Package 'biblioview'

Check Abstract Availability Across Providers for a Single DOI

Description

Debugging utility to query external APIs directly for a specific DOI and print abstract availability and character length.

Usage

check_doi_abstracts(doi, email_contact = Sys.getenv("POLITE_EMAIL"))

Arguments

doi	Character string. Raw or clean DOI (e.g., "10.1007/s10452-015-9564-x").
email_contact	Character. Contact email for API headers.

Value

A named list of retrieved abstracts (or NULL per provider).

Examples

# 1. PLOS ONE: "phyloseq: An R Package for Reproducible Interactive Analysis..."
check_doi_abstracts("10.1371/journal.pone.0061217")

# 2. Journal of Statistical Software: "Data Validation Infrastructure for R" (validate package)
check_doi_abstracts("10.18637/jss.v097.i10")

# 3. PLOS ONE: "Dose-Response Analysis Using R" (drc package)
check_doi_abstracts("10.1371/journal.pone.0146021")

---

Clean and Normalize DOI Strings

Description

Strips common URL prefixes (including bare 'doi.org/'), leading/trailing whitespace, and verifies that the resulting string follows standard DOI format.

Usage

clean_doi_string(raw_doi)

Arguments

raw_doi

Character string containing a raw DOI or DOI URL.

Value

Character string containing the clean DOI (e.g., "10.1579/..."), or NULL if input is invalid or missing the '10.' prefix.

---

Enrich Missing Abstracts from External Metadata APIs

Description

Enrich Missing Abstracts from External Metadata APIs

Usage

enrich_missing_abstracts(
  df,
  email_contact = Sys.getenv("POLITE_EMAIL"),
  providers = list(epmc = fetch_abstract_epmc, crossref = fetch_abstract_crossref,
    openalex = fetch_abstract_openalex)
)

Arguments

df	A data frame generated by fetch_all_zotero_data.
email_contact	Character. Valid email address for polite API pools. Defaults to the environment variable POLITE_EMAIL.
providers	Named list of provider fetcher functions executed in list order. Defaults to Europe PMC -> OpenAlex -> Crossref.

Value

Data frame with updated Abstract column where matches were found.

Examples

## Not run: 
# Default usage (Europe PMC -> OpenAlex -> Crossref)
df_enriched <- enrich_missing_abstracts(df = my_zotero_df)

# Custom provider order: OpenAlex primary, Europe PMC secondary
custom_order <- list(
  openalex = fetch_abstract_openalex,
  epmc     = fetch_abstract_epmc
)

df_enriched <- enrich_missing_abstracts(
  df = my_zotero_df,
  providers = custom_order
)

## End(Not run)

---

Extract and Normalize DOI from Zotero Item Data

Description

Inspects a Zotero item's metadata list for a DOI, checking the primary DOI field first, followed by the extra field if necessary. Automatically normalizes URL prefixes and validates the '10.' prefix structure.

Usage

extract_doi(data)

Arguments

data	List. The data element of a Zotero API item list (e.g., item$data).

Value

Clean character string containing the DOI, or NULL if no valid DOI is found.

---

Extract 4-Digit Year from Raw Zotero Date Fields safely

Description

Extract 4-Digit Year from Raw Zotero Date Fields safely

Usage

extract_zotero_year(date_vec)

Arguments

date_vec

Character vector or list item containing raw date string(s).

Value

Character vector of 4-digit years (or NA_character_).

---

Extract Year from Zotero Date Fields (including BCE / Ancient Dates)

Description

Extract Year from Zotero Date Fields (including BCE / Ancient Dates)

Usage

extract_zotero_year_extended(date_vec)

Arguments

date_vec

Character vector of raw date strings from Zotero.

Value

Character vector containing year strings (e.g., "2024", "384 BCE", "-0383", or NA).

---

Fetch Abstract from Crossref

Description

Fetch Abstract from Crossref

Usage

fetch_abstract_crossref(doi, req_template)

Arguments

doi	Clean DOI string.
req_template	httr2 base request.

