Package 'scimetr'

scimetr: Analysis of Scientific Publication Data with R

Description

Tools for quantitative research in scientometrics and bibliometrics. This package provides routines for importing bibliographic data from Clarivate Web of Science (https://www.webofscience.com/wos/) and performing bibliometric analysis. For more information visit https://rubenfcasal.github.io/scimetr/articles/scimetr.html.

Author(s)

Maintainer: Ruben Fernandez-Casal [email protected] (ORCID)

Authors:

• Borja Lafuente-Rego [email protected] (ORCID)

• Maria Jose Lombardia [email protected] (ORCID)

• Javier Tarrio-Saavedra [email protected] (ORCID)

• Julian Costa-Bouzas [email protected] (ORCID)

Other contributors:

• Yesica Fernandez-Ramos [email protected] [contributor]

• Guillermo Lopez-Taboada [email protected] [contributor]

See Also

Useful links:

• https://rubenfcasal.github.io/scimetr/

• https://github.com/rubenfcasal/scimetr/

• Report bugs at https://github.com/rubenfcasal/scimetr/issues/

---

Add JCR data to a bibliographic database

Description

Extends the bibliographic database by adding JCR metrics to sources, per year and WoS category.

Usage

add_jcr(db, jcrdb)

## S3 method for class 'wos.jcr'
plot(
  x,
  filter,
  plot = TRUE,
  all = FALSE,
  ask = plot && all && interactive(),
  ...
)

Arguments

db	a bibliographic database (a wos.db object; typically the output of the function db_bib()).
jcrdb	a JCR database (a jcr.db object; typically the output of the function db_jcr()).
x	a wos.jcr object.
filter	vector of document identifiers (usually a result of get_id_docs()).
plot	logical; if TRUE (default), the plots are drawn, otherwise only the ggplot2 object is (invisibly) returned.
all	logical; if TRUE, function plot.wos.db() is called (additional parameters ... are passed to this function), otherwise only a JCR metrics plot is generated.
ask	logical; if TRUE, the user is asked before each plot (see par(ask=.)).
...	further arguments passed to or from other methods.

Value

An S3 object of class wos.jcr. A wos.db object with additional components JCRSour and JCRCatSour.

See Also

db_bib, db_jcr.

---

Bibliographic data base creation

Description

db_bib.wos.data() converts a data.frame with WoS variables (as returned by import_wos; see wosdf) into a relational database (a list of data.frames).

Usage

db_bib(data, ...)

## S3 method for class 'wos.data'
db_bib(data, label = "", progress = interactive(), verbose = FALSE, ...)

## S3 method for class 'wos.db'
print(x, ...)

## S3 method for class 'wos.db'
plot(
  x,
  filter,
  which = 1:3,
  plot = TRUE,
  warning = FALSE,
  ask = plot && (length(which) > 1) && interactive(),
  ...
)

Arguments

data	a data.frame with bibliographic data.
...	further arguments passed to or from other methods.
label	character string describing the data.
progress	logical; if TRUE the progress is printed.
verbose	logical; if TRUE additional information is printed.
x	an object used to select a method.
filter	vector of document identifiers (usually a result of get_id_docs).
which	if a subset of the plots is required, specify a subset of the numbers 1:3.
plot	logical; if TRUE (default), the plots are drawn, otherwise only the list of ggplot2 objects is (invisibly) returned.
warning	logical; if FALSE (default), warnings are ignored.
ask	logical; if TRUE, the user is asked before each plot (see par(ask=.)).

Value

An S3 object of class wos.db. A list with the following components:

• Docs: document-level records (year, type, citations, identifiers).

• Authors and AutDoc: author dictionary and document-author links.

• OI and OIDoc: ORCID identifiers and their linkage to documents.

• RI and RIDoc: ResearcherID identifiers and their linkage to documents.

• Affiliations and AffDoc: affiliation dictionary and document links.

• Addresses and AddAutDoc: address and document-author-address links.

• Sources: document sources (journals, books, proceedings, ...).

• Categories, Areas, CatSour and AreaSour: thematic classifications and their linkage to sources.

• WSIndex and SourWSI: Web of Science indexes and their linkage to sources.

