Bibliometrics (12): Introduction to the Bibliometrix package of R

[@RESEARCHHUB]

If you are using the latest version of “bibliometrix”, you do not need the “readFiles” command anymore. For example, D

[@sumantaghosh5899]

Recently, I'm tried with these code.. it's works.. but sir, where I found the entire codes, as u said the SOP. In recent versions, there is no such doc files inside the R-folder... I also checked Research HUB website, it's not there also... please help me.. I need this entire script. Biblioshiny is ok but it's better to go with R, as u suggest. So I'm trying tht.. Thanks in adv sir. Ur video really help me a lots..

[@filipacastilho7344]

Hi! I am having trouble using the new version of bibliometrix as I have 3 documents and it doesn't seem to accept it, the error is: Error: unexpected ','

[@salvon.960]

Your R tutorial is pure gold. Thanks for sharing your knowledge and skills.

[@ziaulhaquemunim]

Hi, I would suggest to everyone not to run the codes all together. When doing the analysis for the first time, please run one by one code, and function by function. And play with each of the commands when running, checkout the "help" command to understand what can be done with each of the function provided by the #Bibliometrix package! Also, I would suggest not to just copy paste the codes, but to write them, all of them, and one by one, even though they are the same! #ResearchHUB

[@AhmedSWafi]

I used latest version of R studio and I do not find the doc file in R. What should I do ?

[@sjanani9696]

Not sure if this is possible with the bibliometrix R package...but can we use co-word network analysis to get a breakdown of where the author keywords (ID) are being primarily used? More specifically, to figure out how and how much the countries are using these terms. Thanks in advance...the package and video are quite useful.

[@adeoyeraphael2868]

After loading my plain text, it says error : invalid 'times' argument. What am I supposed to do

[@Divya_new]

Hi, you were talking about sample. Could you plz suggest about sample file.. I want to do bib analysis but I don't know how to arrange articles in a list for R. Regards.

[@mariaalejandrareyesparga2797]

Thank you. It was really helpfull. So helpful that It moved me to write my first comment ever on a KZbin video.

[@RESEARCHHUB]

Thank you very much!

[@ArjunCPArjun]

Hai, Thank you for the wonderful video. While downloading data from Web of Science using key work eg. The human-wildlife conflict there will be articles from different areas of conflict that may include conflict in Syria etc. how I can remove those irrelevant articles from my data set? Do you have any specific codes for that? Please consider this as a request and reply me, I think many of your viewers also have the same doubt

[@mustafaali5222]

D

[@alekoseleftherios]

Please i need help, when i opne my file i get this "Error in `$

[@RESEARCHHUB]

Yes, that could be problem.

[@valentinereiss-woolever5200]

Hi there, currently doing a systematic map, and have classified several hundred papers by hand after examination of their abstract and full paper. Bibliometrix produces a lot of the analysis I'm looking for, but can I use my own cvs file of classifications rather than papers imported from web of science? Thanks a lot in advance!

[@sabrinabdelghany9137]

W = convert2df("WoS.bib", dbsource = "wos", format = "bib") Converting your wos collection into a bibliographic dataframe 'format' argument is not properly specified 'format' argument has to be a character string matching one among: api bibtex csv endnote excel plaintext pubmed Error in "PY" %in% names(M) : object 'M' not found What does this error message means and how to be fixed please?

[@MrJJacobs152]

Thanks for making this video. When I run my .bib file I get "Converting your ISI collection into a bibliographic dataframe", but then I get an error which reads: Error in as.character (text): cannot coerce type 'closure' to vector of type 'character'. Any suggestions on how to fix this? Using R Studio 1.1.383 on iOS El Capitan 10.11.6. It seem as if the bibliometrix-vignette.R package I'm using is saying there are problems with the entire code. :(

[@shahibulahyan4307]

Why error when I check ✅ in Bibliometrix? I have just installed the rstudio & bibliometrix package.

[@JayachandranPR]

I am unable to download my trifield plot in Bibliometrix. The website hangs when I click the download button. Please help.

[@gyanajeetyumnam5841]

How to correct this error please help me "Error in seq.default(min(df2$year), max(df2$year), by = 2) : 'from' must be a finite number In addition: There were 15 warnings (use warnings() to see them)"

[@valerionetophdcandidate]

How can I wrte the synonyms in the txt file?

