default: list()

Details

Please see https://oeysan.github.io/c2z/

Value

A Zotero-type matrix (tibble)

See Also

http_error, GET, RETRY rename, html_attr, html_text, reexports, html_children, html_name bind, arrange

Examples

# Simple use of `ZoteroDoi`
  example <- ZoteroDoi("10.1126/sciadv.abd1705")

  # Print index using `ZoteroIndex`
  if (any(nrow(example$data))) {
  ZoteroIndex(example$data) |>
    dplyr::select(name) |>
    print(width = 80)
  }

---

Export Zotero items to bibliography

Description

Export Zotero items to a specified format (e.g., BibLaTeX) using a CSL format (e.g., APA7)

Usage

ZoteroExport(
  zotero,
  csl.type = NULL,
  csl.name = "style",
  locale = "en-US",
  format = "biblatex",
  bib.name = "references",
  save.data = FALSE,
  save.path = NULL,
  silent = FALSE
)

Arguments

zotero	A list with information on the specified Zotero library (e.g., id, API key, collections, and items)
csl.type	Specify a CSL type to Official repository for Citation Style Language (CSL), Default: NULL
csl.name	Name of saved CSL file, Default: 'style'
locale	Desired language format of bibliography, Default: 'en-US'
format	Export format of Zotero items, Default: 'biblatex'
bib.name	Name of exported bibliography, Default: 'references'
save.data	Save data (e.g., bibliography) to disk, Default: FALSE
save.path	Location to store data on disk, Default: NULL
silent	c2z is noisy, tell it to be quiet, Default: FALSE

Details

Please see https://oeysan.github.io/c2z/

Value

A list with information on the specified Zotero library (e.g., exported items, bibliography and citations)

See Also

select where

Examples

# Define Zotero list according to default group
  zotero = Zotero(
    user = FALSE,
    id = "4827927",
    api = "RqlAmlH5l1KPghfCseAq1sQ1",
    item.type = "-attachment || note",
    max.result = 1,
    library = TRUE
  )

  # Export 1 items from the default group
  example <- ZoteroExport(
    zotero
  )
  # Display exported
  cat(example$export, fill = 80)

---

Make a Zotero friendly format of input data

Description

Make a Zotero friendly format of input data, will add a zotero key.

Usage

ZoteroFormat(
  data = NULL,
  format = NULL,
  prefix = NULL,
  check.structure = FALSE,
  silent = FALSE
)

Arguments

data	A list of metadata or something else, Default: NULL
format	The format of the input data (e.g., 'JSON', 'versions', 'keys). , Default: NULL
prefix	Add a prefix to the metadata (e.g., user/userID), Default: NULL
check.structure	Check that the structure of a data frame is correct according to the Zotero type, Default: FALSE
silent	c2z is noisy, tell it to be quiet, Default: TRUE

Value

A zotero friendly tibble if requested otherwise format the data according to format.

See Also

tibble, as_tibble toJSON, fromJSON mutate_all, na_if, mutate, across, reexports, select map

Examples

ZoteroFormat(
    list(title = "This is a test", itemType = "document")
  )

---

Get collections and items from a Zotero library

Description

Get

Usage

ZoteroGet(
  zotero,
  use.collection = TRUE,
  use.item = FALSE,
  append.collections = FALSE,
  append.items = FALSE,
  append.top = FALSE,
  append.file = FALSE,
  custom.url = NULL,
  open.query = NULL,
  limit = 100,
  start = 0,
  format = "json",
  item.keys = NULL,
  collection.keys = NULL,
  item.type = NULL,
  library.type = NULL,
  linkwrap = 1,
  style = "apa",
  locale = "en-US",
  all.results = TRUE,
  max.results = NULL,
  result.type = NULL,
  force = FALSE,
  silent = FALSE
)

