An R-tool for comprehensive science mapping analysis. A package for quantitative research in scientometrics and bibliometrics.
Home Page: https://www.bibliometrix.org
License: Other
This is my first time working with bibliometrix, but I'm stumbling over an issue with pubmed2df() that seems to suggest a broken URL specification or perhaps a problem with too many queries.
When running this code:
library(bibliometrix)
library(RISmed)
search.topic <- "movement ecology"
search.query <- EUtilsSummary(search.topic)
summary(search.query) # 3181 results as of 02.07.19
D <- EUtilsGet(search.query)
M <- pubmed2df(D)
I get the following error:
Downloading updated citations from PubMed/MedLine...
Error in readLines(the_url) :
cannot open the connection to 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?retmode=xml&dbfrom=pubmed&id=30718292&cmd=neighbor'
In addition: Warning message:
In readLines(the_url) :
cannot open URL 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?retmode=xml&dbfrom=pubmed&id=30718292&cmd=neighbor': HTTP status was '429 Unknown Error'
I can navigate to that eutils URL in my web browser, but I don't know enough about what pubmed2df() is trying to do to know if that's where it should be pointing. I was also unable to replicate published vignettes using different query terms (i.e., https://rpubs.com/ronaldofsalves/414306) due to the same readLines() error.
Hi,
I downloaded three .bib files from ISI, converted them to a data frame, and stitched them together with the following command:
data <- rbind(isibib2df(readFiles("results_1to500.bib")),
isibib2df(readFiles("results_501to1000.bib")),
isibib2df(readFiles("results_1001to1461.bib")))
When I tried to run a co-occurence analysis on abstracts I was given the following error:
biblioNetwork(data, analysis = "co-occurrences", network = "abstracts")
[1] "Field AB_TM is not a column name of input data frame"
Error in crossprod(x, y) :
requires numeric/complex matrix/vector arguments
data$AB is present in the data frame, but not data$AB_TM. Is there any way to chose the specific variable to use to override "abstracts"?
Hi,
I have a problem with the cited references.
CR <- citations(M, field = "article", sep = "; ") (or with authors field)
Cited articles and its authors appear in my data slightly in different ways between manuscripts. (so, for example, in the list of most cited articles the same article appears twice)
Its a problem of the scopus data, but do you have any solution?
Thank you!
Hi,
great work so far! I tested the new functionality regarding the function duplicatedMatching(). I encountered a problem where the function is removing columns instead of the rows as intended. I set up a quick minimal example:
data.frame.test <- data.frame(TI = I(c("A1","A2","A3","A4")), test = I(c("a","b","c","d")))
data.frame.test <- rbind(data.frame.test, data.frame.test)
data.frame.test <- duplicatedMatching(data.frame.test, Field = "TI", tol = 0.95)
data.frame.test
TI
1 A1
2 A2
3 A3
4 A4
5 A1
6 A2
7 A3
8 A4
We would expect the function to remove half of the rows. Instead the function is removing one column.
Kind Regards & keep up the good work!
The R source code file (bibliometrix-vignette.R) located in the vignettes directory does not seem to reflect the latest update found in its corresponding Rmd file.
Would you mind adding the knitr::purl() command for your vignette Rmd file in Travis CI to keep followers updated about any latest demo codes?
Appreciatively!
When I convert a bib with 500 records from WoS to dataframe in bibliometrix 2.0.3 , an Error occurs as follow
> dt <- convert2df(readFiles("./Data/data_science_2005_7501_8000.bib"),dbsource = "isi", format = "bibtex")
Converting your isi collection into a bibliographic dataframe
Articles extracted 100
Error in seq.default(POS, (POS + END - 1)) : 'to' must be a finite numberBut this code runs well in bibliometrix 2.0.2 .
data_science_2005_7501_8000.zip
metaTagExtraction fails with AU1_CO field extraction
It returns "GEORGIA" for first authors with "GEORGIA INST TECHNOL" in C1 field
I attach an example data frame
(see rows 28 42 52 116 150 186)
plot(x = results, k = 10, pause = FALSE)
Error in seq.default(min(x$Years), max(x$Years)) :
'from' must be a finite number
it drew only two graphs and face with the mentioned error.
Hi,
I try:
NetMatrix <- biblioNetwork(M, analysis = "co-citation", network = "references", sep = ". ")
net=networkPlot(NetMatrix, n = 30, Title = "Co-Citation Network", type = "vosviewer", size=T, remove.multiple=FALSE, labelsize=0.7,edgesize = 5)
from the documentation (just modify the plot type to vosviewer) and got this error:
Error in networkPlot(NetMatrix, n = 30, Title = "Co-Citation Network", :
object 'net_groups' not found
Also, in a computer the vosviewer is executed (even with that warning) but not in another computer.
How to solve this issue?
Hi,
I merged a Scopus and a WoS database thanks to the function mergeDbSources. I need to merge them in order to use a unique database in Biblioshiny.
Quite everything works, except the "most cited source". In this graph are reported both sources and authors. Probably an error in the merge of the database occurred, but I can't understand which database column it uses to generate the "most cited sources".