• label and date: metadata that helps tracking the dataset identity over time.

This object has specialized print and plot methods.

See Also

wosdf, import_wos.

summary.wos.db.

plot.summary.wos.db, plot.summary.year.wos

Examples

db <- db_bib(wosdf)
print(db)
summary(db)

---

Import JCR data from Web of Science (WoS)

Description

Reads JCR data from excel files downloaded from WoS and generates a relational database (a list of data.frames). It is assumed that the file name format is JCR_[WE]_[PY], where [WE] is the WoS index (SCIE, SSCI, ...) and [PY] the JCR year.

Usage

db_jcr(path = ".", files = dir(path, pattern = "*.xlsx"), verbose = TRUE)

Arguments

path	character; path to the directory containing the files. Defaults to the working directory.
files	character vector with the file names. Defaults to filenames in directory path with extension .xlsx".
verbose	logical; indicating whether the name of the file being processed is printed. Defaults to TRUE.

Details

A subscription to Web of Science is required to download JCR data. For successful execution, Excel files must retain the original header fields from Clarivate exports: Title20, ISO_ABBREV, TITLE, ISSN, EISSN, ISSUES/YEAR, COUNTRY, LANGUAGE, ⁠1ST_YR_PUB⁠, categories, TOT_CITES, CITES_JCR_YR, CITES_JCR_YR1, CITES_JCR_YR2, IF_NUMERATOR, CITES_JCR_YR3, CITES_JCR_YR4, CITES_JCR_YR5, ⁠5YR_IF_NUMERATOR⁠, ITEMS_JCR_YR, ITEMS_JCR_YR1, ITEMS_JCR_YR2, IF_DENOMINATOR, ITEMS_JCR_YR3, ITEMS_JCR_YR4, ITEMS_JCR_YR5, ⁠5YR_IF_DENOMINATOR⁠, IMPACT_FACTOR, IMMEDIACY_INDEX, CITED_HALF_LIFE, ⁠5YR_IMPACT_FACTOR⁠, EIGENFACTOR, NORM_EIGENFACTOR, ARTL_INFLUENCE, FREQUENCY, PUBCODE, PUBLISHER_NAME, CATEGORY_CODE, CATEGORY_DESCRIPTION, CATEGORY_RANKING, QUARTILE_RANK, JIF_PERCENTILE.

Value

An S3 object of class jcr.db. A list with components: Sources, Categories, JCRSour and JCRCatSour.

See Also

db_bib, add_jcr.

---

Mathematics UDC 2018-2023 bibliographic database

Description

Bibliographic database with JCR metrics (a wos.jcr S3 object) corresponding to a WoS search by the Affiliation field of Universidade da Coruña (UDC) in the research area "Mathematics" during the years 2018–2023 (generated fom wosdf data set, using the functions db_bib, db_jcr and add_jcr).

Usage

dbjcr

Format

An object of class wos.jcr (inherits from wos.db) of length 22.

---

Get table identifiers

Description

Retrieve internal identifiers (entity keys) for the corresponding relational table (authors, sources, categories, areas, ...). Any field in the target table can be used as a condition, and multiple conditions are combined with & (only IDs for which all conditions evaluate to TRUE are returned). Tidy evaluation can be used to construct the logical expressions, see dplyr::filter().

Usage

get_id_docs(
  db,
  ...,
  id_sources,
  id_authors,
  id_addresses,
  id_oi,
  id_ri,
  id_affiliations
)

get_id_authors(db, ...)

get_id_addresses(db, ...)

get_id_areas(db, ...)

get_id_categories(db, ...)

get_id_wsi(db, ...)

get_id_sources(db, ..., id_categories, id_areas, id_wsi)

get_id_oi(db, ...)

get_id_ri(db, ...)

get_id_affiliations(db, ...)