Arguments

zotero	A list with information on the specified Zotero library (e.g., id, API key, collections, and items)
use.collection	Use collection key if present in Zotero list, Default: TRUE
use.item	Use item key if present in Zotero list, Default: FALSE
append.collections	Append '/collections/' to Zotero API url, Default: FALSE
append.items	Append '/items/' to Zotero API url, Default: FALSE
append.top	Append '/top/' to Zotero API url, Default: FALSE
append.file	Append '/file/' to Zotero API url, Default: FALSE
custom.url	Use a custom Zotero API url, Default: NULL
open.query	Use your own query, Default: NULL
limit	Number of results per query (max 100), Default: 100
start	Starting position of query (0 = first result), Default: 0
format	Format of response from the Zotero API, Default: 'json'
item.keys	Specified vector of items keys, Default: NULL
collection.keys	Specified vector of collection keys, Default: NULL
item.type	Items to search for (NULL = everything), Default: NULL
library.type	Commma-separated data from Zotero (i.e., data, bib, citation), Default: NULL
linkwrap	Set URL (e.g., DOI) as HTML link (1 = yes), Default: 1
style	Citation style to use for appended bibliography and/or citations, Default: apa
locale	Desired language format of bibliography, Default: 'en-US'
all.results	Find all results in query, Default: TRUE
max.results	Do you need a limit?, Default: NULL
result.type	Pointless linguistics to display result type (default = 'result'), Default: NULL
force	Force is seldom wise, but sometimes..., Default: FALSE
silent	c2z is noisy, tell it to be quiet, Default: FALSE

Details

Please see https://oeysan.github.io/c2z/

Value

A list with information on the specified Zotero library (e.g., collections and items)

See Also

RETRY

Examples

# Define Zotero list according to default setings
  zotero = Zotero(
    user = FALSE,
    id = "5250382",
    api = "RqlAmlH5l1KPghfCseAq1sQ1"
  )

  # Query default group Zotero library for 1 item
  example <- ZoteroGet(
    zotero,
    max.results = 1
  )

  # Print index using `ZoteroIndex`
  if (any(nrow(example$results))) {
  ZoteroIndex(example$results) |>
    dplyr::select(name) |>
    print(width = 80)
  }

---

Wrangle regjeringen.no metadata into Zotero-type format

Description

Query regjeringen by search word and type and fetch metadata

Usage

ZoteroGov(search, type = "NOU", meta = list(), silent = TRUE, log = list())

Arguments

search	Search term (e.g., 2018: 2)
type	type of query (e.g., white paper, official norwegian reports), Default: "NOU"
meta	A list collecting all metadata used to create , Default: list()
silent	c2z is noisy, tell it to be quiet, Default: TRUE
log	A list for storing log elements, Default: list()

Details

Please see https://oeysan.github.io/c2z/

Value

A Zotero-type matrix (tibble)

See Also

RETRY reexports bind, arrange

Examples

# Search the default entity, Norwegian official reports in regjeringen.no
  example <- ZoteroGov("2001:4")
  # Print index using `ZoteroIndex`
  if (any(nrow(example$data))) {
  ZoteroIndex(example$data) |>
    dplyr::select(name) |>
    print(width = 80)
  }

---

Create an index of Zotero items

Description

The function creates a index containing key information about the present Zotero items

Usage

ZoteroIndex(data)

Arguments

data	Tibble containing Zotero-type metadata (e.g., from Cristin)

Details

Please see https://oeysan.github.io/c2z/

Value

A tibble

See Also

filter, mutate, across, na_if, case_when, arrange, group_by, context, select everything pmap

Examples

# Access the default group library
  example = Zotero(
    user = FALSE,
    id = "4827927",
    api = "RqlAmlH5l1KPghfCseAq1sQ1",
    library = TRUE
  )
  # Print index using `ZoteroIndex`
  if (any(nrow(example$items))) {
  ZoteroIndex(example$items) |>
    dplyr::select(name) |>
    print(width = 80)
  }

---

Search libraries using ISBN or MMS ID

Description

Query libraries using ISBN (or MMS ID) and fetch metadata

Usage

ZoteroIsbn(keys, meta = list(), silent = TRUE, log = list())

Arguments

keys	Keys to search with (e.g., ISBN or MMS ID)
meta	A list collecting all metadata used to create , Default: list()
silent	c2z is noisy, tell it to be quiet, Default: TRUE
log	A list for storing log elements, Default: list()