Here my database and the wrong graph
Issue.xlsx
Thanks
Hi,
I have the following error when I want to use my own bib file. It has been created via Mendeley.
Error in summary.bibliometrix(object = results, k = 10, pause = FALSE) : object 'AAA' not found
But the code works if I use the bib file of the documentation ("http://www.bibliometrix.org/datasets/savedrecs.bib").
In the documentation it is said the package works for the "four main bibliographic databases..". Does it mean the package does not support all .bib files ?
My code:
library(bibliometrix)
sessionInfo()
packageVersion("bibliometrix")
D <- readFiles("AMEM.bib")
M <- convert2df(D, dbsource = "isi", format = "bibtex")
results <- biblioAnalysis(M, sep = ";")
S <- summary(object = results, k = 10, pause = FALSE)
My bib file can be downloaded here .
Additional info:
R version 3.5.0 (2018-04-23)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)
packageVersion("bibliometrix")
[1] ‘2.0.3’
Thank you !
Thanks for de the great job!
My question: is possible unite two bib files (for example wos.bib and scopus.bib)?
Best regards,
Felipe Smolski
Version 1.9 includes provision for reading the doi field when data is extracted from the Scopus database. However, this field is not present in the data structure created by the scopus2df function. Tested with this data file: http://www.bibliometrix.org/datasets/scopus.bib.
When I try and perform histNetwork function on M, i get the following message:
"Sorry, but for the moment histNetwork works only with WoS collections". Can you provide histNetwork for Spopus as well?
Hi!
What is this error:
Error in cocMatrix(M, Field = "ID", type = "matrix", sep = ";", binary = binary) : object 'M' not found
Dear all,
I'm currently working with bibliometrix (thanks for providing this awesome package!) and was wondering whether it's possible to extract information on the respective authors' first names (i.e., not only the first letter but the full name)?
Thanks in advance!
Hi,
What is this error means?
Error in if (V(bsk.network)$community[x[1]] == V(bsk.network)$community[x[2]]) { :
argument is of length zero
in some data frame, it is OK.
I copy the code to create and visualize the affiliation collaboration network for affiliation collaboration network as followed:
M <- metaTagExtraction(M, Field= "AU_CO", sep = ";")
NetMatrix <- biblioNetwork(M, analysis = "collaboration", network = "countries", sep = ";")
net = networkPlot(NetMatrix,n = 20,Title = "Country Collaboration",type="circle",size = TRUE, remove.multiple = FALSE, labelsize = 1)
However, error happens as followed:
M <- metaTagExtraction(M, Field= "AU_UN", sep = ";")
NetMatrix <- biblioNetwork(M, analysis = "collaboration", network = "affiliations", sep = ";")
Error in NetMatrix[nchar(colnames(NetMatrix)) != 0, nchar(colnames(NetMatrix)) != :
incorrect number of dimensions
Another question , why there are several affiliations in "AU_UN" field and most of them are the same name?
M$AU_UN[1:10]
[1] "PORTLAND STATE UNIV;PORTLAND STATE UNIV"
[2] "UNIV STELLENBOSCH;UNIV STELLENBOSCH;UNIV ESSEX"
[3] "UNIV MALAYA;UNIV MALAYA;SEOUL NATL UNIV"
[4] "INST PHILOSOPHY;INST PHILOSOPHY"
[5] "NATL CHENG KLING UNIV;NATL CHENG KLING UNIV;NATL CHENG KLING UNIV;NATL CHENG KLING UNIV"
[6] "UNIV TUN HUSSEIN ONN MALAYSIA;UNIV TUN HUSSEIN ONN MALAYSIA"
[7] "UNIV SASSARI;UNIV SASSARI;TECH UNIV DENMARK;UNIV UTRECHT"
[8] "HELMUT SCHMIDT UNIV;HELMUT SCHMIDT UNIV"
[9] ""
[10] "HANYANG UNIV;HANYANG UNIV;HANYANG UNIV;HANYANG UNIV"
The textdata is from WOS in bibtex filetype .
plot.bibliometrix(), one of the S3 methods, generates five plots while returning only data.frame object of any given bibliometrix class.
Would you mind making its return type as a list including each five graph object alongside the original data.frame?
That way would allow users to selectively save desired graphs out of the function.
I have followed the steps laid out in the documentation and get the following error when I try to run NetMatrix:
Error in NetMatrix[nchar(colnames(NetMatrix)) != 0, nchar(colnames(NetMatrix)) != :
incorrect number of dimensions
Can anyone help me with what I'm doing wrong? I have looked around the internet for discussions but can't find anything specific. Thanks!
Lex
Code below:
_D1 <- readFiles("data/savedrecs.bib") #reads in the citation file
D2 <- readFiles("data/savedrecs1.bib") #reads in the citation file
DataF1 <- convert2df(D1, dbsource="isi", format="bibtex") #converts to data frame
DataF2 <- convert2df(D2, dbsource="isi", format="bibtex") #converts to data frame
Data_Clean <- rbind(DataF1,DataF1) #creates one dataset
Cocitation <- biblioNetwork(Data_Clean, analysis = "Co-Citation Network", network = "references", sep = ". ")_
Hello
First of all, many thanks for this package. It is awesome.
