Package ‘bibliometrix’

October 9, 2018
Type Package
Title An R-Tool for Comprehensive Science Mapping Analysis
Version 2.0.1
Date 2018-10-09
Description Tool for quantitative research in scientometrics and bibliometrics.
It provides various routines for importing bibliographic data from SCO-
PUS (<http://scopus.com>),
Clarivate Analytics Web of Science (<http://www.webofknowledge.com/>), Cochrane Li-
brary (<http://www.cochranelibrary.com/>)
and PubMed (<https://www.ncbi.nlm.nih.gov/pubmed/>) databases, performing bibliomet-
ric analysis
and building networks for co-citation, coupling, scientific collaboration and co-word analysis.
License GPL-3

URL http://www.bibliometrix.org
LazyData FALSE
Encoding UTF-8
Depends R (>= 3.3.0)
Imports stats, dplyr, DT, factoextra, FactoMineR, ggraph, ggplot2,
ggrepel, igraph, Matrix, networkD3, RColorBrewer, RISmed,
rscopus, shiny, shinycssloaders, shinythemes, SnowballC,
stringdist, stringr
Suggests knitr, rmarkdown,
RoxygenNote 6.1.0
NeedsCompilation no
Author Massimo Aria [cre, aut],
Corrado Cuccurullo [aut]
Maintainer Massimo Aria <[email protected]>
VignetteBuilder knitr,
Repository CRAN
Date/Publication 2018-10-09 12:50:03 UTC

1
2 R topics documented:

R topics documented:
bibliometrix-package . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
biblio . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
biblioAnalysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
biblioNetwork . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
biblioshiny . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
biblio_df . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
citations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
cochrane2df . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
cocMatrix . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
conceptualStructure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
convert2df . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
countries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
dominance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
duplicatedMatching . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
garfield . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Hindex . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
histNetwork . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
histPlot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
idByAuthor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
isi2df . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
isibib2df . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
isiCollection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
keywordAssoc . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
KeywordGrowth . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
localCitations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
lotka . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
mergeDbSources . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
metaTagExtraction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
networkPlot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
networkStat . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
normalizeSimilarity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
plot.bibliometrix . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
plotThematicEvolution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
pubmed2df . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
readFiles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
retrievalByAuthorID . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
rpys . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
scientometrics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
scientometrics_text . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
scopus2df . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
scopusCollection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
sourceGrowth . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
stopwords . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
summary.bibliometrix . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
summary.bibliometrix_netstat . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
tableTag . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
bibliometrix-package 3

termExtraction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
thematicEvolution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
thematicMap . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
timeslice . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
trim . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
trim.leading . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59

Index 61

bibliometrix-package An R-Tool for Comprehensive Science Mapping Analysis

Description
Tool for quantitative research in scientometrics and bibliometrics. It provides various routines for
importing bibliographic data from SCOPUS (<http://scopus.com>), Clarivate Analytics Web of Sci-
ence (<http://www.webofknowledge.com/>), Cochrane Library (<http://www.cochranelibrary.com/>)
and PubMed (<https://www.ncbi.nlm.nih.gov/pubmed/>) databases, performing bibliometric anal-
ysis and building networks for co-citation, coupling, scientific collaboration and co-word analysis.

Details
INSTALLATION
- Stable version from CRAN:
install.packages("bibliometrix")
- Or development version from GitHub:
install.packages("devtools") devtools::install_github("massimoaria/bibliometrix")
- Load "bibliometrix"
library(’bibliometrix’)
DATA LOADING AND CONVERTING
The export file can be read by R using the function *readFiles*: (An example from bibliometrix
vignettes)
D <- readFiles("http://www.bibliometrix.org/datasets/savedrecs.bib")
D is a large character vector. *readFiles* argument contains the name of files downloaded from
SCOPUS, Clarivate Analytics WOS, or Cochrane CDSR website.
The function *readFiles* combines all the text files onto a single large character vector. Further-
more, the format is converted into UTF-8.
es. D <- readFiles("file1.txt","file2.txt", ...)
The object D can be converted in a data frame using the function *convert2df*:
M <- convert2df(D, dbsource = "isi", format = "bibtex")
*convert2df* creates a bibliographic data frame with cases corresponding to manuscripts and vari-
ables to Field Tag in the original export file. Each manuscript contains several elements, such as
4 bibliometrix-package

authors’ names, title, keywords and other information. All these elements constitute the biblio-
graphic attributes of a document, also called metadata. Data frame columns are named using the
standard Clarivate Analytics WoS Field Tag codify.
BIBLIOMETRIC ANALYSIS
The first step is to perform a descriptive analysis of the bibliographic data frame. The function
*biblioAnalysis* calculates main bibliometric measures using this syntax:
results <- biblioAnalysis(M, sep = ";")
The function *biblioAnalysis* returns an object of class "bibliometrix".
To summarize main results of the bibliometric analysis, use the generic function *summary*. It dis-
plays main information about the bibliographic data frame and several tables, such as annual scien-
tific production, top manuscripts per number of citations, most productive authors, most productive
countries, total citation per country, most relevant sources (journals) and most relevant keywords.
*summary* accepts two additional arguments. *k* is a formatting value that indicates the number
of rows of each table. *pause* is a logical value (TRUE or FALSE) used to allow (or not) pause in
screen scrolling. Choosing k=10 you decide to see the first 10 Authors, the first 10 sources, etc.
S <- summary(object = results, k = 10, pause = FALSE)
Some basic plots can be drawn using the generic function plot:
plot(x = results, k = 10, pause = FALSE)
BIBLIOGRAPHIC NETWORK MATRICES
Manuscript’s attributes are connected to each other through the manuscript itself: author(s) to jour-
nal, keywords to publication date, etc. These connections of different attributes generate bipartite
networks that can be represented as rectangular matrices (Manuscripts x Attributes). Furthermore,
scientific publications regularly contain references to other scientific works. This generates a fur-
ther network, namely, co-citation or coupling network. These networks are analyzed in order to
capture meaningful properties of the underlying research system, and in particular to determine the
influence of bibliometric units such as scholars and journals.
*biblioNetwork* function
The function *biblioNetwork* calculates, starting from a bibliographic data frame, the most fre-
quently used networks: Coupling, Co-citation, Co-occurrences, and Collaboration. *biblioNet-
work* uses two arguments to define the network to compute: - *analysis* argument can be "co-
citation", "coupling", "collaboration", or "co-occurrences". - *network* argument can be "authors",
"references", "sources", "countries", "universities", "keywords", "author_keywords", "titles" and
"abstracts".
i.e. the following code calculates a classical co-citation network:
NetMatrix <- biblioNetwork(M, analysis = "co-citation", network = "references", sep = ". ")
VISUALIZING BIBLIOGRAPHIC NETWORKS
All bibliographic networks can be graphically visualized or modeled. Using the function *network-
Plot*, you can plot a network created by *biblioNetwork* using R routines.
The main argument of *networkPlot* is type. It indicates the network map layout: circle, kamada-
kawai, mds, etc.
In the following, we propose some examples.
### Country Scientific Collaboration
bibliometrix-package 5

# Create a country collaboration network

M <- metaTagExtraction(M, Field = "AU_CO", sep = ";")
NetMatrix <- biblioNetwork(M, analysis = "collaboration", network = "countries", sep = ";")
# Plot the network
net=networkPlot(NetMatrix, n = dim(NetMatrix)[1], Title = "Country Collaboration", type = "cir-
cle", size=TRUE, remove.multiple=FALSE,labelsize=0.8)
### Co-Citation Network
# Create a co-citation network
NetMatrix <- biblioNetwork(M, analysis = "co-citation", network = "references", sep = ". ")
# Plot the network
net=networkPlot(NetMatrix, n = 30, Title = "Co-Citation Network", type = "fruchterman", size=T,
remove.multiple=FALSE, labelsize=0.7,edgesize = 5)
### Keyword co-occurrences
# Create keyword co-occurrences network
NetMatrix <- biblioNetwork(M, analysis = "co-occurrences", network = "keywords", sep = ";")
# Plot the network
net=networkPlot(NetMatrix, normalize="association", weighted=T, n = 30, Title = "Keyword Co-
occurrences", type = "fruchterman", size=T,edgesize = 5,labelsize=0.7)
CO-WORD ANALYSIS: THE CONCEPTUAL STRUCTURE OF A FIELD
The aim of the co-word analysis is to map the conceptual structure of a framework using the word
co-occurrences in a bibliographic collection. The analysis can be performed through dimensionality
reduction techniques such as Multidimensional Scaling (MDS), Correspondence Analysis (CA) or
Multiple Correspondence Analysis (MCA). Here, we show an example using the function *concep-
tualStructure* that performs a CA or MCA to draw a conceptual structure of the field and K-means
clustering to identify clusters of documents which express common concepts. Results are plotted
on a two-dimensional map. *conceptualStructure* includes natural language processing (NLP) rou-
tines (see the function *termExtraction*) to extract terms from titles and abstracts. In addition, it
implements the Porter’s stemming algorithm to reduce inflected (or sometimes derived) words to
their word stem, base or root form.
# Conceptual Structure using keywords (method="CA")
CS <- conceptualStructure(M,field="ID", method="CA", minDegree=4, k.max=8, stemming=FALSE,
labelsize=10, documents=10)
HISTORICAL DIRECT CITATION NETWORK
The historiographic map is a graph proposed by E. Garfield to represent a chronological network
map of most relevant direct citations resulting from a bibliographic collection. The function histNet-
work generates a chronological direct citation network matrix which can be plotted using *histPlot*:
# Create a historical citation network
histResults <- histNetwork(M, n = 20, sep = ". ")
# Plot a historical co-citation network
net <- histPlot(histResults, size = FALSE,label=TRUE, arrowsize = 0.5)
6 biblio