Details

Please see https://oeysan.github.io/c2z/

Value

A Zotero-type matrix (tibble)

See Also

rename, html_children, html_attr, html_text, reexports bind, distinct, arrange tibble RETRY setNames toJSON, fromJSON

Examples

# Search libraries for ISBN metadata
  example <- ZoteroIsbn("978-1529797138")

  # Print index using `ZoteroIndex`
  if (any(nrow(example$data))) {
  ZoteroIndex(example$data) |>
    dplyr::select(name) |>
    print(width = 80)
  }

---

Create Zotero key or write token

Description

Create an identifier for Zotero items/collections or a write token to library

Usage

ZoteroKey(token = FALSE)

Arguments

token

Create a write token, Default: FALSE

Details

Please see https://oeysan.github.io/c2z/

Value

Will return a 8 character Zotero key or 32 character write token

Examples

# Create a Zotero key
key <- ZoteroKey()
# Create a write token
token <- ZoteroKey(TRUE)

---

Access the Zotero library

Description

The function uses information stored in the 'zotero' list to access specified collections and items in the Zotero library

Usage

ZoteroLibrary(
  zotero,
  case.insensitive = TRUE,
  ancestor = FALSE,
  recursive = FALSE,
  create = FALSE,
  limit = 100,
  start = 0,
  search.collections = TRUE,
  get.collections = TRUE,
  get.items = TRUE,
  item.type = NULL,
  all.results = TRUE,
  max.results = NULL,
  library.type = NULL,
  linkwrap = 1,
  style = "apa",
  locale = "en-US",
  force = FALSE,
  silent = FALSE
)

Arguments

zotero	A list with information on the specified Zotero library (e.g., id, API key, collections, and items)
case.insensitive	Disregard letter casing when searching for collections, Default: TRUE
ancestor	Trace the lineage of a collection (i.e., find the top-level collection), Default: FALSE
recursive	Find all nested collections, Default: FALSE
create	Create missing collections, Default: FALSE
limit	Number of results per query (max 100), Default: 100
start	Starting position of query (0 = first result), Default: 0
search.collections	Search all collections if collection.key fails, Default: TRUE
get.collections	Fetch collections, Default: TRUE
get.items	Fetch items, Default: TRUE
item.type	Items to search for (NULL = everything), Default: NULL
all.results	Find all results in query, Default: TRUE
max.results	Do you need a limit?, Default: NULL
library.type	Commma-separated data from Zotero (i.e., data, bib, citation), Default: NULL
linkwrap	Set URL (e.g., DOI) as HTML link (1 = yes), Default: 1
style	Citation style to use for appended bibliography and/or citations, Default: apa
locale	Desired language format of bibliography, Default: 'en-US'
force	Force is seldom wise, but sometimes..., Default: FALSE
silent	c2z is noisy, tell it to be quiet, Default: FALSE

Details

Please see https://oeysan.github.io/c2z/

Value

A list with information on the specified Zotero library (e.g., collections and items)

See Also

toJSON, fromJSON distinct, arrange tibble

Examples

# Access the default group library
  example <- ZoteroLibrary(
    Zotero(
      user = FALSE,
      id = "4827927",
      api = "RqlAmlH5l1KPghfCseAq1sQ1"
    )
  )
  # Print index using `ZoteroIndex`
  if (any(nrow(example$items))) {
    ZoteroIndex(example$items) |>
      dplyr::select(name) |>
      print(width = 80)
  }

---

Search or match items using CrossRef

Description

Use the CrossRef API to match data (e.g., Cristin metadata with Crossref metadata) or search by title, authors and date

Usage

ZoteroMatch(
  title,
  authors,
  date,
  haystack = NULL,
  haystack.size = 3,
  crossref.search = FALSE,
  autosearch = FALSE,
  cristin.data = NULL,
  external.data = NULL,
  polite = TRUE,
  silent = FALSE,
  prefer.semantic = FALSE,
  log = list()
)