Value

Character string containing abstract or NULL if not found.

---

Fetch Abstract from Europe PMC API

Description

Queries Europe PMC for an article's abstract using its DOI. Requires resultType = "core" in the query parameters to ensure abstract text is included.

Usage

fetch_abstract_epmc(encoded_doi, base_req)

Arguments

encoded_doi	Character string. Clean or URL-encoded DOI.
base_req	An httr2 request object configured with user-agent/headers.

Value

Character string containing abstract text, or NULL if not found.

---

Fetch Abstract from OpenAlex

Description

Fetch Abstract from OpenAlex

Usage

fetch_abstract_openalex(doi, req_template)

Arguments

doi	Clean DOI string.
req_template	httr2 base request.

Value

Character string containing abstract or NULL if not found.

---

Fetch Abstract from Semantic Scholar

Description

Fetch Abstract from Semantic Scholar

Usage

fetch_abstract_semanticscholar(doi, base_req)

Arguments

doi	Clean DOI string.
base_req	httr2 base request.

Value

Character string containing abstract or NULL if not found.

---

Fetch All Data from a Zotero Group Library

Description

Loops through specified or all collections in a Zotero group library, retrieves their items, formats them into a tabular structure, and appends the collection name.

Usage

fetch_all_zotero_data(group_id, api_key, collection_id = NULL)

Arguments

group_id	Character or numeric. The target Zotero Group ID.
api_key	Character. Your secret Zotero Web API v3 key.
collection_id	Optional character vector. Unique Zotero collection keys (hashes) to pull down. If NULL (default), all collections in the library are processed.

Value

A data frame containing structured reference data with columns: Sub_Collection, Authors, Year, Title, DOI, APA_Citation, and Abstract.

---

Fetch Citation Counts from OpenAlex via Batch Queries

Description

Scans a data frame for a DOI column, extracts all valid identifiers, and queries the OpenAlex API in batches of up to 50 items to retrieve up-to-date citation metrics (cited_by_count). The results are joined back to the original data frame under a new citations column.

Usage

fetch_citation_counts(df, email_contact = Sys.getenv("POLITE_EMAIL"))

Arguments

df	A data frame containing bibliographic data, typically generated by fetch_all_zotero_data().
email_contact	Character string containing the contact email used to gain entry to the OpenAlex "Polite Pool." Defaults to the system environment variable Sys.getenv("POLITE_EMAIL").

Value

A data frame identical to the input, but with an added integer column named citations containing the citation metrics. Rows with missing or unmatched DOIs will default to NA.

Examples

## Not run: 
enriched_data <- fetch_citation_counts(raw_data)

## End(Not run)

---

Fetch All Items Within a Specific Zotero Collection

Description

Handles paginated API requests (100 items per page) to retrieve all top-level items from a specific Zotero collection key.

Usage

fetch_collection_items(group_id, api_key, collection_key)

Arguments

group_id	Character or numeric. The target Zotero Group ID.
api_key	Character. Your secret Zotero Web API v3 key.
collection_key	Character. The unique alphanumeric key for the sub-collection.

Value

A data frame of processed items belonging to the collection.

---

Fetch Bibliography Metadata in RIS Format from Crossref

Description

Takes a vector of DOIs and retrieves their bibliographic data formatted as RIS using Crossref Content Negotiation. Includes robust error handling and automatic retry logic for network rate-limiting.

Usage

fetch_ris_from_crossref(dois, email = NULL)

Arguments

dois	Character vector of DOIs.
email	Optional email address for Crossref's polite pool (recommended).

Value

A character vector of RIS formatted entries.

See Also

write_ris()

Examples

## Not run: 
ris <- fetch_ris_from_crossref(
  dois = c("10.1016/j.ecolmodel.2020.109282", "10.1111/gcb.15000"),
  email = "[email protected]"
)
write_ris(ris, "export.ris")

## End(Not run)

---

Fetch Sub-Folders (Collections) from a Zotero Group

Description

Connects to the Zotero API and retrieves a named vector of all sub-folders (collections) within the specified group library.