Using an Scopus database I've been getting this error when using either histNetwork or localCitations:
Articles analysed 100
Articles analysed 200
Articles analysed 300
Error in grep(x, M$CR[M$PY >= Year]) :
invalid regular expression, reason 'Invalid character range'
I think it may be due to grep inside the histNetwork not playing well with a particular pattern in title fields. Some non-English articles have the title in a second language between "[ ]" as in "PREJUDICE AGAINST FAT PEOPLE [PREJUICIO CONTRA PERSONAS OBESAS]". The brackets are interpreted as special characters.
I worked it around replacing all "[...]" for "(...)" in titles within the output of readFiles before using convert2df, but it surely deserved to be noticed in case it could be avoided in the package itself.
Not sure if the better solution would be the one I used, or maybe escaping those brackets before pos = grep(x, M$CR[M$PY >= Year]) within histNetwork, but it may be useful to implement either of those.
Best
Manuel
Offtopic: I created a couple of helping functions to allow me homogeneise titles within the Scopus database more easily. Not sure where I could share it with others in case they are helpful.
Dear authors,
Thank you for the continued development of the bibliometrix.
Is it possible to build a direct citation network from references in bibliometrix?
I am assuming that a direct citation network consists of citation between the articles returned in the query, as presented by Boyak and Klavans (2010), Figure 1.
Boyack, K. W., & Klavans, R. (2010). Co‐citation analysis, bibliographic coupling, and direct citation: Which citation approach represents the research front most accurately?. Journal of the American Society for Information Science and Technology, 61(12), 2389-2404.
thanks
Hi! Thanks for a great package!
While working with it I did the following and suggest the following:
I made a separate function specifically for zotero bib output to df (due to case sensitivity in the isibib2df() matching and non-capitalised field names from zotero (same as from Papers)), but it would likely be better to have one generally functioning bib to df function (e.g. bibtex2df) (i.e. it should not matter where the bibtex comes from).
My function here:
https://github.com/opetchey/bibliometrix/blob/master/R/zoterobib2df.R
Original one here:
https://github.com/opetchey/bibliometrix/blob/master/R/isibib2df.R
Owen
I try to understand difference between Authors per Document and Co-authors per Document in a summary object. I think that short explanation of $MainInformation items is necessary in this wonderful package.
I cant import data from Scielo. The error: Error in seq.default(iStart, iStop) : 'from' must be a finite number.
Loading txt or bib files into R environment
D <- readFiles("D:/Educ/novaeconomia.txt")
Converting the loaded files into a R bibliographic dataframe
M <- convert2df(D, dbsource="isi",format="plaintext")
How can I solve?
Thanks
novaeconomia.txt
I try to convert Scopus RIS file to data frame using the command:
D <- readFiles("~/Desktop/scopus.ris")
M <- convert2df(D, dbsource = "scopus", format = "plaintext")
Unfortunately, I get the error:
Error in seq.default(iP, iPs) : 'to' must be a finite number
I try with default version of bibliometrix on CRAN and with recent GitHub version. Any idea what's wrong?
Andrej
Hello, I run into problems again.
When I input the codes below:
NetMatrix <- biblioNetwork(M, analysis = "collaboration", network = "authors", sep = ";")
net <- networkPlot(NetMatrix, n=30, type="vosviewer", Title = "Authors collaboration", labelsize = 0.5)
Error in networkPlot(NetMatrix, n = 30, type = "vosviewer", Title = "Authors collaboration", :
object 'bsk.network1' not found
The vosviewer is executed, but an error occurs and there is no connection between nodes.
However, in another case, when I put the codes below:
NetMatrix <- biblioNetwork(M,analysis = "co-citation", network = "references",sep = ";")
net <- networkPlot(NetMatrix, n=30, Title = "Co-Citation Network", type = "vosviewer",size = T, remove.multiple = FALSE, edgesize = 5, labelsize = 0.9)
Error in networkPlot(NetMatrix, n = 30, Title = "Co-Citation Network", :
object 'bsk.network1' not found
The vosviewer is executed and the network is plotted correctly, but the error still occurs.
I installed bibliometrix from CRAN a few days ago and the vosviewer is the version 1.6.10 released on January 10, 2019.
How to solve this issue and plot networks correctly in Vosviewer?
Thank you for this awesome work!
While installing this package, error happened.
Error : object 'author_df_orig' is not exported by 'namespace:rscopus'
Thank you again
Hi,
I tried the new function bib2df with scopus database. It give me this error when I create the network plot.
Error in if (V(bsk.network)$community[x[1]] == V(bsk.network)$community[x[2]]) { :
argument is of length zero
It works fine with the previous version of convert2df or scopus2df.
Is there something error in the db conversion?
thanks for the solution.
regards,
I'm trying to import a .bib file generated by Scopus and modified in Excel (just to delete some documents). As soon as I import it in Biblioshiny it gives me this error: 'to' must be a finite number.
I read previous "issues" on the topic but seems I have no problem with tab character or @
How can I solve?
Thank you!