Author(s)
Massimo Aria [cre, aut], Corrado Cuccurullo [aut]
Maintainer: Massimo Aria <[email protected]>

References
Aria, M. & Cuccurullo, C. (2017). *bibliometrix*: An R-tool for comprehensive science mapping
analysis, *Journal of Informetrics*, 11(4), pp 959-975, Elsevier, DOI: 10.1016/j.joi.2017.08.007
(https://doi.org/10.1016/j.joi.2017.08.007).
Cuccurullo, C., Aria, M., & Sarto, F. (2016). Foundations and trends in performance management.
A twenty-five years bibliometric analysis in business and public administration domains, *Sciento-
metrics*, DOI: 10.1007/s11192-016-1948-8 (https://doi.org/10.1007/s11192-016-1948-8).
Cuccurullo, C., Aria, M., & Sarto, F. (2015). Twenty years of research on performance management
in business and public administration domains. Presentation at the *Correspondence Analysis and
Related Methods conference (CARME 2015)* in September 2015 (http://www.bibliometrix.org/documents/2015Carme_cucc
Sarto, F., Cuccurullo, C., & Aria, M. (2014). Exploring healthcare governance literature: systematic
review and paths for future research. *Mecosan* (http://www.francoangeli.it/Riviste/Scheda_Rivista.aspx?IDarticolo=52780&
Cuccurullo, C., Aria, M., & Sarto, F. (2013). Twenty years of research on performance management
in business and public administration domains. In *Academy of Management Proceedings* (Vol.
2013, No. 1, p. 14270). Academy of Management (https://doi.org/10.5465/AMBPP.2013.14270abstract).

biblio Dataset of "Bibliometrics" scientific documents.

Description
The set of manuscripts which the title containing the word "bibliometrics" and published in a jour-
nal indexed by ISI WoK database.
Period: 2006 - 2015
Database: ISI Web of Knowledge

Format
A large character with 9014 rows.
Data has been imported by an ISI Export file in bibtex format using the function readLines.

Source
http://www.webofknowledge.com
biblioAnalysis 7

biblioAnalysis Bibliometric Analysis

Description
It performs a bibliometric analysis of a dataset imported from SCOPUS and Thomson Reuters’ ISI
Web of Knowledge databases.

Usage
biblioAnalysis(M, sep = ";")

Arguments
M is a bibliographic data frame obtained by the converting function convert2df.
It is a data matrix with cases corresponding to manuscripts and variables to Field
Tag in the original SCOPUS and Thomson Reuters’ ISI Web of Knowledge file.
sep is the field separator character. This character separates strings in each column
of the data frame. The default is sep = ";".

Value
biblioAnalysis returns an object of class "bibliometrix".
The functions summary and plot are used to obtain or print a summary and some useful plots of the
results.
An object of class "bibliometrix" is a list containing the following components:

Articles the total number of manuscripts

Authors the authors’ frequency distribution
AuthorsFrac the authors’ frequency distribution (fractionalized)
FirstAuthors first author of each manuscript
nAUperPaper the number of authors per manuscript
Appearances the number of author appearances
nAuthors the number of authors
AuMultiAuthoredArt the number of authors of multi-authored articles
MostCitedPapers The list of manuscripts sorted by citations
Years pubblication year of each manuscript
FirstAffiliation the affiliation of the first author
Affiliations the frequency distribution of affiliations (of all co-authors for each paper)
Aff_frac the fractionalized frequency distribution of affiliations (of all co-authors for each paper)
CO the affiliation country of the first author
Countries the affiliation countries’ frequency distribution
CountryCollaboration Intracountry (SCP) and intercountry (MCP) collaboration indices
TotalCitation the number of times each manuscript has been cited
TCperYear the yearly average number of times each manuscript has been cited
Sources the frequency distribution of sources (journals, books, etc.)
DE the frequency distribution of authors’ keywords
ID the frequency distribution of keywords associated to the manuscript bySCOPUS and Thomson Reu
8 biblioNetwork

See Also

convert2df to import and convert an ISI or SCOPUS Export file in a bibliographic data frame.
summary to obtain a summary of the results.
plot to draw some useful plots of the results.

Examples

data(scientometrics)

results <- biblioAnalysis(scientometrics)

summary(results, k = 10, pause = FALSE)

biblioNetwork Creating Bibliographic networks

Description

biblioNetwork creates different bibliographic networks from a bibliographic data frame.

Usage

biblioNetwork(M, analysis = "coupling", network = "authors",

sep = ";")

Arguments

M is a bibliographic data frame obtained by the converting function convert2df.

It is a data matrix with cases corresponding to manuscripts and variables to Field
Tag in the original SCOPUS and Thomson Reuters’ ISI Web of Knowledge file.
analysis is a character object. It indicates the type of analysis have to be performed.
analysis argument can be "collaboration", "coupling", "co-occurrences"
or "co-citation". Default is analysis = "coupling".
network is a character object. It indicates the network typology. The network aurgument
can be "authors", "references", "sources", "countries","keywords", "author_keywords",
"titles", or "abstracts". Default is network = "authors".
sep is the field separator character. This character separates strings in each column
of the data frame. The default is sep = ";".
biblioNetwork 9

Details
The function biblioNetwork can create a collection of bibliographic networks following the ap-
proach proposed by Batagely and Cerinsek (2013).

Typical networks output of biblioNetwork are:

#### Collaboration Networks ############

– Authors collaboration (analysis = "collaboration", network = "authors")
– University collaboration (analysis = "collaboration", network = universities")
– Country collabortion (analysis = "collaboration", network = "countries")

#### Co-citation Networks ##############

– Authors co-citation (analysis = "co-citation", network = "authors")
– Reference co-citation (analysis = "co-citation", network = "references")
– Source co-citation (analysis = "co-citation", network = "sources")

#### Coupling Networks ################

– Manuscript coupling (analysis = "coupling", network = "references")
– Authors coupling (analysis = "coupling", network = "authors")
– Source coupling (analysis = "coupling", network = "sources")
– Country coupling (analysis = "coupling", network = "countries")

#### Co-occurrences Networks ################

– Authors co-occurrences (analysis = "co-occurrences", network = "authors")
– Source co-occurrences (analysis = "co-occurrences", network = "sources")
– Keyword co-occurrences (analysis = "co-occurrences", network = "keywords")
– Author-Keyword co-occurrences (analysis = "co-occurrences", network = "author_keywords")
– Title content co-occurrences (analysis = "co-occurrences", network = "titles")
– Abstract content co-occurrences (analysis = "co-occurrences", network = "abstracts")

Value
It is a squared network matrix. It is an object of class dgMatrix of the package Matrix.

See Also
convert2df to import and convert a SCOPUS and Thomson Reuters’ ISI Web of Knowledge export
file in a data frame.
cocMatrix to compute a co-occurrence matrix.
biblioAnalysis to perform a bibliometric analysis.

Examples
# EXAMPLE 1: Authors collaboration network

# data(scientometrics)
10 biblio_df

# NetMatrix <- biblioNetwork(scientometrics, analysis = "collaboration",

# network = "authors", sep = ";")

# net <- networkPlot(NetMatrix, n = 30, type = "kamada", Title = "Collaboration",labelsize=0.5)

# EXAMPLE 2: Co-citation network

data(scientometrics)

NetMatrix <- biblioNetwork(scientometrics, analysis = "co-citation",

network = "references", sep = ";")

net <- networkPlot(NetMatrix, n = 30, type = "kamada", Title = "Co-Citation",labelsize=0.5)

biblioshiny Shiny UI for bibliometrix package

Description
biblioshiny performs science mapping analysis using the main functions of the bibliometrix pack-
age.

Usage
biblioshiny()

Examples

#biblioshiny()

biblio_df Dataset of "Bibliometrics" manuscripts.

Description
The set of manuscripts which the title containing the word "bibliometrics" and published in a jour-
nal indexed by ISI WoK database.
Period: 2006 - 2015
Database: ISI Web of Knowledge
citations 11

Format
#’ A data frame with 99 rows (manuscripts) and 16 variables (ISI tag field):
AU Authors
TI Document Title
SO Publication Name (or Source)
JI ISO Source Abbreviation
DT Document Type
DE Author Keywords
ID Keywords associated by ISI or SCOPUS database
AB Abstract
C1 Author Address
RP Reprint Address
CR Cited References
TC Times Cited
PY Year
SC Subject Category
UT Unique Article Identifier
DB Database

Source
http://www.webofknowledge.com

citations Citation frequency distribution

Description
It calculates frequency distribution of citations.

Usage
citations(M, field = "article", sep = ";")

Arguments
M is a bibliographic data frame obtained by the converting function convert2df.
It is a data matrix with cases corresponding to manuscripts and variables to Field
Tag in the original SCOPUS and Thomson Reuters’ ISI Web of Knowledge file.
field is a character. It can be "article" or "author" to obtain frequency distribution of
cited citations or cited authors (only first authors for ISI database) respectively.
The default is field = "article".
sep is the field separator character. This character separates citations in each string
of CR column of the bibiographic data frame. The default is sep = ";".
12 cochrane2df

Value
an object of class "list" containing the following components:

Cited the most frequent cited manuscripts or authors

Year the pubblication year (only for cited article analysis)
Source the journal (only for cited article analysis)

See Also
biblioAnalysis function for bibliometric analysis.
summary to obtain a summary of the results.
plot to draw some useful plots of the results.