Usage

fetch_zotero_collections(group_id, api_key)

Arguments

group_id	Character or numeric string containing the Zotero Group ID.
api_key	Character string containing the Zotero API access key.

Value

A named character vector where the values are the unique Zotero collection hashes (e.g., "A8F3X2Z9") and the names are the human-readable folder titles (e.g., "Marine Biology"). Returns an empty vector if no folders exist.

Examples

## Not run: 
folders <- fetch_zotero_collections("1234567", "your_api_key")

## End(Not run)

---

Format DOI and URL Columns into Clickable HTML Anchors

Description

Scans a data frame for columns matching "doi" or "url" (case-insensitive) and transforms their string values into active HTML anchor tags (<a href="...">). It automatically protects existing full URLs inside the DOI column from being duplicated with the DOI resolver prefix.

Usage

format_hyperlinks(df)

Arguments

df	A data frame containing bibliographic data, typically generated by fetch_all_zotero_data().

Value

A data frame with the matched identifier columns transformed into HTML link strings.

Examples

## Not run: 
# Assuming raw_data contains columns named 'DOI' and 'url'
clean_df <- format_hyperlinks(raw_data)

## End(Not run)

---

Launch the Biblioview Dashboard Locally

Description

Launch the Biblioview Dashboard Locally

Usage

launch_dashboard(group = NULL, key = NULL, folder = NULL, title = NULL)

Arguments

group	Optional character string containing a default Zotero Group ID.
key	Optional character string containing a default Zotero API Key.
folder	Optional character string containing a sub-collection (folder) of the group library.
title	Optional character string to override the default portal header title.

---

Create Standard Biblioview DataTable

Description

Handles hyperlink formatting, JS tooltips, column truncation, and export button configurations uniformly.

Usage

render_biblioview_table(df, title = "export", show_buttons = TRUE)

Arguments

df	Data frame containing reference entries.
title	Character. Export filename prefix.
show_buttons	Logical. Include Copy/CSV/Excel export buttons.

---

Sync Missing Abstracts Back to Zotero API

Description

Scans a Zotero group library (or specific collections) for top-level items missing abstracts, fetches them from external APIs, sanitizes formatting, and writes them back to Zotero.

Usage

sync_missing_abstracts_to_zotero(
  group_id,
  api_key,
  collections = NULL,
  force_overwrite = FALSE,
  email_contact = Sys.getenv("POLITE_EMAIL"),
  providers = list(epmc = fetch_abstract_epmc, crossref = fetch_abstract_crossref,
    openalex = fetch_abstract_openalex)
)

Arguments

group_id	Character or Numeric. The Zotero Group ID.
api_key	Character. A Zotero API key with write access to the group.
collections	Character vector (optional). One or more Zotero folder/collection names. If NULL (default), scans the entire group library.
force_overwrite	Logical. If TRUE, re-fetches and overwrites pre-existing abstracts. Defaults to FALSE.
email_contact	Character. Contact email used for polite external API pools. Defaults to environment variable POLITE_EMAIL.
providers	Named list of provider functions passed to external APIs.

Value

A named list containing summary statistics of the sync operation and details on any unresolvable items.

---

Export RIS Entries to File

Description

Writes a character vector of RIS records to a file.

Usage

write_ris(ris_data, file)

Arguments

ris_data	Character vector of RIS records (e.g. from fetch_ris_from_crossref).
file	Path to the destination file.

Value

The file path invisibly.

See Also

fetch_ris_from_crossref()

---

Convert Zotero Item Data to Simplified Plain-Text APA 7 Format

Description

Parses Zotero JSON items across articles, books, chapters, reports, and webpages, enforcing APA 7th rules without rich text (no italics or bolding).

Usage

zotero_to_apa(item)

Arguments

item	List. A single raw item element from the Zotero JSON API.

Value

A single-row data frame with standardized bibliographic columns.

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