Dear all,
I just discovered your package... thank you very much for your work. It's great!
For my first steps I have used the attached bib-file (zipped for Github) downloaded from Web of Science.
Using
library (bibliometrix)
D <- readFiles("C:/Users/u991726/Downloads/savedrecs (3).bib")
M <- convert2df(D, dbsource = "isi", format = "bibtex")
results <- biblioAnalysis(M, sep = ";")
results$Affiliation delivers 628 "NR".... So many of the affiliation were not parsed correctly(?).
Did I missed something?
Best regards and thank you very much !
Juergen
Hi,
using the attached WOS plaintext file and the following code
library (bibliometrix)
D <- readFiles("C:/Users/u991726/Downloads/savedrecs (1).txt")
M <- convert2df(D, dbsource = "isi", format = "plaintext")
an error is thrown:
Articles extracted 100
Articles extracted 200
Articles extracted 300
Articles extracted 400
Articles extracted 499
Error in $<-.data.frame(*tmp*, "TC", value = numeric(0)) :
replacement has 0 rows, data has 499
Do you know the reason for this error?
Best regards,
Jürgen
savedrecs (1).zip
Hi,
I downloaded three .bib files from ISI, converted them to a data frame, and stitched them together with the following command:
data <- rbind(isibib2df(readFiles("results_1to500.bib")),
isibib2df(readFiles("results_501to1000.bib")),
isibib2df(readFiles("results_1001to1461.bib")))
When I attempted to run a conceptual structure analysis I was given the following error:
> CS <- conceptualStructure(data)
Error in which(unlist(lapply(listModa, is.numeric))) :
argument to 'which' is not logical
I'm trying to extract citation data of clinical guidelines (currently focusing on American and European hypertension guidelines) from Web Of Science.
I found that I couldn't extract whole citations of the guideline (WoS showed 615 citations, but only metadata from about 500 articles can be extracted). It is not a problem of this package, but is their anyone who have an experience like this?
Hello,
I have downloaded the latest version of "bibliometrix" package from this GitHub repo.
It seems like there is an error in Hindex() function. It fails even when example code is invoked.
Please refer to the following reproducible code created by reprex package.
library(bibliometrix)
#> To cite bibliometrix in publications, please use:
#>
#> Aria, M. & Cuccurullo, C. (2017) bibliometrix: An R-tool for comprehensive science mapping analysis, Journal of Informetrics, 11(4), pp 959-975, Elsevier.
#>
#>
#> http:\\www.bibliometrix.org
#>
#>
#> To start with the shiny web-interface, please digit:
#> biblioshiny()
example(Hindex)
#>
#> Hindex> ### EXAMPLE 1: ###
#> Hindex>
#> Hindex> data(scientometrics)
#>
#> Hindex> authors <- c("SMALL H", "CHEN DZ")
#>
#> Hindex> Hindex(scientometrics, field = "author", elements = authors, sep = ";")$H
#> Error in data.frame(Element = elements, h_index = 0, g_index = 0, m_index = 0, : arguments imply differing number of rows: 0, 1Created on 2019-01-17 by the reprex package (v0.2.1.9000)
devtools::session_info()
#> - Session info ----------------------------------------------------------
#> setting value
#> version R version 3.5.2 (2018-12-20)
#> os Windows 10 x64
#> system x86_64, mingw32
#> ui RTerm
#> language (EN)
#> collate English_United States.1252
#> ctype English_United States.1252
#> tz America/New_York
#> date 2019-01-17
#>
#> - Packages --------------------------------------------------------------
#> package * version date lib
#> assertthat 0.2.0 2017-04-11 [1]
#> backports 1.1.3 2018-12-14 [1]
#> bibliometrix * 2.1.1 2019-01-17 [1]
#> callr 3.1.1 2018-12-21 [1]
#> cli 1.0.1 2018-09-25 [1]
#> cluster 2.0.7-1 2018-04-13 [1]
#> colorspace 1.4-0 2019-01-13 [1]
#> crayon 1.3.4 2017-09-16 [1]
#> desc 1.2.0 2018-05-01 [1]
#> devtools 2.0.1.9000 2019-01-12 [1]
#> digest 0.6.18 2018-10-10 [1]
#> dplyr 0.8.0 2019-01-17 [1]
#> DT 0.5 2018-11-05 [1]
#> evaluate 0.12 2018-10-09 [1]
#> factoextra 1.0.5 2017-08-22 [1]
#> FactoMineR 1.41 2018-05-04 [1]
#> farver 1.1.0 2018-12-31 [1]
#> flashClust 1.01-2 2012-08-21 [1]
#> fs 1.2.6 2018-08-23 [1]
#> ggforce 0.1.3 2018-07-07 [1]
#> ggplot2 3.1.0.9000 2019-01-09 [1]
#> ggraph 1.0.2 2018-07-07 [1]