Examples
## EXAMPLE 1: Cited articles

data(scientometrics)

CR <- citations(scientometrics, field = "article", sep = ";")

CR$Cited[1:10]
CR$Year[1:10]
CR$Source[1:10]

## EXAMPLE 2: Cited first authors

data(scientometrics)

CR <- citations(scientometrics, field = "author", sep = ";")

CR$Cited[1:10]

cochrane2df Convert a Cochrane Database Export file into a data frame

Description
It converts a Cochrane Database Export file and create a data frame from it, with cases correspond-
ing to articles and variables to Field Tag in the original file.

Usage
cochrane2df(D)
cocMatrix 13

Arguments
D is a character array containing data read from a ISI Export file (in plain text
format).

Value
a data frame with cases corresponding to articles and variables to Field Tag in the original ISI file.

See Also
scopus2df for converting SCOPUS Export file (in bibtex format)
Other converting functions: convert2df, isi2df, isibib2df, pubmed2df, scopus2df

Examples
# A group of Cochrane Database Export files can be read using \code{\link{readFiles}} function:

# largechar <- readFiles('filename1.txt','filename2.txt','filename3.txt')

# filename.txt is a Cochrane Database Export file in plain text format.

# scientometrics_text <- readFiles('http://www.bibliometrix.org/datasets/cochrane.txt')

# scient_df <- cochrane2df(cochrane_text)

cocMatrix Co-occurrence matrix

Description
cocMatrix computes co-occurences between elements of a Tag Field from a bibliographic data
frame. Manuscript is the unit of analysis.

Usage
cocMatrix(M, Field = "AU", type = "sparse", sep = ";",
binary = TRUE)

Arguments
M is a data frame obtained by the converting function convert2df. It is a data
matrix with cases corresponding to articles and variables to Field Tag in the
original ISI or SCOPUS file.
Field is a character object. It indicates one of the field tags of the standard ISI WoS
Field Tag codify. Field can be equal to one of this tags:

AU Authors
SO Publication Name (or Source)
14 cocMatrix

JI ISO Source Abbreviation

DE Author Keywords
ID Keywords associated by ISI or SCOPUS database
CR Cited References

for a complete list of filed tags see: Field Tags used in bibliometrix
type indicates the output format of co-occurrences:

type = "matrix" produces an object of class matrix

type = "sparse" produces an object of class dgMatrix of the package Matrix. "sparse" argument generates a compact

sep is the field separator character. This character separates strings in each column
of the data frame. The default is sep = ";".
binary is a logical. If TRUE each cell contains a 0/1. if FALSE each cell contains the
frequency.

Details
This co-occurrence matrix can be tranformed into a collection of compatible networks. Through
matrix multiplication you can obtain different networks. The fuction follows the approach pro-
posed by Batagely and Cerinsek (2013).

Value
a co-occurrence matrix with cases corresponding to manuscripts and variables to the objects ex-
tracted from the Tag Field.

See Also
convert2df to import and convert an ISI or SCOPUS Export file in a data frame.
biblioAnalysis to perform a bibliometric analysis.
biblioNetwork to compute a bibliographic network.

Examples
# EXAMPLE 1: Articles x Authors co-occurrence matrix

data(scientometrics)
WA <- cocMatrix(scientometrics, Field = "AU", type = "sparse", sep = ";")

# EXAMPLE 2: Articles x Cited References co-occurrence matrix

# data(scientometrics)

# WCR <- cocMatrix(scientometrics, Field = "CR", type = "sparse", sep = ";")

# EXAMPLE 3: Articles x Cited First Authors co-occurrence matrix

conceptualStructure 15

# data(scientometrics)
# scientometrics <- metaTagExtraction(scientometrics, Field = "CR_AU", sep = ";")
# WCR <- cocMatrix(scientometrics, Field = "CR_AU", type = "sparse", sep = ";")

conceptualStructure Creating and plotting conceptual structure map of a scientific field

Description
The function conceptualStructure creates a conceptual structure map of a scientific field per-
forming Correspondence Analysis (CA) or Multiple Correspondence Analysis (MCA) and Cluster-
ing of a bipartite network of terms extracted from keyword, title or abstract fields.

Usage
conceptualStructure(M, field = "ID", method = "MCA",
quali.supp = NULL, quanti.supp = NULL, minDegree = 2, k.max = 5,
stemming = FALSE, labelsize = 10, documents = 10, graph = TRUE)

Arguments
M is a data frame obtained by the converting function convert2df. It is a data
matrix with cases corresponding to articles and variables to Field Tag in the
original ISI or SCOPUS file.
field is a character object. It indicates one of the field tags of the standard ISI WoS
Field Tag codify. field can be equal to one of this tags:

ID Keywords Plus associated by ISI or SCOPUS database

DE Author’s keywords
ID_TM Keywords Plus stemmed through the Porter’s stemming algorithm
DE_TM Author’s Keywords stemmed through the Porter’s stemming algorithm
TI Terms extracted from titles
AB Terms extracted from abstracts

method is a character object. It indicates the factorial method used to create the facto-
rial map. Use method="CA" for Correspondence Analysis or method="MCA" for
Multiple Correspondence Analysis. The default is method="MCA"
quali.supp is a vector indicating the indexes of the categorical supplementary variables.
quanti.supp is a vector indicating the indexes of the quantitative supplementary variables.
minDegree is an integer. It indicates the minimun occurrences of terms to analize and plot.
The default value is 2.
k.max is an integer. It indicates the maximum numebr of cluster to keep. The default
value is 5. The max value is 8.
16 convert2df

stemming is logical. If TRUE the Porter’s Stemming algorithm is applied to all extracted
terms. The default is stemming = FALSE.
labelsize is an integer. It indicates the label size in the plot. Default is labelsize=10
documents is an integer. It indicates the numer of documents to plot in the factorial map.
The default value is 10.
graph is logical. If TRUE the function plots the maps otherwise they are saved in the
output object. Default value is TRUE

Value
It is an object of the class list containing the following components:

net bipartite network

res Results of CA or MCA method
km.res Results of cluster analysis
graph_terms Conceptual structure map (class "ggplot2")
graph_documents_Contrib Factorial map of the documents with the highest contributes (class "ggplot2")
graph_docuemnts_TC Factorial map of the most cited documents (class "ggplot2")

See Also
termExtraction to extract terms from a textual field (abstract, title, author’s keywords, etc.) of a
bibliographic data frame.
biblioNetwork to compute a bibliographic network.
cocMatrix to compute a co-occurrence matrix.
biblioAnalysis to perform a bibliometric analysis.

Examples
# EXAMPLE Conceptual Structure using Keywords Plus

data(scientometrics)

CS <- conceptualStructure(scientometrics, field="ID", method="CA",

stemming=FALSE, minDegree=3, k.max = 5)

convert2df Convert a Clarivate Analytics WoS, SCOPUS and COCHRANE

Database Export files or RISmed PubMed/MedLine object into a data
frame

Description
It converts a SCOPUS, Clarivate Analytics WoS and COCHRANE Database export files or RISmed
PubMed/MedLine object into a data frame, with cases corresponding to articles and variables to
Field Tags as used in WoS.
convert2df 17

Usage
convert2df(file, dbsource = "isi", format = "plaintext")

Arguments
file can be: a) a character array containing data read from a Clarivate Analytics WoS
Export file (in plain text or bibtex format) or SCOPUS Export file (exclusively in
bibtex format); b) an object of the class pubmed (package RISmed) containing
a collection obtained from a query performed with RISmed package.
dbsource is a character indicating the bibliographic database. dbsource can be "isi",
"scopus" or pubmed. Default is dbsource = "isi".
format is a character indicating the format of the SCOPUS and Clarivate Analytics WoS
export file. format can be "bibtex" or "plaintext". Default is format = "plaintext".

Details
Actually the function allows to convert both SCOPUS/WoS files in bibtext format and just WoS
files in plain text format.

Value
a data frame with cases corresponding to articles and variables to Field Tags in the original export
file.
data frame columns are named using the standard Clarivate Analytics WoS Field Tag codify. The
main field tags are:

AU Authors
TI Document Title
SO Publication Name (or Source)
JI ISO Source Abbreviation
DT Document Type
DE Authors’ Keywords
ID Keywords associated by SCOPUS or WoS database
AB Abstract
C1 Author Address
RP Reprint Address
CR Cited References
TC Times Cited
PY Year
SC Subject Category
UT Unique Article Identifier
DB Database

for a complete list of field tags see: Field Tags used in bibliometrix
18 countries

See Also

scopus2df for converting SCOPUS Export file (in bibtex format)

isibib2df for converting ISI Export file (in bibtex format)
isi2df for converting ISI Export file (in plain text format)
pubmed2df for converting an object of the class pubmed (RISmed package)
Other converting functions: cochrane2df, isi2df, isibib2df, pubmed2df, scopus2df

Examples

# An ISI or SCOPUS Export file can be read using \code{\link{readLines}} function:

# D <- readFiles('filename1.txt','filename2.txt','filename3.txt')

# filename1.txt, filename2.txt and filename3.txt are WoS or SCOPUS Export file

# in plain text or bibtex format.

# biblio <- readFiles('http://www.bibliometrix.org/datasets/bibliometrics_articles.txt')

data(biblio)

biblio_df_df <- convert2df(file = biblio, dbsource = "isi", format = "bibtex")

countries Index of Countries.

Description

Data frame containing a normalized index of countries.

Data are used by biblioAnalysis function to extract Country Field of Cited References and Au-
thors.

Format

A data frame with 198 rows and 1 variable:

countries country names

dominance 19

dominance Authors’ dominance ranking

Description
It calculates the authors’ dominance ranking from an object of the class ’bibliometrix’ as pro-
posed by Kumar & Kumar, 2008.

Usage
dominance(results, k = 10)

Arguments
results is an object of the class ’bibliometrix’ for which the analysis of the authors’
dominance ranking is desired.
k is an integer, used for table formatting (number of authors). Default value is 10.