[@philippegenois-lefrancois2606]

Thanks very much! What a powerful tool

[@allannhapulo8271]

how can we load the data if we have around 500 .bib files ?

[@sepidehblanch]

When it comes to creating the networks, I don' have lines that connect the dots?

[@muridsemesta4683]

Thanks a lot for this tutorial. I have a question, how to deal with the more than 2000 data which is limited by Scopus? Can we download separately than merge the excel file? Thanks

[@RESEARCHHUB]

yes, you can download separately and merge for analysis.

[@muridsemesta4683]

@@RESEARCHHUB is there any certain method to merge it? Or just merge the CSV files manually?

[@AbcXyz-tw5ir]

How many files can be combined in read file argument. Cux when i am cimbining 29 files its giving error?

[@RESEARCHHUB]

I have combined upto 35 files and it worked fine. //zhmunim

[@anuradhasaikia9305]

I am not able to find doc folder in bibliometrics

[@mizhimo]

Hello, I can't find the file that you use for your demo bibliometrix-vignette.R Im using R 4.22 and bibliometrix 4.0. Even the folder doc does not exist. Does anybody know where I can find it?

[@briansoftware849]

I am with the same problem. 😕

[@elizacortes9028]

I cant combined two files, Its mark error if i conect with a comma, whats wrong?

[@danielnocera9042]

Hello, First congratz for this video. I cant find in C:\Users\Daniel\Documents\R\win-library\3.4\bibliometrix the folder DOC with this files to open in Rstudio. Where can i find it?

[@RESEARCHHUB]

Hi, first you need to install the "bibliometrix" package in R. Then it should work. Also, we will upload another video in more detail by the next weekend. Also, also provide all codes via our website.

[@younisahmed8751]

i sucesssfully installed the bibliometric package but when i try to install libaray its showing error???? can anyone help?

[@rodrigofigueroa4892]

Thanks a lot for this video, it was really helpful!

[@NadeemShafiqueButt]

Great, excellent work

[@RESEARCHHUB]

thanks for appreciation.

[@AbcXyz-tw5ir]

Rstudio fails to analyze more than 5500 records. Why?

[@NadeemShafiqueButt]

Thank you very much for very useful tutorial. Can you please guide me what is NP under author metrics? Author h_index g_index m_index TC NP PY_start

[@Durocarlos]

Hi, Error in "PY" %in% names(M) : object 'M' not found

[@korinziat.8212]

Hello, thanks for the video. But after clicking "Source", I get the following error: Error in data.frame(Description = Description, Results = Results, stringsAsFactors = FALSE) : arguments imply differing number of rows: 15, 11 How can I solve it? Thanks.

[@RESEARCHHUB]

Hi, I would suggest to everyone not to run the codes all together using the 'source' command. When doing the analysis for the first time, please run one by one code, and function by function. And play with each of the commands when running, checkout the "help" command to understand what can be done with each of the function provided by the #Bibliometrix package! Also, I would suggest not to just copy paste the codes, but to write them, all of them, and one by one, even though they are the same! Good luck. Ziaul H. Munim

[@moniquepaez5310]

Hi! Thank you for the video. I'm having some issues with the results, it appears the following error: Error in summary.bibliometrix(object = results, k = 10, pause = FALSE) : object 'AAA' not found How can I fix it?

[@BeVal]

You can't unless you modify the function (but you surely don't want to mess around with it unless you really know what are you doing). It means that your dataset does not have information concerning keywords (at this level you should get a data.frame with the most relevant keywords authors keywords and number of articles along with keywords plus and number of articles)

[@prateekkalia9758]

Can you please make a video on merging wos and Scopus databases into one file?

[@RESEARCHHUB]

Sure! But as I mentioned to you already, merged file usually do not make meaningful bibliometric analysis. It can be used in systematic or content analysis better. Anyway, let me know if your analysis worked with the codes I sent you. Munim.

[@tuansonnguyen3554]

Dear Sir, If I have two bib file, one from Scopus and one from Web of Science, please let me know how I can combine them to run bibliometrics in R. I put like this: file

[@RESEARCHHUB]

It will now run. To the best of our knowledge it is not possible to combine data from two databases. Munim.