#> ggrepel 0.8.0 2018-05-09 [1]
#> glue 1.3.0.9000 2019-01-05 [1]
#> gridExtra 2.3 2017-09-09 [1]
#> gtable 0.2.0 2016-02-26 [1]
#> highr 0.7 2018-06-09 [1]
#> htmltools 0.3.6 2017-04-28 [1]
#> htmlwidgets 1.3 2018-12-31 [1]
#> httpuv 1.4.5.9002 2019-01-12 [1]
#> httr 1.4.0 2018-12-11 [1]
#> igraph 1.2.2 2018-07-27 [1]
#> knitr 1.21.6 2019-01-12 [1]
#> later 0.7.5.9001 2019-01-12 [1]
#> lattice 0.20-38 2018-11-04 [1]
#> lazyeval 0.2.1 2017-10-29 [1]
#> leaps 3.0 2017-01-10 [1]
#> magrittr 1.5 2014-11-22 [1]
#> MASS 7.3-51.1 2018-11-01 [1]
#> Matrix 1.2-15 2018-11-01 [1]
#> memoise 1.1.0 2017-04-21 [1]
#> mime 0.6 2018-10-05 [1]
#> munsell 0.5.0 2018-06-12 [1]
#> networkD3 0.4 2017-03-18 [1]
#> pillar 1.3.1 2018-12-15 [1]
#> pkgbuild 1.0.2.9000 2018-12-31 [1]
#> pkgconfig 2.0.2 2018-08-16 [1]
#> pkgload 1.0.2 2018-10-29 [1]
#> plyr 1.8.4 2016-06-08 [1]
#> prettyunits 1.0.2 2015-07-13 [1]
#> processx 3.2.1 2018-12-05 [1]
#> promises 1.0.1 2018-04-13 [1]
#> ps 1.3.0.9000 2018-12-30 [1]
#> purrr 0.2.99.9000 2019-01-12 [1]
#> R6 2.3.0 2018-10-04 [1]
#> RColorBrewer 1.1-2 2014-12-07 [1]
#> Rcpp 1.0.0.1 2019-01-05 [1]
#> remotes 2.0.2.9000 2018-12-31 [1]
#> RISmed 2.1.7 2017-06-06 [1]
#> rlang 0.3.1.9000 2019-01-12 [1]
#> rmarkdown 1.11.3 2019-01-12 [1]
#> rprojroot 1.3-2 2018-01-03 [1]
#> rscopus 0.6.3 2018-11-19 [1]
#> scales 1.0.0 2018-08-09 [1]
#> scatterplot3d 0.3-41 2018-03-14 [1]
#> sessioninfo 1.1.1 2018-11-05 [1]
#> shiny 1.2.0.9001 2019-01-12 [1]
#> shinycssloaders 0.2.0 2017-05-12 [1]
#> shinythemes 1.1.2 2018-11-06 [1]
#> SnowballC 0.6.0 2019-01-15 [1]
#> stringdist 0.9.5.1 2018-06-08 [1]
#> stringi 1.2.4 2018-07-20 [1]
#> stringr 1.3.1.9000 2019-01-09 [1]
#> testthat 2.0.1 2018-10-13 [1]
#> tibble 2.0.99.9000 2019-01-14 [1]
#> tidyr 0.8.2.9000 2019-01-05 [1]
#> tidyselect 0.2.5.9000 2019-01-05 [1]
#> tweenr 1.0.1 2018-12-14 [1]
#> units 0.6-2 2018-12-05 [1]
#> usethis 1.4.0.9000 2018-12-30 [1]
#> viridis 0.5.1 2018-03-29 [1]
#> viridisLite 0.3.0 2018-02-01 [1]
#> withr 2.1.2 2018-03-15 [1]
#> xfun 0.4 2018-10-23 [1]
#> xtable 1.8-3 2018-08-29 [1]
#> yaml 2.2.0 2018-07-25 [1]
#> source
#> CRAN (R 3.5.2)
#> CRAN (R 3.5.2)
#> Github (massimoaria/bibliometrix@ca98549)
#> CRAN (R 3.5.2)
#> CRAN (R 3.5.2)
#> CRAN (R 3.5.2)
#> CRAN (R 3.5.2)
#> CRAN (R 3.5.2)
#> CRAN (R 3.5.2)
#> Github (r-lib/devtools@bcdde39)
#> CRAN (R 3.5.2)
#> Github (hadley/dplyr@9aa5846)
#> CRAN (R 3.5.2)
#> CRAN (R 3.5.2)
#> CRAN (R 3.5.2)
#> CRAN (R 3.5.2)
#> Github (thomasp85/farver@882bb92)
#> CRAN (R 3.5.2)
#> CRAN (R 3.5.2)
#> CRAN (R 3.5.2)
#> Github (hadley/ggplot2@9eae13b)
#> CRAN (R 3.5.2)
#> CRAN (R 3.5.2)
#> Github (tidyverse/glue@3f7012c)
#> CRAN (R 3.5.2)
#> CRAN (R 3.5.2)
#> CRAN (R 3.5.2)
#> CRAN (R 3.5.2)
#> Github (ramnathv/htmlwidgets@5db27ad)
#> Github (rstudio/httpuv@14f0b97)
#> CRAN (R 3.5.2)
#> CRAN (R 3.5.2)
#> Github (yihui/knitr@2814058)
#> Github (r-lib/later@7dc879a)
#> CRAN (R 3.5.2)
#> CRAN (R 3.5.2)
#> CRAN (R 3.5.2)
#> CRAN (R 3.5.2)
#> CRAN (R 3.5.2)
#> CRAN (R 3.5.2)
#> CRAN (R 3.5.2)
#> CRAN (R 3.5.2)
#> CRAN (R 3.5.2)
#> CRAN (R 3.5.2)
#> CRAN (R 3.5.2)
#> Github (r-lib/pkgbuild@6e4ebdf)
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#> CRAN (R 3.5.2)
#> CRAN (R 3.5.2)
#> CRAN (R 3.5.2)
#> Github (r-lib/ps@7d17711)
#> Github (hadley/purrr@57dd213)
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#> Github (RcppCore/Rcpp@0c9f683)
#> Github (r-lib/remotes@a0d6cd5)
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#> Github (r-lib/rlang@923c789)
#> Github (rstudio/rmarkdown@170d048)
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#> CRAN (R 3.5.2)
#> CRAN (R 3.5.2)
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#> CRAN (R 3.5.2)
#> Github (rstudio/shiny@8ae31eb)
#> CRAN (R 3.5.2)
#> CRAN (R 3.5.2)
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#> CRAN (R 3.5.2)
#> Github (hadley/stringr@cec6a66)
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#> [1] C:/Program Files/R/R-3.5.2/libraryI'm trying to convert my Scopus database in R studio, but it's not working. Maybe there's a problem in some lines? If yes, how do I find it? It worked fine for my WoS database...