Value
The function dominance returns a data frame with cases corresponding to the first k most productive
authors and variables to typical field of a dominance analysis.
the data frame variables are:

Dominance Factor Dominance Factor (DF = FAA / MAA)

Multi Authored N. of Multi-Authored Articles (MAA)
First Authored N. of First Authored Articles (FAA)
Rank by Articles Author Ranking by N. of Articles
Rank by DF Author Ranking by Dominance Factor

See Also

biblioAnalysis function for bibliometric analysis

summary method for class ’bibliometrix’

Examples

data(scientometrics)
results <- biblioAnalysis(scientometrics)
DF=dominance(results)
DF
20 duplicatedMatching

duplicatedMatching Searching of duplicated records in a bibliographic database

Description

Search duplicated records in a dataframe.

Usage

duplicatedMatching(M, Field = "TI", tol = 0.95)

Arguments

M is the bibliographic data frame.

Field is a character object. It indicates one of the field tags used to identify duplicated
records. Field can be equal to one of this tags: TI (title), AB (abstract), UT
(manuscript ID).
tol is a numeric value giving the minimum relative similarity to match two manuscripts.
Default value is tol = 0.95.

Details

A bibliographic data frame is obtained by the converting function convert2df. It is a data matrix
with cases corresponding to manuscripts and variables to Field Tag in the original SCOPUS and
Thomson Reuters’ ISI Web of Knowledge file. The function identifies duplicated records in a
bibliographic data frame and deletes them. Duplicate entries are identified through the restricted
Damerau-Levenshtein distance. Two manuscripts that have a relative similarity measure greater
than tol argument are stored in the output data frame only once.

Value

the value returned from duplicatedMatching is a data frame without duplicated records.

See Also

convert2df to import and convert an ISI or SCOPUS Export file in a bibliographic data frame.
biblioAnalysis function for bibliometric analysis.
summary to obtain a summary of the results.
plot to draw some useful plots of the results.
garfield 21

Examples

data(scientometrics)

M=rbind(scientometrics[1:20,],scientometrics[10:30,])

newM <- duplicatedMatching(M, Field = "TI", tol = 0.95)

dim(newM)

garfield Eugene Garfield’s manuscripts.

Description
All manuscripts published by Eugene Garfield.
Period: 1954 - 2014
Database: SCOPUS source

Format
A data frame with 147 rows and 15 variables:
AU Authors
TI Document Title
SO Publication Name (or Source)
JI ISO Source Abbreviation
DT Document Type
DE Author Keywords
ID Keywords associated by ISI or SCOPUS database
AB Abstract
C1 Author Address
RP Reprint Address
CR Cited References
TC Times Cited
PY Year
UT Unique Article Identifier
DB Database

Source
http://www.scopus.com
22 Hindex

Hindex h-index calculation

Description
It calculates the authors’ h-index and its variants.

Usage
Hindex(M, authors, sep = ";", years = 10)

Arguments
M is a bibliographic data frame obtained by the converting function convert2df.
It is a data matrix with cases corresponding to manuscripts and variables to Field
Tag in the original SCOPUS and Thomson Reuters’ ISI Web of Knowledge file.
authors is a character vector. It contains the the authors’ names list for which you
want to calculate the H-index. The aurgument has the form C("SURNAME1
N","SURNAME2 N",...), in other words, for each author: surname and initials
separated by one blank space. i.e for the auhtors SEMPRONIO TIZIO CAIO
and ARIA MASSIMO authors argument is authors = c("SEMPRONIO TC", "ARIA M").
sep is the field separator character. This character separates auhtors in each string of
AU column of the bibiographic data frame. The default is sep = ";".
years is a integer. It indicates the number of years to consider for Hindex calculation.
Default is 10.

Value
an object of class "list". It contains two elements: H is a data frame with h-index, g-index and
m-index for each author; CitationList is a list with the bibliographic collection for each author.

See Also
convert2df to import and convert an ISI or SCOPUS Export file in a bibliographic data frame.
biblioAnalysis function for bibliometric analysis.
summary to obtain a summary of the results.
plot to draw some useful plots of the results.

Examples

### EXAMPLE 1: ###

data(scientometrics)

authors <- c("SMALL H", "CHEN DZ")

histNetwork 23

Hindex(scientometrics, authors, sep = ";")$H

### EXAMPLE 2: Garfield h-index###

data(garfield)

indices=Hindex(garfield, authors="GARFIELD E", sep = ";")

# h-index, g-index and m-index of Eugene Garfield

indices$H

# Papers and total citations

indices$CitationList[[1]]

histNetwork Historical co-citation network

Description
histNetwork creates a historical citation network from a bibliographic data frame.

Usage
histNetwork(M, min.citations = 0, sep = ";")

Arguments
M is a bibliographic data frame obtained by the converting function convert2df.
It is a data matrix with cases corresponding to manuscripts and variables to Field
Tag in the original SCOPUS and Clarivate Analitics’ Web of Knowledge file.
min.citations is an integer. It sets the minimum number of citations for the documents in-
cluded in the analysis. The default is min.citations = 0.
sep is the field separator character. This character separates strings in CR column of
the data frame. The default is sep = ";".

Value
histNetwork returns an object of class "list" containing the following components:

NetMatrix the historical co-citation network matrix

histData the set of n most cited references
M the bibliographic data frame

See Also
convert2df to import and convert an ISI or SCOPUS Export file in a bibliographic data frame.
24 histPlot

summary to obtain a summary of the results.

plot to draw some useful plots of the results.
biblioNetwork to compute a bibliographic network.

Examples
data(scientometrics)

histResults <- histNetwork(scientometrics, min.citations = 10, sep = ";")

histPlot Plotting historical co-citation network

Description
histPlot plots a historical co-citation network.

Usage
histPlot(histResults, n = 20, size.cex = TRUE, size = 5,
labelsize = 0.8, arrowsize = 0.1, edgesize = 2, color = TRUE)

Arguments
histResults is an object of class "list" containing the following components:

NetMatrix the historical citation network matrix

Degree the min degree of the network
histData the set of n most cited references
M the bibliographic data frame

is a network matrix obtained by the function histNetwork.

n is integer. It defines the numebr of vertices to plot.
size.cex is logical. If TRUE the point size of each vertex is proportional to its degree.
Default value is TRUE.
size is an integer. It define the point size of the vertices. Default value is 5.
labelsize is an integer. It indicates the label size in the plot. Default is labelsize=1
arrowsize is numerical. It indicates the edge arrow size.
edgesize is numerical. It indicates the edge size.
color is logical. If TRUE, egdes are colored according to citing references.

Details
The function histPlot can plot a historical co-citation network previously created by histNetwork.
idByAuthor 25

Value
It is a network object of the class igraph.

See Also
histNetwork to compute a historical co-citation network.
cocMatrix to compute a co-occurrence matrix.
biblioAnalysis to perform a bibliometric analysis.

Examples
# EXAMPLE Citation network

data(scientometrics)

histResults <- histNetwork(scientometrics, sep = ";")

net <- histPlot(histResults, n=20, size.cex=TRUE, size = 5, arrowsize=0.3)

idByAuthor Get Complete Author Information and ID from Scopus

Description
Uses SCOPUS API author search to identify author identification information.

Usage
idByAuthor(df, api_key)

Arguments
df is a dataframe composed of three columns:

lastname author’s last name

firstname author’s first name
affiliation Part of the affiliation name (university name, city, etc.)

i.e. df[1,1:3]<-c("aria","massimo","naples") When affiliation is not specified,

the field df$affiliation have to be NA. i.e. df[2,1:3]<-c("cuccurullo","corrado",
NA)

api_key is a character. It contains the Elsvier API key. Information about how to obtain
an API Key Elsevier API website
26 isi2df

Value
a data frame with cases corresponding to authors and variables to author’s information and ID got
from SCOPUS.

See Also
retrievalByAuthorID for downloading the complete author bibliographic collection from SCO-
PUS

Examples
## Request a personal API Key to Elsevier web page https://dev.elsevier.com/sc_apis.html
#
# api_key="your api key"

## create a data frame with the list of authors to get information and IDs
# i.e. df[1,1:3]<-c("aria","massimo","naples")
# df[2,1:3]<-c("cuccurullo","corrado", NA)

## run idByAuthor function

#
# authorsID <- idByAuthor(df, api_key)

isi2df Convert an ISI WoK Export file into a data frame

Description
It converts an ISI Wok Export file and create a data frame from it, with cases corresponding to
articles and variables to Field Tag in the original file.

Usage
isi2df(D)

Arguments
D is a character array containing data read from a ISI Export file (in plain text
format).

Value
a data frame with cases corresponding to articles and variables to Field Tag in the original ISI file.

See Also
scopus2df for converting SCOPUS Export file (in bibtex format)
Other converting functions: cochrane2df, convert2df, isibib2df, pubmed2df, scopus2df
isibib2df 27

Examples
# A group of ISI Export files can be read using \code{\link{readFiles}} function:

# largechar <- readFiles('filename1.txt','filename2.txt','filename3.txt')

# scientometrics_text <- readFiles('http://www.bibliometrix.org/datasets/scientometrics.txt')

# data(scientometrics_text)
# scient_df <- isi2df(scientometrics_text)

isibib2df Convert an Clarivate Analitycs WoS Export file into a data frame

Description
It converts an Clarivate Analitycs WoS Export file and create a data frame from it, with cases
corresponding to articles and variables to Field Tag in the original file.

Usage
isibib2df(D)

Arguments
D is a character array containing data read from an WoS Export file (in bibtex
format).

Value
a data frame with cases corresponding to articles and variables to Field Tag in the original SCOPUS
file.