[@tuansonnguyen3554]

@@RESEARCHHUB Thanks.

[@cvsccau7384]

Hi! I exported dimesions.ai data in xlsx format. I did what you did in 5.02 in the video i.e., pasted the file location.xlsx, changed the dbsource="dimensions" format= "xlsx". When i clicked "run" it gave me the following errors -> Error in readFiles("C:/Users/store/Documents/R/Dimensions-Publication-2020-01-24_10-02-02.xlsx") : could not find function "readFiles" and > M

[@RESEARCHHUB]

Hi, to the best of our knowledge, bibliometrix works with only bibtext or plaintext files. see how to extract at kzbin.info/www/bejne/rYOqkoB5jp2bj5Y

[@চটপটঝটপট]

Hi can I load 2 extracted plain text files together when one is from web of science and another from Scopus?

[@RESEARCHHUB]

Not likely to work. But you can give a try and let us know if it works.

[@bussub8778]

Thanks for these excellent tutorials, @@RESEARCHHUB! I was wondering if you could find any solution to combine different two sources as it was mentioned above before (one is from web of science and another from Scopus)? I am trying but it seems that it is not possible to load two different files into biblioshiny also :/

[@mohammedalrezq4923]

Dose this bibliometrics analyze files from other platforms/database such as ProQuest or Engineering Village?

[@RESEARCHHUB]

Unfortunately, no.

[@mohammedalrezq4923]

Thank you for your reply. But I noticed these platforms (ProQuest and Engineering village) can generate plain text files format, isn't that enough to analyze these file using biblimetrics library?

[@RESEARCHHUB]

@@mohammedalrezq4923 That is not enough. Data in plaintext needs to be formatted in a certain way.

[@mohammedalrezq4923]

Thank you for your great works and I hope to see more platforms to be included in the future

[@paolabalbi9200]

Molto chiaro e facile

[@sumeyyearkan2089]

Hi! Thanks for your work. I couldnt find the “doc” in bibliometrix file. What should I do?

[@RESEARCHHUB]

you can download the r-script from researchhub.org/store/

[@AbcXyz-tw5ir]

I am combining 28 bibtex files n all the articles are extracted which is 13,811 but 5500 are analyzed n then got an error.

[@RESEARCHHUB]

did you collect data properly? pls see this video for proper data extraction from scopus at kzbin.info/www/bejne/iKjZenxui6yYY7s //zhmunim

[@nageshwarpatel2668]

Hello, Please help me here, When I am trying to upload the data, it is showing that "Error in readFiles("C:/Users/patel/Documents/savedrecs.bib") : could not find function "readFiles"" What is the problem here. I am unable to figure it out.

[@RESEARCHHUB]

Hi, have you used the library(bibliometrix) command to initiate the package?

[@nageshwarpatel2668]

@@RESEARCHHUB Yes, I followed every step again and again. Installed the package, run the library. but problem is still persisting.

[@RESEARCHHUB]

@@nageshwarpatel2668 can you post a screen shot of your R window here? or send via message to facebook.com/research.hub.org/

[@RESEARCHHUB]

Usually the problem is fixed after reinstalling the program.@@nageshwarpatel2668

[@Footyfanati-y2o]

i am getting an error when running my code and the error is:Error in seq.default(iStart, iStop) : 'from' must be a finite number

[@ankea27]

I Have the same mistake :( , have you found a solution?

[@eriklankut4107]

Hi, sorry for late reply! do you still have the same issue? please copy your whole command you were trying to run!

[@Shenilaz]

Error in grep(x, M$CR[M$PY >= Year]) : invalid regular expression, reason 'Missing ')'' I am getting the above error. What should I do?

[@RESEARCHHUB]

when are you getting this error? can you please post the command?