Arguments

db	Object of class wos.db, as returned by db_bib.
...	Logical predicates. Multiple conditions are combined with & (see filter).
id_sources	optional; sources identifiers.
id_authors	optional; author identifiers (values of db$Authors$ids).
id_addresses	optional; addresses identifiers.
id_oi	optional; ORCID identifiers or codes (values of db$OI$OI).
id_ri	optional; RI identifiers or codes (values of db$RI$RI).
id_affiliations	optional; affiliations identifiers or names (values of db$Affiliations$C3).
id_categories	optional; categories identifiers or names (values of db$Categories$WC)
id_areas	optional; research area identifiers or names (values of db$Areas$SC)
id_wsi	optional; WoS Index identifiers or names (values of db$WSI$WE)

Value

An integer vector of identifiers. For instance, get_id_docs returns the document identifiers (values of the db$Docs$idd variable) corresponding to identifiers of authors, categories, areas, addresses and/or sources. Logical expressions defined in terms of the variables in db$Docs can also be used as arguments.

See Also

db_bib, filter.

---

Get JCR metrics

Description

get_jcr() combines document indexes with their source JCR metrics per year.

get_jcr_cat() combines document indexes with their source JCR metrics per year and WoS category.

Usage

get_jcr(db, filter)

get_jcr_cat(db, filter, best = TRUE)

Arguments

db	a bibliographic database with JCR information (a wos.jcr object; typically the output of the function add_jcr()).
filter	vector of document identifiers (usually a result of get_id_docs()).
best	logical; if TRUE (default), only the results for the WoS category with the best ranking for each document are returned.

Value

A data.frame with document indexes and their source JCR metrics.

See Also

add_jcr(), db_jcr(), db_bib().

Examples

head(get_jcr(dbjcr))
head(get_jcr_cat(dbjcr, best = TRUE))

---

Import bibliographic data downloaded from Web of Science (WoS).

Description

Reads bibliography entries from UTF-8 encoded Tab-delimited files containing "Full Record and Cited References" (see wosdf and vignette Downloading data from the Web of Science).

Usage

import_wos(path = ".", pattern = "*.txt", all = TRUE, progress = NULL)

Arguments

path	character; path to the directory containing the files.
pattern	regular expression; only matching files will be loaded. Defaults to "*.txt".
all	logical; indicating whether sources without ISSN are included (TRUE) or not (FALSE) in the result. Defaults to TRUE.
progress	logical; indicating whether a progress bar should be displayed. Defaults to TRUE when R is used interactively and there is more than one file, and FALSE otherwise.

Details

A subscription to Web of Science is required to download bibliometric data.

Value

A data.frame with rows corresponding to sources and columns to WoS variables.

See Also

wosdf, db_bib().

---

Summaries per year

Description

The summary_year methods return summaries by year of a bibliometric database.

Usage

summary_year(object, ...)

## S3 method for class 'wos.db'
summary_year(object, filter, ...)

## S3 method for class 'summary.year.wos'
print(x, ...)

## S3 method for class 'summary.year.wos'
plot(
  x,
  which = 1:3,
  boxplot = FALSE,
  plot = TRUE,
  ask = plot && length(which) > 1 && interactive(),
  ...
)

## S3 method for class 'wos.jcr'
summary_year(object, filter, all = FALSE, ...)

## S3 method for class 'summary.year.jcr'
print(x, digits = 3, all = TRUE, ...)

## S3 method for class 'summary.year.jcr'
plot(x, plot = TRUE, all = FALSE, ask = plot && interactive(), ...)

Arguments

object	an object for which a summary is desired.
...	further arguments passed to or from other methods.
filter	vector of document identifiers (optional, usually a result of get_id_docs).
x	an object used to select a method.
which	if a subset of the plots is required, specify a subset of the numbers 1:3.
boxplot	logical; if TRUE, boxplots are drawn (for plots from 2 to 3).
plot	logical; if TRUE (default), the plots are drawn, otherwise only the list of ggplot2 objects is (invisibly) returned.
ask	logical; if TRUE, the user is asked before each plot, see par(ask=.).
all	logical; if TRUE, the corresponding wos.db method is called (additional parameters ... are passed to it), otherwise only results of JCR metrics are returned.
digits	minimal number of significant digits, see print.default.

Value

A list of summary statistics (an object of class summary.year.wos and/or summary.year.jcr), which has specialized print() and plot() methods.

See Also

db_bib(), add_jcr().