See Also
isi2df for converting ISI Export file (in plain text format)
Other converting functions: cochrane2df, convert2df, isi2df, pubmed2df, scopus2df

Examples
# A ISI Export file can be read using \code{\link{readLines}} function:

# largechar <- readFiles('filename1.bib','filename2.bib2,...)

# filename.bib is a Clarivate Analytics WoS Export file in plain text format.

# largechar <- readFiles('http://www.bibliometrix.org/datasets/ranking.bib')

# ranking <- isibib2df(largechar)

28 isiCollection

isiCollection "Bibliometrics" manuscripts from ISI WOS.

Description

Manuscripts including the term "bibliometrics" in the title.

Period: 1985 - 2017
Database: ISI Web of Knowledge
Format: bibtex

Format

A data frame with 329 rows and 16 variables:

AU Authors
TI Document Title
SO Publication Name (or Source)
JI ISO Source Abbreviation
DT Document Type
DE Author Keywords
ID Keywords associated by ISI or SCOPUS database
AB Abstract
C1 Author Address
RP Reprint Address
CR Cited References
TC Times Cited
PY Year
SC Subject Category
UT Unique Article Identifier
DB Database

Source

http://www.webofknowledge.com
keywordAssoc 29

keywordAssoc ID and DE keyword associations

Description
It associates authors’ keywords to keywords plus.

Usage
keywordAssoc(M, sep = ";", n = 10, excludeKW = NA)

Arguments
M is a bibliographic data frame obtained by the converting function convert2df.
It is a data matrix with cases corresponding to manuscripts and variables to Field
Tag in the original SCOPUS and Thomson Reuters’ ISI Web of Knowledge file.
sep is the field separator character. This character separates keywords in each string
of ID and DE columns of the bibiographic data frame. The default is sep = ";".
n is a integer. It indicates the number of authors’ keywords to associate to each
keyword plus. The default is n = 10.
excludeKW is character vector. It contains authors’ keywords to exclude from the analysis.

Value
an object of class "list".

See Also
convert2df to import and convert an ISI or SCOPUS Export file in a bibliographic data frame.
biblioAnalysis function for bibliometric analysis.
summary to obtain a summary of the results.
plot to draw some useful plots of the results.

Examples

data(scientometrics)

KWlist <- keywordAssoc(scientometrics, sep = ";",n = 10, excludeKW = NA)

# list of first 10 Keywords plus

names(KWlist)

# list of first 10 authors' keywords associated to the first Keyword plus

KWlist[[1]][1:10]
30 KeywordGrowth

KeywordGrowth Yearly occurrences of top keywords/terms

Description
It calculates yearly occurrences of top keywords/terms.

Usage
KeywordGrowth(M, Tag = "ID", sep = ";", top = 10, cdf = TRUE)

Arguments
M is a data frame obtained by the converting function convert2df. It is a data
matrix with cases corresponding to articles and variables to Field Tag in the
original ISI or SCOPUS file.
Tag is a character object. It indicates one of the keyword field tags of the standard
ISI WoS Field Tag codify (ID or DE) or a field tag created by termExtraction
function (TI_TM, AB_TM, etc.).
sep is the field separator character. This character separates strings in each keyword
column of the data frame. The default is sep = ";".
top is a numeric. It indicates the number of top keywords to analize. The default
value is 10.
cdf is a logical. If TRUE, the function calculates the cumulative occurrences distri-
bution.

Value
an object of class data.frame

Examples

data(scientometrics)
topKW=KeywordGrowth(scientometrics, Tag = "ID", sep = ";", top=5, cdf=TRUE)
topKW

# Plotting results
#
# library(reshape2)
# library(ggplot2)
# DF=melt(topKW, id='Year')
# ggplot(DF,aes(Year,value, group=variable, color=variable))+geom_line()
localCitations 31

localCitations Author local citations

Description
It calculates local citations (LCS) of authors and documents of a bibliographic collection.

Usage
localCitations(M, sep = ";")

Arguments
M is a bibliographic data frame obtained by the converting function convert2df.
It is a data matrix with cases corresponding to manuscripts and variables to Field
Tag in the original SCOPUS and Thomson Reuters’ ISI Web of Knowledge file.
sep is the field separator character. This character separates citations in each string
of CR column of the bibiographic data frame. The default is sep = ";".

Details
Local citations measure how many times an author (or a document) included in this collection have
been cited by the documents also included in the collection.

Value
an object of class "list" containing author local citations and docuemnt local citations.

See Also
citations function for citation frequency distribution.
biblioAnalysis function for bibliometric analysis.
summary to obtain a summary of the results.
plot to draw some useful plots of the results.

Examples

data(scientometrics)

CR <- localCitations(scientometrics, sep = ";")

CR$Authors[1:10,]
CR$Papers[1:10,]
32 mergeDbSources

lotka Lotka’s law coefficient estimation

Description
It estimates Lotka’s law coefficients for scientific productivity (Lotka A.J., 1926 )

Usage
lotka(results)

Arguments
results is an object of the class ’bibliometrix’ for which the analysis of the authors’
dominance ranking is desired.

Value
The function lotka returns a list of summary statistics of the Lotka’s law estimation of an object of
class bibliometrix.
the list contains the following objects:

Beta Beta coefficient

C Constant coefficient
R2 Goodness of Fit
fitted Fitted Values
p.value Pvalue of two-sample Kolmogorov-Smirnov test between the empirical and the theorical Lotka’s Law distrib
AuthorProd Authors’ Productivity frequency table

See Also
biblioAnalysis function for bibliometric analysis
summary method for class ’bibliometrix’

Examples
data(scientometrics)
results <- biblioAnalysis(scientometrics)
L=lotka(results)
L

mergeDbSources Merge bibliographic data frames from SCOPUS and ISI WOS
mergeDbSources 33

Description

Merge bibliografic data frames from different databases (ISI and SCOPUS) into a single one.

Usage

mergeDbSources(..., remove.duplicated = TRUE)

Arguments

... are the bibliographic data frames to merge.

remove.duplicated
is logical. If TRUE duplicated documents will be deleted from the bibliographic
collection.

Details

bibliographic data frames are obtained by the converting function convert2df. The function
merges data frames identifying common tag fields and duplicated records.

Value

the value returned from mergeDbSources is a bibliographic data frame.

See Also

convert2df to import and convert an ISI or SCOPUS Export file in a bibliographic data frame.
biblioAnalysis function for bibliometric analysis.
summary to obtain a summary of the results.
plot to draw some useful plots of the results.

Examples

data(isiCollection)

data(scopusCollection)

M <- mergeDbSources(isiCollection, scopusCollection, remove.duplicated=TRUE)

dim(M)
34 metaTagExtraction

metaTagExtraction Meta-Field Tag Extraction

Description
It extracts other field tags, different from the standard ISI/SCOPUS codify.

Usage
metaTagExtraction(M, Field = "CR_AU", sep = ";", aff.disamb = TRUE)

Arguments
M is a data frame obtained by the converting function convert2df. It is a data
matrix with cases corresponding to articles and variables to Field Tag in the
original ISI or SCOPUS file.
Field is a character object. New tag exctracted from aggregated data is specified by
this string. Field can be equal to one of this tags:

"CR_AU" First Author of each cited reference

"CR_SO" Source of each cited reference
"AU_CO" Country of affiliation for each co-author
"AU1_CO" Country of affiliation for the first author
"AU_UN" University of affiliation for each co-author and the corresponding author (AU1_UN)
"SR" Short tag of the document (as used in reference lists)

sep is the field separator character. This character separates strings in each column
of the data frame. The default is sep = ";".
aff.disamb is a logical. If TRUE and Field="AU_UN", then a disambiguation algorithm
is used to identify and match scientific affiliations (univ, research centers, etc.).
The default is aff.disamb=TRUE.

Value
the bibliometric data frame with a new column containing data about new field tag indicated in the
argument Field.

See Also
scopus2df for converting ISO or SCPUS Export file into a data frame.
biblioAnalysis function for bibliometric analysis

Examples
# Example 1: First Authors for each cited reference

data(scientometrics)
networkPlot 35

scientometrics <- metaTagExtraction(scientometrics, Field = "CR_AU", sep = ";")

unlist(strsplit(scientometrics$CR_AU[1], ";"))

#Example 2: Source for each cited reference

data(scientometrics)
scientometrics <- metaTagExtraction(scientometrics, Field = "CR_SO", sep = ";")
unlist(strsplit(scientometrics$CR_SO[1], ";"))

#Example 3: Affiliation country for co-author

data(scientometrics)
scientometrics <- metaTagExtraction(scientometrics, Field = "AU_CO", sep = ";")
scientometrics$AU_CO[1:10]

networkPlot Plotting Bibliographic networks

Description
networkPlot plots a bibliographic network.