Arguments

title	Title of reference
authors	creators of the reference
date	publication date of the reference
haystack	Potential matches for search term (i.e., needle), Default: NULL
haystack.size	Number of items in the haystack, Default: 3
crossref.search	Search CrossRef if needle not found in haystack, Default: FALSE
autosearch	Match automatically or compare needle with haystack, Default: FALSE
cristin.data	Metadata from Cristin, Default: NULL
external.data	Metadata from external source (e.g., CrossRef), Default: NULL
polite	Will use an email stored in '.Renviron', Default: TRUE
silent	Running silent, running deep, Default: FALSE
prefer.semantic	Prefer metadata from Semantic Scholar, Default: FALSE
log	A list for storing log elements, Default: list()

Details

Please see https://oeysan.github.io/c2z/

Value

A Zotero-type matrix (tibble) if match is found otherwise NULL

See Also

select, reexports, mutate, coalesce, pull sym RETRY toJSON, fromJSON adist, head map

Examples

# Conduct an autosearch in CrossRef using title, authors and date
  example <- ZoteroMatch(
    title = "Nonreplicable publications",
    authors = "Serra-Garcia & Gneezy",
    date = "2021",
    autosearch = TRUE
  )

  # Print index using `ZoteroIndex`
  if (any(nrow(example$data))) {
  ZoteroIndex(example$data) |>
    dplyr::select(name) |>
    print(width = 80)
  }

---

Post collections and items to a Zotero library

Description

Create or update collections and items in a specified library

Usage

ZoteroPost(
  zotero,
  post.collections = TRUE,
  post.items = TRUE,
  post.attachments = TRUE,
  post.limit = 50,
  force = FALSE,
  silent = FALSE
)

Arguments

zotero	A list with information on the specified Zotero library (e.g., id, API key, collections, and items)
post.collections	Try to copy specified collections, Default: TRUE
post.items	Try to copy specified items?, Default: TRUE
post.attachments	Try to copy specified extras (i.e., attachments and notes)?, Default: TRUE
post.limit	Number of collections/items to post per request (max 50), Default: 50
force	Force is seldom wise, but sometimes..., Default: FALSE
silent	c2z is noisy, tell it to be quiet, Default: FALSE

Details

Please see https://oeysan.github.io/c2z/

Value

A list with information on the specified Zotero library (e.g., posted collections and items)

See Also

select, bind, mutate add_headers, RETRY toJSON, fromJSON as_tibble, add_column stack setNames

Examples

# Connect to the public group "c2z_delete"
  # NB! This process can be done using only `Zotero` (see README)
  zotero <- Zotero(
    user = FALSE,
    id = "4988497",
    api = "RqlAmlH5l1KPghfCseAq1sQ1"
  )

  # Create a new collection for POST
  zotero$collections <- tibble::tibble(
    key = ZoteroKey(),
    version = 0,
    name = "Post-test",
    parentCollection = "FALSE"
  )

  # Add item to post using `ZoteroAdd` (and `ZoteroDoi`)
  zotero <- ZoteroAdd(
    zotero,
    doi = "10.1126/sciadv.abd1705"
  )

  # Post a DOI to the public group "c2z_delete"
  post.example <- ZoteroPost(
    zotero,
    post.collections = TRUE,
    post.items = TRUE
  )

  # Delete collections and items using `ZoteroDelete`
  delete.example <- ZoteroDelete(
    post.example,
    delete.collections = TRUE,
    delete.items = TRUE
  )

  # Print index using `ZoteroIndex`
  if (any(nrow(post.example$items))) {
    ZoteroIndex(post.example$items) |>
      dplyr::select(name) |>
      print(width = 80)
  }

---

List with empty zotero-items

Description

Each tibble in the list represents a zotero-item

Usage

ZoteroTypes(type = NULL, names = TRUE)

Arguments

type	Type of zotero-item, Default: NULL
names	return only column names if set to TRUE, Default: TRUE

Format

A list with 36 tibbles with zero rows and various columns

Details

Used to create Zotero-items from list of metadata

Value

Either list of zotero-items or specified item

Examples

# All zotero-items
names(ZoteroTypes())
# Column names of item-type `book`
ZoteroTypes("book")

---