Examples

# Bibliographic database
db <- db_bib(wosdf)
summary_year(db)
# Bibliographic database with JCR metrics
summary_year(dbjcr)

---

Summaries of a bibliographic database

Description

summary() methods for bibliometric databases.

Usage

## S3 method for class 'wos.db'
summary(object, filter, index = c("H", "G"), nmax = 10, ...)

## S3 method for class 'summary.wos.db'
print(x, ...)

author_metrics(db, id_authors)

## S3 method for class 'summary.wos.db'
plot(
  x,
  which = 1:5,
  pie = FALSE,
  others = !pie,
  accuracy = 0.1,
  plot = TRUE,
  ask = length(which) > 1 && interactive(),
  ...
)

## S3 method for class 'wos.jcr'
summary(object, filter, all = FALSE, ...)

## S3 method for class 'summary.wos.jcr'
print(x, digits = 2, all = TRUE, ...)

## S3 method for class 'summary.wos.jcr'
plot(x, plot = TRUE, all = FALSE, ask = plot && all && interactive(), ...)

Arguments

object	an object for which a summary is desired.
filter	vector of document identifiers (optional, usually a result of get_id_docs()).
index	citation indexes.
nmax	number of top levels.
...	further arguments passed to or from other methods.
x	an object used to select a method.
db	Object of class wos.db, as returned by db_bib.
id_authors	optional; author identifiers
which	if a subset of the plots is required, specify a subset of the numbers 1:5.
pie	logical; if TRUE, pie charts are drawn.
others	logical; if FALSE, only nmax top levels categories are shown.
accuracy	numerical scalar; see label_number(accuracy=.).
plot	logical; if TRUE (default), the plots are drawn, otherwise only the list of ggplot2 objects is (invisibly) returned.
ask	logical; if TRUE, the user is asked before each plot, see par(ask=.).
all	logical; if TRUE, the corresponding wos.db method is called (additional parameters ... are passed to it), otherwise only results of JCR metrics are returned.
digits	minimal number of significant digits, see print.default.

Value

A list of summary statistics (an object of class summary.wos.db and/or summary.wos.jcr), which has specialized print() and plot() methods.

See Also

db_bib(), add_jcr().

Examples

# Bibliographic database
db <- db_bib(wosdf)
summary(db)
# Bibliographic database with JCR metrics
summary(dbjcr)

---

Mathematics UDC WoS Core Collection 2018-2023 data

Description

The data set consists of 293 publications corresponding to a WoS search by the Affiliation field of Universidade da Coruña (UDC) (Affiliation: OG = Universidade da Coruna) in the research area "Mathematics" (SC = Mathematics), indexed in the Web of Science Core Collection:

• Science Citation Index Expanded (SCI-EXPANDED).

• Social Sciences Citation Index (SSCI).

• Arts & Humanities Citation Index (A&HCI).

in the years 2018-2023 (generated using the import_wos function).

Usage

wosdf

Format

A data frame with 293 rows and 48 columns:

PT

Publication Type

AU

Author

AF

Author Full Name

TI

Article Title

SO

Source Title

SE

Book Series Title

BS

Book Series Subtitle

LA

Language

DT

Document Type

C1

Address

C3

Affiliation

RI

Researcher Ids

OI

ORCID

NR

Cited Reference Count

TC

Times Cited, WoS Core

Z9

Times Cited, All Databases

U1

180 Day Usage Count

U2

Since 2013 Usage Count

PU

Publisher

PI

Publisher City

PA

Publisher Address

SN

ISSN

EI

eISSN

BN

ISBN

J9

Journal Abbreviation

JI

Journal ISO Abbreviation

PD

Publication Date

PY

Publication Year

VL

Volume

IS

Issue

PN

Part Number

SU

Supplement

SI

Special Issue

MA

Meeting Abstract

BP

Start Page

EP

End Page

AR

Article Number

DI

DOI

D2

Book DOI

EA

Early Access Date

PG

Number of Pages

WC

WoS Category

WE

Web of Science Index

SC

Research Area

HC

Highly Cited Status

HP

Hot Paper Status

DA

Date of Export

UT

Unique WOS ID

Source

Clarivate Web of Science: https://www.webofscience.com/wos/.

See Also

import_wos, db_bib

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