Usage
networkPlot(NetMatrix, normalize = NULL, n = NULL, degree = NULL,
Title = "Plot", type = "kamada", label = TRUE, labelsize = 1,
label.cex = FALSE, label.color = FALSE, label.n = NULL,
halo = FALSE, cluster = "walktrap", vos.path = NULL, size = 3,
size.cex = FALSE, curved = FALSE, noloops = TRUE,
remove.multiple = TRUE, remove.isolates = FALSE, weighted = NULL,
edgesize = 1, edges.min = 0)

Arguments
NetMatrix is a network matrix obtained by the function biblioNetwork.
normalize is a character. It can be "association", "jaccard", "inclusion","salton" or "equiva-
lence" to obtain Association Strength, Jaccard, Inclusion, Salton or Equivalence
similarity index respectively. The default is type = NULL.
n is an integer. It indicates the number of vertices to plot.
degree is an integer. It idicates the min frequency of a vertex. If degree is not NULL, n
is ignored.
Title is a character indicating the plot title.
36 networkPlot

type is a character object. It indicates the network map layout:

type="auto" Automatic layout selection

type="circle" Circle layout
type="sphere" Sphere layout
type="mds" Multidimensional Scaling layout
type="fruchterman" Fruchterman-Reingold layout
type="kamada" Kamada-Kawai layout
type="vosviewer" Network is plotted using VOSviewer software

label is logical. If TRUE vertex labels are plotted.

labelsize is an integer. It indicates the label size in the plot. Default is labelsize=1
label.cex is logical. If TRUE the label size of each vertex is proportional to its degree.
label.color is logical. If TRUE, for each vertex, the label color is the same as its cluster.
label.n is an integer. It indicates the number of vertex labels to draw.
halo is logical. If TRUE communities are plotted using different colors. Default is
halo=FALSE
cluster is a character. It indicates the type of cluster to perform among ("none", opti-
mal", "lovain","infomap","edge_betweenness","walktrap").
vos.path is a character indicating the full path whre VOSviewer.jar is located.
size is integer. It defines the size of each vertex. Default is size=3.
size.cex is logical. If TRUE the size of each vertex is proportional to its degree.
curved is a logical. If TRUE edges are plotted with an optimal curvature. Default is
curved=FALSE
noloops is logical. If TRUE loops in the network are deleted.
remove.multiple
is logical. If TRUE multiple links are plotted using just one edge.
remove.isolates
is logical. If TRUE isolates vertices are not plotted.
weighted This argument specifies whether to create a weighted graph from an adjacency
matrix. If it is NULL then an unweighted graph is created and the elements
of the adjacency matrix gives the number of edges between the vertices. If it
is a character constant then for every non-zero matrix entry an edge is created
and the value of the entry is added as an edge attribute named by the weighted
argument. If it is TRUE then a weighted graph is created and the name of the
edge attribute will be weight.
edgesize is an integer. It indicates the network edge size.
edges.min is an integer. It indicates the min frequency of edges between two vertices. If
edge.min=0, all edges are plotted.

Details
The function networkPlot can plot a bibliographic network previously created by biblioNetwork.
The network map can be plotted using internal R routines or using VOSviewer by Nees Jan van Eck
and Ludo Waltman.
networkStat 37

Value
It is a list containing the following elements:

graph a network object of the class igraph

cluster_obj a communities object of the package igraph
cluster_res a data frame with main results of clustering procedure.

See Also
biblioNetwork to compute a bibliographic network.
cocMatrix to compute a co-occurrence matrix.
biblioAnalysis to perform a bibliometric analysis.

Examples
# EXAMPLE Co-citation network

data(scientometrics)

NetMatrix <- biblioNetwork(scientometrics, analysis = "co-citation",

network = "references", sep = ";")

net <- networkPlot(NetMatrix, n = 30, type = "kamada", Title = "Co-Citation",labelsize=0.5)

networkStat Calculating network summary statistics

Description
networkStat calculates main network statistics.

Usage
networkStat(object)

Arguments
object is a network matrix obtained by the function biblioNetwork or an graph object
of the class igraph.

Details
The function networkStat can calculate the main network statistics from a bibliographic network
previously created by biblioNetwork.
38 networkStat

Value
It is a list containing the following elements:
normalizeSimilarity 39

graph a network object of the class igraph

network a communities a list with the main statistics of the network
vertex a data frame with the main measures of centrality and prestige of vertices.

See Also

biblioNetwork to compute a bibliographic network.

cocMatrix to compute a co-occurrence matrix.
biblioAnalysis to perform a bibliometric analysis.

Examples
# EXAMPLE Co-citation network

# to run the example, please remove # from the beginning of the following lines
# data(scientometrics)

# NetMatrix <- biblioNetwork(scientometrics, analysis = "co-citation",

# network = "references", sep = ";")

# netstat <- networkStat(NetMatrix)

normalizeSimilarity Calculate similarity indices

Description

It calculates a relative measure of bibliographic co-occurrences.

Usage

normalizeSimilarity(NetMatrix, type = "association")

Arguments

NetMatrix is a coupling matrix obtained by the network functions biblioNetwork or cocMatrix.

type is a character. It can be "association", "jaccard", "inclusion","salton" or "equiva-
lence" to obtain Association Strength, Jaccard, Inclusion, Salton or Equivalence
similarity index respectively. The default is type = "association".
40 plot.bibliometrix

Details
couplingSimilarity calculates Association strength, Inclusion, Jaccard or Salton similarity from
a co-occurrence bibliographic matrix.
The association strength is used by Van Eck and Waltman (2007) and Van Eck et al. (2006). Several
works refer to the measure as the proximity index, while Leydesdorff (2008)and Zitt et al. (2000)
refer to it as the probabilistic affinity (or activity) index.
The inclusion index, also called Simpson coefficient, is an overlap measure used in information
retrieval.
The Jaccard index (or Jaccard similarity coefficient) gives us a relative measure of the overlap of
two sets. It is calcultated as the ratio between the intersection and the union of the reference lists
(of two manuscripts).
The Salton index, instead, relates the intersection of the two lists to the geometric mean of the size
of both sets. The square of Salton index is also called Equivalence index.
The indices are equal to zero if the intersection of the reference lists is empty.

Value
a similarity matrix.

See Also
biblioNetwork function to compute a bibliographic network.
cocMatrix to compute a bibliographic bipartite network.

Examples

data(scientometrics)
NetMatrix <- biblioNetwork(scientometrics, analysis = "co-occurrences",
network = "keywords", sep = ";")
S=normalizeSimilarity(NetMatrix, type = "association")

plot.bibliometrix Plotting bibliometric analysis results

Description
plot method for class ’bibliometrix’

Usage
## S3 method for class 'bibliometrix'
plot(x, ...)
plotThematicEvolution 41

Arguments
x is the object for which plots are desired.
... can accept two arguments:
k is an integer, used for plot formatting (number of objects). Default value is 10.
pause is a logical, used to allow pause in screen scrolling of results. Default
value is pause = FALSE.

Value
The function plot returns a set of plots of the object of class bibliometrix and a dataframe of
citation analysis.

See Also
The bibliometric analysis function biblioAnalysis.
summary to compute a list of summary statistics of the object of class bibliometrix.

Examples
data(scientometrics)

results <- biblioAnalysis(scientometrics)

plot(results, k = 10, pause = FALSE)

plotThematicEvolution Plot a Thematic Evolution Analysis

Description
It plot a Thematic Evolution Analysis performed using the thematicEvolution function.

Usage
plotThematicEvolution(Nodes, Edges)

Arguments
Nodes is a list of nodes obtained by thematicEvolution function.
Edges is a list of edges obtained by thematicEvolution function.

Value
a sankeyPlot
42 pubmed2df

See Also
thematicMap function to create a thematic map based on co-word network analysis and clustering.
thematicMap function to perform a thematic evolution analysis.
networkPlot to plot a bibliographic network.

Examples

data(scientometrics)
years=c(2000)

nexus <- thematicEvolution(scientometrics,years,n=100,minFreq=2)

#plotThematicEvolution(nexus$Nodes,nexus$Edges)

pubmed2df Convert a PubMed/MedLine collection into a data frame

Description
It converts a PubMed/MedLine collection (obtained through a query performed with RISmed pack-
age) and create a data frame from it, with cases corresponding to articles and variables to Field Tags
as proposed by Clarivate Analytics WoS.

Usage
pubmed2df(D)

Arguments
D is an object of class MedLine (package "RISmed") containing data resulting of
a query performed on MedLine using the package RISmed.

Value
a data frame with cases corresponding to articles and variables to Field Tags as proposed by Clari-
vate Analytics WoS.

See Also
scopus2df for converting SCOPUS Export file (in bibtex format)
isi2df for converting Clarivate Analitics WoS Export file (in plaintex format)
isibib2df for converting Clarivate Analitics WoS Export file (in bibtex format)
Other converting functions: cochrane2df, convert2df, isi2df, isibib2df, scopus2df
readFiles 43

Examples
# library(RISmed)
# search_topic <- 'epidermolysis bullosa'
# search_query <- EUtilsSummary(search_topic, retmax=200, mindate=2014, maxdate=2014)
# summary(search_query)
# D <- EUtilsGet(search_query)

# M <- pubmed2df(D)

readFiles Load a sequence of ISI or SCOPUS Export files into a large character
object

Description
It loads a sequence of SCOPUS and Thomson Reuters’ ISI Web of Knowledge export files and
create a large character vector from it.

Usage
readFiles(...)

Arguments
... is a sequence of names of files downaloaded from ISI WOS.(in plain text or
bibtex format) or SCOPUS Export file (exclusively in bibtex format).

Value
a character vector of length the number of lines read.

See Also
convert2df for converting SCOPUS of ISI Export file into a dataframe

Examples
# ISI or SCOPUS Export files can be read using \code{\link{readFiles}} function:

# largechar <- readFiles('filename1.txt','filename2.txt','filename3.txt')

# filename1.txt, filename2.txt and filename3.txt are ISI or SCOPUS Export file

# in plain text or bibtex format.

# D <- readFiles('http://www.bibliometrix.org/datasets/bibliometrics_articles.txt')
44 retrievalByAuthorID

retrievalByAuthorID Get Author Content on SCOPUS by ID

Description
Uses SCOPUS API search to get information about documents on a set of authors using SCOPUS
ID.

Usage
retrievalByAuthorID(id, api_key, remove.duplicated = TRUE,
country = TRUE)

Arguments
id is a vector of characters containing the author’s SCOPUS IDs. SCOPUS IDs
con be obtained using the function idByAuthor.
api_key is a character. It contains the Elsvier API key. Information about how to obtain
an API Key Elsevier API website
remove.duplicated
is logical. If TRUE duplicated documents will be deleted from the bibliographic
collection.
country is logical. If TRUE authors’ country information will be dowloaded from SCO-
PUS.