"Converting your scopus collection into a bibliographic dataframe
Error in seq.default(iP, iPs) : 'to' must be a finite number"
I have found that the current biblioAnalysis() function categorizes the same author with a different punctuation style into two different individuals.
For example, there is "John Smith" denoted with Smith J. in journal A; Smith J in journal B.
Even though "Smith J" and "Smith J." are the same person, the internal function of bibliometrix counts them towards two different individuals just because of the punctuation (.).
Would there be anyway to identify the same individual regardless of their punctuation?
It would be great to have the option to customize the Field Tags included in the ...2df functions. I'd really like to be able to include a DOI code, which I have in my downloaded WoS search, but can't seem to transfer into the R data frame with the current functions.
Thank you for the package. It is a great resource for scientometric analysis.
Related to the function "bib2df", I checked that all semicolons are replaced by comma on the fields "Funding-Text" and "Funding-Acknowledgement" (bib files from Web of Science). The function work properly with other fields that also have semicolon, such as Author and Address.
Hi, I experiment with your bibliometrix package immediately after coming across it through a search engine. I like it very much so far. Most of the functions work great. However, I have an issue with the output of conceptualStructure. The font size within each cluster is too small to be readable. One example is shown in link.
The function is using the default setting.
CS <- conceptualStructure(M,field="ID", minDegree=4, k.max=5, stemming=FALSE)
Your example file shows clear image. I am wondering is it related to system setting or there are more keywords in my search file? If it is later, is there an option to increase font size of the keywords within the plot?
Thanks,
Rick
When I convert a bib file from WoS with 1 record in bibliometrix 2.0.3, an Error occurs as follow
> convert2df(readFiles("./Data/data_science_2014_b_26001_26001.bib"),dbsource = "isi", format = "bibtex")
Converting your isi collection into a bibliographic dataframe
Articles extracted 1
Error in `$<-.data.frame`(`*tmp*`, "AU", value = character(0)) :
replacement has 0 rows, data has 23 the trackback is
6. stop(sprintf(ngettext(N, "replacement has %d row, data has %d",
"replacement has %d rows, data has %d"), N, nrows), domain = NA)
5 .`$<-.data.frame`(`*tmp*`, "AU", value = character(0))
4. `$<-`(`*tmp*`, "AU", value = character(0))
3. postprocessing(DATA, dbsource)
2. bib2df(file, dbsource = "isi")
1. convert2df(readFiles("./Data/data_science_2014_b_26001_26001.bib"),
dbsource = "isi", format = "bibtex") The measure stability is a possible argument value in function plotThematicEvolution(). E.g., plotThematicEvolution(..., measure="stability), yet there is no reference or definition/explanation of this measure option in the package documentation on CRAN.
Can you please add a reference or more information on this option to the package documentation?
Thanks!
I have PhD students that need to import their clean citation data from the Bibexcel in order to Bibliometrix package to read it. I can provide a sample of text to illustrate what the Bibexcel outputs.
In the latest version of R (3.5.2.) on Windows 64-bit system, convert2df() function prompts an error.
I have found that there is no error when R console is started with --vanilla flag though.