[@Shenilaz]

@@RESEARCHHUB If I just run then its okay but when i press the source button for plotting the graphs i get this error. Error in grep(x, M$CR[M$PY >= Year]) : invalid regular expression, reason 'Missing ')'' In addition: Warning messages: 1: Removed 1 rows containing missing values (position_stack). 2: Removed 1 rows containing missing values (geom_path). 7: grep(x, M$CR[M$PY >= Year]) 6: histNetwork(M, sep = sep) 5: localCitations(M, sep = ";") at bibliometrix-vignette.R#39 4: eval(ei, envir) 3: eval(ei, envir) 2: withVisible(eval(ei, envir)) 1: source("C:/Program Files/R/R-3.5.2/library/bibliometrix/doc/bibliometrix-vignette.R")

[@RESEARCHHUB]

Source button is to run all codes in the script at once (and not to plot the graphs) which you should never do. Can you please run each of the code lines one by one and tell us after which code you are getting the errors? @@Shenilaz

[@Shenilaz]

I get a warning "Removed 1 rows containing missing values (position_stack)" "Removed 1 rows containing missing values (geom_path)" What does this mean?

[@RESEARCHHUB]

As it is not an error, your analysis may still be valid. Without looking at your example data, this is a typical warning from ggplot that is simply telling you that for some combination of the data frame you tried to plot, there was some missing data (NAs). It's nothing to worry about unless you weren't expecting any missing data. To know that, you'll need to look at your data set.

[@JayachandranPR]

@@RESEARCHHUB I am unable to download my trifield plot in Bibliometrix. The website hangs when I click the download button. Please help.

[@khizratariq1423]

when i perss the source ... Access Denied..please help me

[@RESEARCHHUB]

Hi, I would suggest to everyone not to run the codes all together using the 'source' command. When doing the analysis for the first time, please run one by one code, and function by function. And play with each of the commands when running, checkout the "help" command to understand what can be done with each of the function provided by the #Bibliometrix package! Also, I would suggest not to just copy paste the codes, but to write them, all of them, and one by one, even though they are the same! Good luck. Ziaul H. Munim

[@amirhosseinyaghoubi1202]

I followed every step as instructed. However, this error happens every time: Error in if (min(M$PY) < past) { : missing value where TRUE/FALSE needed after running this line of the command: ## ----h-index---------------------------------------------------------------------------------------------------------- indices

[@GerogeMathew]

Did you find a solution to this? @ResearchHub any suggestions?

[@amirhosseinyaghoubi1202]

@@GerogeMathew Yeah I found one. The error occurs when ever there is a missing year in the data frame. Column PY is for showing the year of the publication in data frame M( you can view data frame M by double clicking on it.) somehow, in the process of extracting data from web of science, some of the years are not recorded and these years are shown as NA. To solve the problem: 1. You need to find out which publications are not having a year. Type: which(is.na(M$PY)) It shows you what rows (paper) are having NA as the year of publication. 2. Now to replace it: edit(M) the editor allows you to change NA value to the year of the publication.

[@GerogeMathew]

@@amirhosseinyaghoubi1202 Thank you for your reply and suggestion. There was some problem with the WoS file that I was using. I had done another search and the new file did not give me this problem. I had not bothered to examine the older file but now I know just what to do...I appreciate your response.

[@RESEARCHHUB]

@@amirhosseinyaghoubi1202 Thank you very much for solving the issue.

[@pushpadm4755]

plz help me analysis pubmed data in bibliometrix package

[@RESEARCHHUB]

Hi, at the moment bibliometrix works only with web of science and scopus data. Please try other software. For example, bibexcel and gephi. Have a look on this video kzbin.info/www/bejne/lX2rk42wnN2dfpo

[@BeVal]

If you can export your data in bibtext format or in .csv, you can still use bibliometrix; you just use format="bibtext" or "generic" and it runs. You probably will not have all the information you get when using scopus or web of science, but you will have useful data for a more than a basic analyisis.

[@lorikmucolli2496]

How can I access the codebase?

[@RESEARCHHUB]

You can access from here bibliometrix.org/documents/bibliometrix_Report.html

[@lorikmucolli2496]

Thank you!

[@AbcXyz-tw5ir]

R studio is not a good tool to use

[@RESEARCHHUB]

Please try using the new user friendly #biblioshiny app. See video at kzbin.info/www/bejne/b4rah5t8etSpeaM

[@haochengwang2720]

I saw lol

[@mechram4609]

cant find the bibliometrix-vignette.r anywhere in my entire drive ... i cant even download it from somewhere else