Value
a list containing two objects: (i) M which is a data frame with cases corresponding to articles and
variables to main Field Tags named using the standard ISI WoS Field Tag codify. M includes the
entire bibliographic collection downloaded from SCOPUS. The main field tags are:

AU Authors
TI Document Title
SO Publication Name (or Source)
DT Document Type
DE Authors’ Keywords
ID Keywords associated by SCOPUS or ISI database
AB Abstract
C1 Author Address
RP Reprint Address
TC Times Cited
PY Year
UT Unique Article Identifier
DB Database
rpys 45

(ii) authorDocuments which is a list containing a bibliographic data frame for each author.
LIMITATIONS: Currently, SCOPUS API does not allow to download document references. As
consequence, it is not possible to perform co-citation analysis (the field CR is empty).

See Also
idByAuthor for downloading auhtor information and SCOPUS ID.

Examples
## Request a personal API Key to Elsevier web page https://dev.elsevier.com/sc_apis.html

## api_key="your api key"

## create a data frame with the list of authors to get information and IDs
# i.e. df[1,1:3] <- c("aria","massimo","naples")
# df[2,1:3] <- c("cuccurullo","corrado", "naples")

## run idByAuthor function

#
# authorsID <- idByAuthor(df, api_key)
#

## extract the IDs

#
# id <- authorsID[,3]
#

## create the bibliographic collection

#
# res <- retrievalByAuthorID(id, api_key)
#
# M <- res$M # the entire bibliographic data frame
# M <- res$authorDocuments # the list containing a bibliographic data frame for each author

rpys Reference Publication Year Spectroscopy

Description
rpys computes a Reference Publication Year Spectroscopy for detecting the Historical Roots of
Research Fields. The method was introduced by Marx et al., 2014.

(Marx, W., Bornmann, L., Barth, A., & Leydesdorff, L. (2014). Detecting the historical roots
of research fields by reference publication year spectroscopy (RPYS). Journal of the Association
for Information Science and Technology, 65(4), 751-764.)
46 scientometrics

Usage
rpys(M, sep = ";", timespan = NULL, graph = T)

Arguments
M is a data frame obtained by the converting function convert2df. It is a data
matrix with cases corresponding to articles and variables to Field Tag in the
original ISI or SCOPUS file.
sep is the cited-references separator character. This character separates cited-references
in the CR column of the data frame. The default is sep = ";".
timespan is a numeric vector c(min year,max year). The default value is NULL (the entire
timespan is considered).
graph is a logical. If TRUE the function plot the spectrography otherwise the plot is
created but not drawn down.

Value
a list containing the spectroscopy (class ggplot2) and two dataframes with the number of citation
per year and the list of the cited-references for each year, respectively.

See Also
convert2df to import and convert an ISI or SCOPUS Export file in a data frame.
biblioAnalysis to perform a bibliometric analysis.
biblioNetwork to compute a bibliographic network.

Examples

data(scientometrics)
res <- rpys(scientometrics, sep=";", graph = TRUE)

scientometrics "Co-citation analysis" and "Coupling analysis" manuscripts.

Description
Manuscripts about the topics "co-citation analysis" and "coupling analysis" published on Sciento-
metrics Journal.
Period: 1985 - 2015
Database: ISI Web of Knowledge
scientometrics_text 47

Format
A data frame with 147 rows and 17 variables:
AU Authors
TI Document Title
SO Publication Name (or Source)
JI ISO Source Abbreviation
DT Document Type
DE Author Keywords
ID Keywords associated by ISI or SCOPUS database
AB Abstract
C1 Author Address
RP Reprint Address
CR Cited References
TC Times Cited
PY Year
SC Subject Category
UT Unique Article Identifier
DB Database
SR Short Reference

Source
http://www.webofknowledge.com

scientometrics_text "Co-citation analysis" and "Coupling analysis" manuscripts.

Description
Manuscripts about the topics "co-citation analysis" and "coupling analysis" published on Sciento-
metrics Journal.
Period: 1985 - 2015
Database: ISI Web of Knowledge

Format
A large character with 12731 rows.
Data has been imported by an ISI Export file in plain text format using the function readLines.

Source
http://www.webofknowledge.com
48 scopus2df

scopus2df Convert a SCOPUS Export file into a data frame

Description

It converts a SCOPUS Export file and create a data frame from it, with cases corresponding to
articles and variables to Field Tag in the original file.

Usage

scopus2df(D)

Arguments

D is a character array containing data read from a SCOPUS Export file (in bibtex
format).

Value

a data frame with cases corresponding to articles and variables to Field Tag in the original SCOPUS
file.

See Also

isi2df for converting ISI Export file (in plain text format)
Other converting functions: cochrane2df, convert2df, isi2df, isibib2df, pubmed2df

Examples

# A SCOPUS Export file can be read using \code{\link{readFiles}} function:

# largechar <- readFiles('filename1.bib','filename2.bib2,...)

# filename.bib is a SCOPUS Export file in plain text format.

#largechar <- readFiles('http://www.bibliometrix.org/datasets/scopus.bib')

#scopus_df <- scopus2df(largechar)

scopusCollection 49

scopusCollection "Bibliometrics" manuscripts from SCOPUS.

Description

Manuscripts including the term "bibliometrics" in the title.

Period: 1975 - 2017
Database: SCOPUS
Format: bibtex

Format

A data frame with 487 rows and 15 variables:

AU Authors
TI Document Title
SO Publication Name (or Source)
JI ISO Source Abbreviation
DT Document Type
DE Author Keywords
ID Keywords associated by ISI or SCOPUS database
AB Abstract
C1 Author Address
RP Reprint Address
CR Cited References
TC Times Cited
PY Year
UT Unique Article Identifier
DB Database

Source

http://www.scopus.com
50 sourceGrowth

sourceGrowth Number of documents published annually per Top Sources

Description

It calculates yearly published docuemnts of the top sources.

Usage

sourceGrowth(M, top = 5, cdf = TRUE)

Arguments

M is a data frame obtained by the converting function convert2df. It is a data

matrix with cases corresponding to articles and variables to Field Tag in the
original ISI or SCOPUS file.
top is a numeric. It indicates the number of top sources to analize. The default value
is 5.
cdf is a logical. If TRUE, the function calculates the cumulative occurrences distri-
bution.

Value

an object of class data.frame

Examples

data(scientometrics)
topSO=sourceGrowth(scientometrics, top=1, cdf=TRUE)
topSO

# Plotting results
#
# library(reshape2)
# library(ggplot2)
# DF=melt(topSO, id='Year')
# ggplot(DF,aes(Year,value, group=variable, color=variable))+geom_line()
stopwords 51

stopwords List of English stopwords.

Description
A character vector containing a complete list of English stopwords
Data are used by biblioAnalysis function to extract Country Field of Cited References and Au-
thors.

Format
A character vector with 665 rows.

summary.bibliometrix Summarizing bibliometric analysis results

Description
summary method for class ’bibliometrix’

Usage
## S3 method for class 'bibliometrix'
summary(object, ...)

Arguments
object is the object for which a summary is desired.
... can accept two arguments:
k integer, used for table formatting (number of rows). Default value is 10.
pause locical, used to allow pause in screen scrolling of results. Default value
is pause = FALSE.
width integer, used to define screen output width. Default value is width = 120.
verbose logical, used to allow screen output. Default is TRUE.

Value
The function summary computes and returns a list of summary statistics of the object of class
bibliometrics.
the list contains the following objects:

MainInformation Main Information about Data

AnnualProduction Annual Scientific Production
AnnualGrowthRate Annual Percentage Growth Rate
52 summary.bibliometrix_netstat

MostProdAuthors Most Productive Authors

MostCitedPapers Top manuscripts per number of citations
MostProdCountries Most Productive Countries
TCperCountries Total Citation per Countries
MostRelSources Most Relevant Sources
MostRelKeywords Most Relevant Keywords

See Also
biblioAnalysis function for bibliometric analysis
plot to draw some useful plots of the results.

Examples
data(scientometrics)

results <- biblioAnalysis(scientometrics)

summary(results)

summary.bibliometrix_netstat
Summarizing network analysis results

Description
summary method for class ’bibliometrix_netstat’

Usage
## S3 method for class 'bibliometrix_netstat'
summary(object, ...)

Arguments
object is the object for which a summary is desired.
... can accept two arguments:
k integer, used for table formatting (number of rows). Default value is 10.

Value
The function summary computes and returns on display severa statistics both at netowrk and vertex
level.
tableTag 53

Examples

# to run the example, please remove # from the beginning of the following lines
#data(scientometrics)

#NetMatrix <- biblioNetwork(scientometrics, analysis = "collaboration",

# network = "authors", sep = ";")
#netstat <- networkStat(NetMatrix)
#summary(netstat)

tableTag Tabulate elements from a Tag Field column

Description
It tabulates elements from a Tag Field column of a bibliographic data frame.

Usage
tableTag(M, Tag = "CR", sep = ";")

Arguments
M is a data frame obtained by the converting function convert2df. It is a data
matrix with cases corresponding to articles and variables to Field Tag in the
original ISI or SCOPUS file.
Tag is a character object. It indicates one of the field tags of the standard ISI WoS
Field Tag codify.
sep is the field separator character. This character separates strings in each column
of the data frame. The default is sep = ";".

Details
tableTag is an internal routine of main function biblioAnalysis.

Value
an object of class table

Examples

data(scientometrics)
Tab <- tableTag(scientometrics, Tag = "CR", sep = ";")
Tab[1:10]
54 termExtraction

termExtraction Term extraction tool from textual fields of a manuscript

Description
It extracts terms from a textual field (abstract, title, author’s keywords, etc.) of a bibliographic data
frame.