> ## ----bibliometrix loading------------------------------------------------
> library(bibliometrix) ### load bibliometrix package
To cite bibliometrix in publications, please use:
Aria, M. & Cuccurullo, C. (2017) bibliometrix: An R-tool for comprehensive science mapping analysis, Journal of Informetrics, 11(4), pp 959-975, Elsevier.
http:\\www.bibliometrix.org
To start with the shiny web-interface, please digit:
biblioshiny()
> ## ----Data loading--------------------------------------------------------
> D <- readFiles("http://www.bibliometrix.org/datasets/savedrecs.bib")
>
> ## ----Data converting-----------------------------------------------------
> M <- convert2df(D, dbsource = "isi", format = "bibtex")
Converting your isi collection into a bibliographic dataframe
Error in seq.default(iP, iPs) : 'to' must be a finite number
Calls: convert2df -> bib2df -> seq -> seq.default
Execution halted
>
> ## Session Info
> devtools::session_info()
- Session info ---------------------------------------------------------------
setting value
version R version 3.5.2 (2018-12-20)
os Windows 10 x64
system x86_64, mingw32
ui RTerm
language (EN)
collate English_United States.1252
ctype English_United States.1252
tz America/New_York
date 2019-01-17
- Packages -------------------------------------------------------------------
package * version date lib
assertthat 0.2.0 2017-04-11 [1]
backports 1.1.3 2018-12-14 [1]
bibliometrix * 2.1.1 2019-01-17 [1]
callr 3.1.1 2018-12-21 [1]
cli 1.0.1 2018-09-25 [1]
cluster 2.0.7-1 2018-04-13 [1]
colorspace 1.4-0 2019-01-13 [1]
crayon 1.3.4 2017-09-16 [1]
desc 1.2.0 2018-05-01 [1]
devtools 2.0.1.9000 2019-01-12 [1]
digest 0.6.18 2018-10-10 [1]
dplyr 0.8.0 2019-01-17 [1]
DT 0.5 2018-11-05 [1]
factoextra 1.0.5 2017-08-22 [1]
FactoMineR 1.41 2018-05-04 [1]
farver 1.1.0 2018-12-31 [1]
flashClust 1.01-2 2012-08-21 [1]
fs 1.2.6 2018-08-23 [1]
ggforce 0.1.3 2018-07-07 [1]
ggplot2 3.1.0.9000 2019-01-09 [1]
ggraph 1.0.1.9999 2019-01-17 [1]
ggrepel 0.8.0 2018-05-09 [1]
glue 1.3.0.9000 2019-01-05 [1]
gridExtra 2.3 2017-09-09 [1]
gtable 0.2.0 2016-02-26 [1]
htmltools 0.3.6 2017-04-28 [1]
htmlwidgets 1.3 2018-12-31 [1]
httpuv 1.4.5.9002 2019-01-12 [1]
httr 1.4.0 2018-12-11 [1]
igraph 1.2.2 2018-07-27 [1]
later 0.7.5.9001 2019-01-12 [1]
lattice 0.20-38 2018-11-04 [1]
lazyeval 0.2.1 2017-10-29 [1]
leaps 3.0 2017-01-10 [1]
magrittr 1.5 2014-11-22 [1]
MASS 7.3-51.1 2018-11-01 [1]
Matrix 1.2-15 2018-11-01 [1]
memoise 1.1.0 2017-04-21 [1]
mime 0.6 2018-10-05 [1]
munsell 0.5.0 2018-06-12 [1]
networkD3 0.4 2017-03-18 [1]
pillar 1.3.1 2018-12-15 [1]
pkgbuild 1.0.2.9000 2018-12-31 [1]
pkgconfig 2.0.2 2018-08-16 [1]
pkgload 1.0.2 2018-10-29 [1]
plyr 1.8.4 2016-06-08 [1]
prettyunits 1.0.2 2015-07-13 [1]
processx 3.2.1 2018-12-05 [1]
promises 1.0.1 2018-04-13 [1]
ps 1.3.0.9000 2018-12-30 [1]
purrr 0.2.99.9000 2019-01-12 [1]
R6 2.3.0 2018-10-04 [1]
RColorBrewer 1.1-2 2014-12-07 [1]
Rcpp 1.0.0.1 2019-01-05 [1]
remotes 2.0.2.9000 2018-12-31 [1]
RISmed 2.1.7 2017-06-06 [1]
rlang 0.3.1.9000 2019-01-12 [1]
rprojroot 1.3-2 2018-01-03 [1]
rscopus 0.6.3 2018-11-19 [1]
scales 1.0.0 2018-08-09 [1]
scatterplot3d 0.3-41 2018-03-14 [1]
sessioninfo 1.1.1 2018-11-05 [1]
shiny 1.2.0.9001 2019-01-12 [1]
shinycssloaders 0.2.0 2017-05-12 [1]
shinythemes 1.1.2 2018-11-06 [1]
SnowballC 0.6.0 2019-01-15 [1]
stringdist 0.9.5.1 2018-06-08 [1]
stringi 1.2.4 2018-07-20 [1]
stringr 1.3.1.9000 2019-01-09 [1]
testthat 2.0.1 2018-10-13 [1]
tibble 2.0.99.9000 2019-01-14 [1]
tidygraph 1.1.1 2019-01-17 [1]
tidyr 0.8.2.9000 2019-01-05 [1]
tidyselect 0.2.5.9000 2019-01-05 [1]
tweenr 1.0.1 2018-12-14 [1]
units 0.6-2 2018-12-05 [1]
usethis 1.4.0.9000 2018-12-30 [1]
viridis 0.5.1 2018-03-29 [1]
viridisLite 0.3.0 2018-02-01 [1]
withr 2.1.2 2018-03-15 [1]
xtable 1.8-3 2018-08-29 [1]
source
CRAN (R 3.5.2)
CRAN (R 3.5.2)
