[R] Help with bibliometrix and biblioshiny

Sun Sep 5 18:02:05 CEST 2021

Please read and follow the posting guide, which says:

"For questions about functions in standard packages distributed with R
(see the FAQ Add-on packages in R), ask questions on R-help.
If the question relates to a contributed package , e.g., one
downloaded from CRAN, try contacting the package maintainer first. You
can also use find("functionname") and
packageDescription("packagename") to find this information. Only send
such questions to R-help or R-devel if you get no reply or need
further assistance. "

So for a specialized package like bibliometrix, though you might get
lucky here, you should probably contact the maintainers. I also noted
that the package has its own web page with a FAQ and other resources.
Have you consulted them yet?  There might also be a user community
that could help, but I did not see it in my brief look around.

Bert Gunter

"The trouble with having an open mind is that people keep coming along
and sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )

On Sun, Sep 5, 2021 at 8:20 AM Bruno César Juliatti
<brunojuliatti using gmail.com> wrote:
>
> Hi, everyone. I'm new in this R language universe. I want to use
> bibliometric as a research in m Master's program. I run the code in R
> studio and works just fine. But, in the web-interface (biblioshiny), I load
> the table in .csv and keeps showing this message: Error: object 'M' not
> found
> PS: I already exported the searches in Web of Science and Scopus.
>
> This is the code and below the console's messages.
>
> *install.packages("bibliometrix")* # Baixar o pacote. S? precisa fazer isso
> uma #vez! E demora muito, por vezes muitos minutos!
>
> #library(bibliometrix)  # carregar o pacote na mem?ria para utiliz?-lo
> agora.
>
> # D?vidas de uso do Bibliometrix, execute  o comando que segue:
> help(bibliometrix)
>
> #Artigo: CAPACIDADE ESTATAL
> #AUTORES: PATRÃ CIA ROSVADOSKI-DA-SILVA, WELLES ABREU
> #OBJETIVO -> Caracterizar e clusterizar os trabalhos de capacidade estatal
>
>
> #######COLETA DOS DADOS ##############
>
> #WEB OF SCIENCE
> #Pesquisa BÃ¡sica
> # variÃ¡veis da pesquisa: BOLEADORES -> AND, OR , NOT
> ############ ATENÃ‡ÃƒO: ASPAS (") E *
> # configuraÃ§Ãµes
> #Filtros ##########ATENÃ‡ÃƒO: ANOTAR TODOS OS PASSOS
> # EXPORTAR -> Outros formatos de arquivo
> # Registro completo de referÃªncias citadas (mÃ¡ximo de 500)
> # bibtex. OBS-> Salvar arquivo: serÃ¡ gerado um arquivo #â€œsavedrecs.bibâ€
> na Ã¡rea de downloads
>
> #SCOPUS
> #PESQUISA
> #CAMPOS
> #  FILTROS -> Data range, document type, Access type
> #FILTROS
> #EXPORT -> Bibtex (citation information, Bibliographical information,
> Abstract & keywords, Funding details, Other information -> Export)
> #limite de 2000 artigos, Salvar arquivo: serÃ¡ gerado um arquivo
> #â€œscopus.bibâ€ na Ã¡rea de downloads
>
>
>
>
>
>
>
>
> ############### ETAPA 1 - CARREGAMENTO E CONVERS?O DOS DADOS ###############
>
> # WEB OF SCIENCE (ISI): Converter os dados para o padr?o do bibliometrix
>
> *W <- convert2df("C:/Users/bruno/Desktop/Bibliometria/wos_scielo.bib",
> dbsource = "isi", format = "bibtex")*
> #W1 <- convert2df("/Users/user/OneDrive/Curriculum/Artigos em
> andamento/Cooperativismo/WOS/savedrecs (12).bib", dbsource = "isi", format
> = "bibtex")
> #W2 <- convert2df("/Users/user/OneDrive/Curriculum/Artigos em
> andamento/Cooperativismo/WOS/savedrecs (13).bib", dbsource = "isi", format
> = "bibtex")
> #W3 <- convert2df("/Users/user/OneDrive/Curriculum/Artigos em
> andamento/Cooperativismo/WOS/savedrecs (14).bib", dbsource = "isi", format
> = "bibtex")
> #W4 <- convert2df("/Users/user/OneDrive/Curriculum/Artigos em
> andamento/Cooperativismo/WOS/savedrecs (15).bib", dbsource = "isi", format
> = "bibtex")
>
>
>
>
> #W <- mergeDbSources(W1, W2, W3, W4)