Usage
termExtraction(M, Field = "TI", stemming = FALSE,
language = "english", remove.numbers = TRUE, remove.terms = NULL,
keep.terms = NULL, synonyms = NULL, verbose = TRUE)

Arguments
M is a data frame obtained by the converting function convert2df. It is a data
matrix with cases corresponding to articles and variables to Field Tag in the
original ISI or SCOPUS file.
Field is a character object. It indicates the field tag of textual data :

"TI" Manuscript title

"AB" Manuscript abstract
"ID" Manuscript keywords plus
"DE" Manuscript author’s keywords

The default is Field = "TI".

stemming is logical. If TRUE the Porter Stemming algorithm is applied to all extracted
terms. The default is stemming = FALSE.
language is a character. It is the language of textual contents ("english", "german","italian","french","spanish").
The default is language="english".
remove.numbers is logical. If TRUE all numbers are deleted from the documents before term
extraction. The default is remove.numbers = TRUE.
remove.terms is a character vector. It contains a list of additional terms to delete from the
documents before term extraction. The default is remove.terms = NULL.
keep.terms is a character vector. It contains a list of compound words "formed by two or
more terms" to keep in their original form in the term extraction process. The
default is keep.terms = NULL.
synonyms is a character vector. Each element contains a list of synonyms, separeted by
";", that will be merged into a single term (the first word contained in the vector
element). The default is synonyms = NULL.
verbose is logical. If TRUE the function prints the most frequent terms extracted from
documents. The default is verbose=TRUE.
termExtraction 55

Value
the bibliometric data frame with a new column containing terms about the field tag indicated in the
argument Field.

See Also
convert2df to import and convert an ISI or SCOPUS Export file in a bibliographic data frame.
biblioAnalysis function for bibliometric analysis

Examples
# Example 1: Term extraction from titles

data(scientometrics)

# vector of compound words

keep.terms <- c("co-citation analysis","bibliographic coupling")

# term extraction
scientometrics <- termExtraction(scientometrics, Field = "TI",
remove.numbers=TRUE, remove.terms=NULL, keep.terms=keep.terms, verbose=TRUE)

# terms extracted from the first 10 titles

scientometrics$TI_TM[1:10]

#Example 2: Term extraction from abstracts

data(scientometrics)

# vector of terms to remove

remove.terms=c("analysis","bibliographic")

# term extraction
scientometrics <- termExtraction(scientometrics, Field = "AB", stemming=TRUE,language="english",
remove.numbers=TRUE, remove.terms=remove.terms, keep.terms=NULL, verbose=TRUE)

# terms extracted from the first abstract

scientometrics$AB_TM[1]

# Example 3: Term extraction from keywords with synonyms

data(scientometrics)

# vector of synonyms
synonyms <- c("citation; citation analysis", "h-index; index; impact factor")

# term extraction
scientometrics <- termExtraction(scientometrics, Field = "ID",
synonyms=synonyms, verbose=TRUE)
56 thematicEvolution

thematicEvolution Perform a Thematic Evolution Analysis

Description
It performs a Thematic Evolution Analysis based on co-word network analysis and clustering. The
methodology is inspired by the proposal of Cobo et al. (2011).

Usage
thematicEvolution(M, years, n = 250, minFreq = 2)

Arguments
M is a bibliographic data frame obtained by the converting function convert2df.
years is a numeric vector of two or more unique cut points.
n is numerical. It indicates the number of words to use in the network analysis
minFreq is numerical. It indicates the min frequency of words included in to a cluster.

Details
thematicEvolution starts from two or more thematic maps created by thematicMap function.

Value
a list containing:

nets The thematic nexus graph for each comparison

incMatrix Some useful statistics about the thematic nexus

See Also
thematicMap function to create a thematic map based on co-word network analysis and clustering.
cocMatrix to compute a bibliographic bipartite network.
networkPlot to plot a bibliographic network.

Examples

data(scientometrics)
years=c(2000)

nexus <- thematicEvolution(scientometrics,years,n=100,minFreq=2)

thematicMap 57

thematicMap Create a thematic map

Description
It creates a thematic map based on co-word network analysis and clustering. The methodology is
inspired by the proposal of Cobo et al. (2011).

Usage
thematicMap(Net, NetMatrix, S = NULL, minfreq = 5)

Arguments
Net is a igraph object created by networkPlot function.
NetMatrix is a co-occurence matrix obtained by the network functions biblioNetwork or
cocMatrix.
S is a similarity matrix obtained by the normalizeSimilarity function. If S is
NULL, map is created using co-occurrence counts.
minfreq is a integer. It indicates the minimun frequency of a cluster.

Details
thematicMap starts from a co-occurrence keyword network to plot in a two-dimesional map the
typological themes of a domain.

Value
a list containing:

map The thematic map as ggplot2 object

clusters Centrality and Density values for each cluster.
words A list of words following in each cluster

See Also
biblioNetwork function to compute a bibliographic network.
cocMatrix to compute a bibliographic bipartite network.
networkPlot to plot a bibliographic network.

Examples

data(scientometrics)
NetMatrix <- biblioNetwork(scientometrics, analysis = "co-occurrences",
network = "keywords", sep = ";")
58 timeslice

S <- normalizeSimilarity(NetMatrix, type = "association")

net <- networkPlot(S, n = 100, Title = "co-occurrence network",type="fruchterman",
labelsize = 0.7, halo = FALSE, cluster = "walktrap",remove.isolates=FALSE,
remove.multiple=FALSE, noloops=TRUE, weighted=TRUE)
res <- thematicMap(net, NetMatrix, S)
plot(res$map)

timeslice Bibliographic data frame time slice

Description
Divide a bibliographic data frame into time slice

Usage
timeslice(M, breaks = NA, k = 5)

Arguments
M is a bibliographic data frame obtained by the converting function convert2df.
It is a data matrix with cases corresponding to manuscripts and variables to Field
Tag in the original SCOPUS and Thomson Reuters’ ISI Web of Knowledge file.
breaks is a numeric vector of two or more unique cut points.
k is a integer value giving the number of intervals into which the data frame is to
be cut. k is used only in case breaks argument is not provided. The default is
k = 5.

Value
the value returned from split is a list containing the data frames for each sub-period.

See Also
convert2df to import and convert an ISI or SCOPUS Export file in a bibliographic data frame.
biblioAnalysis function for bibliometric analysis.
summary to obtain a summary of the results.
plot to draw some useful plots of the results.

Examples

data(scientometrics)

list_df <- timeslice(scientometrics, breaks = c(1995, 2005))

names(list_df)
trim 59

trim Deleting leading and ending white spaces

Description
Deleting leading and ending white spaces from a character object.

Usage
trim(x)

Arguments
x is a character object.

Details
tableTag is an internal routine of bibliometrics package.

Value
an object of class character

Examples

char <- c(" Alfred", "Mary", " John")

char
trim(char)

trim.leading Deleting leading white spaces

Description
Deleting leading white spaces from a character object.

Usage
trim.leading(x)

Arguments
x is a character object.
60 trim.leading

Details
tableTag is an internal routine of bibliometrics package.

Value
an object of class character

Examples

char <- c(" Alfred", "Mary", " John")

char
trim.leading(char)
Index

∗Topic Science Mapping, isi2df, 13, 18, 26, 27, 42, 48

Bibliometrics, Clarivate isibib2df, 13, 18, 26, 27, 42, 48
Analytics Web of Science, isiCollection, 28
Scopus, citations, co-citation,
citation-network, coupling, keywordAssoc, 29
co-authors, co-occurence, KeywordGrowth, 30
collaboration, co-word
analysis localCitations, 31
bibliometrix-package, 3 lotka, 32

biblio, 6 Matrix, 9, 14
biblio_df, 10 mergeDbSources, 32
biblioAnalysis, 7, 9, 12, 14, 16, 18–20, 22, metaTagExtraction, 34
25, 29, 31–34, 37, 39, 41, 46, 51–53,
55, 58 networkPlot, 35, 36, 42, 56, 57
bibliometrix (bibliometrix-package), 3 networkStat, 37, 37
bibliometrix-package, 3 normalizeSimilarity, 39, 57
biblioNetwork, 8, 9, 14, 16, 24, 35–37, 39,
plot, 7, 8, 12, 20, 22, 24, 29, 31, 33, 52, 58
40, 46, 57
plot.bibliometrix, 40
biblioshiny, 10
plotThematicEvolution, 41
citations, 11, 31 pubmed2df, 13, 18, 26, 27, 42, 48
cochrane2df, 12, 18, 26, 27, 42, 48
readFiles, 43
cocMatrix, 9, 13, 16, 25, 37, 39, 40, 56, 57
readLines, 6, 47
communities, 37, 39
retrievalByAuthorID, 26, 44
conceptualStructure, 15
rpys, 45
convert2df, 7–9, 11, 13–15, 16, 20, 22, 23,
26, 27, 29–31, 33, 34, 42, 43, 46, 48, scientometrics, 46
50, 53–56, 58 scientometrics_text, 47
countries, 18 scopus2df, 13, 18, 26, 27, 34, 42, 48
scopusCollection, 49
dominance, 19
sourceGrowth, 50
duplicatedMatching, 20
stopwords, 51
garfield, 21 summary, 7, 8, 12, 19, 20, 22, 24, 29, 31–33,
41, 58
Hindex, 22 summary.bibliometrix, 51
histNetwork, 23, 24, 25 summary.bibliometrix_netstat, 52
histPlot, 24, 24
tableTag, 53
idByAuthor, 25, 44, 45 termExtraction, 16, 30, 54

61
62 INDEX

thematicEvolution, 41, 56, 56

thematicMap, 42, 56, 57
timeslice, 58
trim, 59
trim.leading, 59