Github (massimoaria/bibliometrix@d336a07)
CRAN (R 3.5.2)
CRAN (R 3.5.2)
CRAN (R 3.5.2)
CRAN (R 3.5.2)
CRAN (R 3.5.2)
CRAN (R 3.5.2)
Github (r-lib/devtools@bcdde39)
CRAN (R 3.5.2)
Github (hadley/dplyr@9aa5846)
CRAN (R 3.5.2)
CRAN (R 3.5.2)
CRAN (R 3.5.2)
Github (thomasp85/farver@882bb92)
CRAN (R 3.5.2)
CRAN (R 3.5.2)
CRAN (R 3.5.2)
Github (hadley/ggplot2@9eae13b)
Github (thomasp85/ggraph@8d23845)
CRAN (R 3.5.2)
Github (tidyverse/glue@3f7012c)
CRAN (R 3.5.2)
CRAN (R 3.5.2)
CRAN (R 3.5.2)
Github (ramnathv/htmlwidgets@5db27ad)
Github (rstudio/httpuv@14f0b97)
CRAN (R 3.5.2)
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CRAN (R 3.5.2)
CRAN (R 3.5.2)
CRAN (R 3.5.2)
CRAN (R 3.5.2)
Github (r-lib/pkgbuild@6e4ebdf)
CRAN (R 3.5.2)
CRAN (R 3.5.2)
CRAN (R 3.5.2)
CRAN (R 3.5.2)
CRAN (R 3.5.2)
CRAN (R 3.5.2)
Github (r-lib/ps@7d17711)
Github (hadley/purrr@57dd213)
CRAN (R 3.5.2)
CRAN (R 3.5.2)
Github (RcppCore/Rcpp@0c9f683)
Github (r-lib/remotes@a0d6cd5)
CRAN (R 3.5.0)
Github (r-lib/rlang@923c789)
CRAN (R 3.5.2)
CRAN (R 3.5.2)
CRAN (R 3.5.2)
CRAN (R 3.5.2)
CRAN (R 3.5.2)
Github (rstudio/shiny@8ae31eb)
CRAN (R 3.5.2)
CRAN (R 3.5.2)
CRAN (R 3.5.2)
CRAN (R 3.5.2)
CRAN (R 3.5.2)
Github (hadley/stringr@cec6a66)
CRAN (R 3.5.2)
Github (hadley/tibble@5a6e727)
Github (thomasp85/tidygraph@277ba22)
Github (hadley/tidyr@503fe85)
Github (tidyverse/tidyselect@19150c0)
CRAN (R 3.5.2)
CRAN (R 3.5.2)
Github (r-lib/usethis@85bf30a)
CRAN (R 3.5.2)
CRAN (R 3.5.2)
CRAN (R 3.5.2)
CRAN (R 3.5.2)
[1] C:/Program Files/R/R-3.5.2/library
> the biblioNetwork function only creates coupling networks list below:
Would you mind providing the readers of bibliometrix-vignette.Rmd with accurate citation references for the following parts? I am looking for the exact articles:
The **Collaboration Index** (CI) is calculated as Total Authors of Multi-Authored Articles/Total Multi-Authored Articles (Elango and Rajendran, 2012; Koseoglu, 2016).
The function *dominance* calculates the authors' dominance ranking as proposed by Kumar & Kumar, 2008.
The historiographic map is a graph proposed by E. Garfield ...
The documentation in your vignette and the documentation for convert2df refer to this file to discern which field tags are used:
http://www.bibliometrix.org/documents/Field_Tags_bibliometrix.pdf
This document does not contain the fields:
[1] "DT2" "PP" "DB" "AU_UN" "AU1_UN"
[6] "AU_UN_NR" "SR_FULL" "SR"
What are these tags?
First of all, thanks for the very usefull bibliometrix package
Recently I have had troubles with the pubmed connection server using the pubmed2df function
When I try to download around more than 15 records the next error appear
"HTTP status was 429 Too Many Requests", months before, I used the function to download around1000 records successfully.
Do you have any idea about the problem and how to solve it?
Thanks in advance
Dago
I think there is a bug in the isi2df function. When importing, for example, the DE and WC fields.
As you can see in the file (wos.txt), when a DE (or WC) starts on one line but ends on the next (after three blank spaces), it becomes two DE or two WC.
DE
Sentiment analysis
Keyword extraction
Graph based model
Centrality measure
Text mining
SENTIMENT ANALYSIS
KEYWORD EXTRACTION
GRAPH BASED MODEL
CENTRALITY
MEASURE
TEXT MINING
WC
Computer Science, Artificial Intelligence
Engineering, Electrical & Electronic
Operations Research & Management Science
COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE
ENGINEERING, ELECTRICAL &
ELECTRONIC
OPERATIONS RESEARCH & MANAGEMENT SCIENCE
React
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🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
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Django
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Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
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