>
>
>
>
> # SCOPUS: Converter os dados   para o padr?o do bibliometrix
>
> *S <-convert2df("C:/Users/bruno/Desktop/Bibliometria/scopus_elsevier.bib",
> dbsource = "scopus", format = "bibtex")*
> #S2 <- convert2df("/Users/user/OneDrive/Curriculum/Artigos em
> andamento/Cooperativismo/Scopus/scopus (2).bib", dbsource = "scopus",
> format = "bibtex")
> #S3 <- convert2df("/Users/user/OneDrive/Curriculum/Artigos em
> andamento/Cooperativismo/Scopus/scopus (4).bib", dbsource = "scopus",
> format = "bibtex")
> #S4 <- convert2df("/Users/user/OneDrive/Curriculum/Artigos em
> andamento/Cooperativismo/Scopus/scopus (5).bib", dbsource = "scopus",
> format = "bibtex")
> #S5 <- convert2df("/Users/user/OneDrive/Curriculum/Artigos em
> andamento/Cooperativismo/Scopus/scopus (6).bib", dbsource = "scopus",
> format = "bibtex")
> #S6 <- convert2df("/Users/user/OneDrive/Curriculum/Artigos em
> andamento/Cooperativismo/Scopus/scopus (7).bib", dbsource = "scopus",
> format = "bibtex")
> #S7 <- convert2df("/Users/user/OneDrive/Curriculum/Artigos em
> andamento/Cooperativismo/Scopus/scopus (8).bib", dbsource = "scopus",
> format = "bibtex")
> #S8 <- convert2df("/Users/user/OneDrive/Curriculum/Artigos em
> andamento/Cooperativismo/Scopus/scopus (9).bib", dbsource = "scopus",
> format = "bibtex")
> #S9 <- convert2df("/Users/user/OneDrive/Curriculum/Artigos em
> andamento/Cooperativismo/Scopus/scopus (10).bib", dbsource = "scopus",
> format = "bibtex")
> #S10 <- convert2df("/Users/user/OneDrive/Curriculum/Artigos em
> #andamento/Cooperativismo/Scopus/scopus (11).bib", dbsource = "scopus",
> #format = "bibtex")
>
>
> #S <- mergeDbSources(S1, S2, S3, S4, S5, S6, S7, S8, S9, S10)
>
> # PUBMED: Se desejar caregar dado, execute o script do PubMed, gerando o
> #arquivo de dados "C"
>
> # COCHRANE: Se desejar carregar dados  execute a linha que segue, gerando
> #o arquivo de dados "D"
> # D <- convert2df("c:/bib/citation-export.bib", dbsource = "isi", format =
> "bibtex")
>
> #### Juntar bases WEB OF SCIENCE (ISI), SCOPUS, PUBMED e #COCHRANE
> *M <- mergeDbSources(W, S, remove.duplicated = TRUE)*
>
> # se precisar juntar dados do Pubmed e Cochrane, execute linha que segue
> # M <- mergeDbSources(A, B, C, D, remove.duplicated = TRUE)
>
> #### Cria um arquivo.csv para importar para o Excel
> *P<- M[,c("AU","TI","SO","AB","DE", "ID", "DI","LA","DT","TC","PY")] * #
> #Cria lista na ordem desejada
> *write.table(P, "C:/Users/bruno/Desktop/Bibliometria/opa.csv", sep=";",
> row.names=FALSE)* # para gerar com separador ";", sem necessidade de
> #ajustar o CSV, quanto ? primeira coluna
>
> #### BiblioAnalysis - Processamento dos dados
> *resultados <- biblioAnalysis(M)*
>
>
>
>
> ############### ETAPA 2 - AN?LISE e VISUALIZA??O DOS DADOS ###############
>
> #### 2.1 - Resumo dos resultados na console do RStudio
>
>
> *Resumo <- summary(object = resultados, k = 10)Resumoplot(resultados, k=10)*
>   # Gr?ficos com dados bibliom?tricos b?sicos
> *plot*
>
>
> # Para visualizar os resultados via web-interface (browser)
> *biblioshiny()*
>
> #### Para mais informa??es, tutoriais e v?deos, acessar
> www.bibliometrix.org/
>
> This is the console's message about the error:
>
>
>
>
>
>
>
>
>
>
>
>
>
> *Warning: Error in eventReactiveValueFunc: object 'M' not found  149:
> eventReactiveValueFunc
> [C:\Users\bruno\OneDrive\Documentos\R\win-library\4.1\bibliometrix\biblioshiny/server.R#321]
> 105: DATAloading  104: exprFunc
> [C:\Users\bruno\OneDrive\Documentos\R\win-library\4.1\bibliometrix\biblioshiny/server.R#330]
> 103: widgetFunc  102: htmlwidgets::shinyRenderWidget  101: func   88:
> renderFunc   87: renderFunc   83: renderFunc   82: output$contents    2:
> runApp*
> *    1: biblioshiny *
>
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help using r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.