diff --git a/BibPlots.Rmd b/BibPlots.Rmd new file mode 100644 index 0000000..7c59d64 --- /dev/null +++ b/BibPlots.Rmd @@ -0,0 +1,23 @@ +--- +title: "BibPlots" +output: html_notebook +--- + +### BibPlots + +https://cran.r-project.org/web/packages/BibPlots/BibPlots.pdf + +- **R package for producing beamplots as a preferred alternative to the h index when assessing single researchers (based on downloads from Web of Science)** + +Haunschild, R., Bornmann, L. & Adams, J. Scientometrics (2019) 120: 925. +https://doi.org/10.1007/s11192-019-03147-3 +https://link.springer.com/article/10.1007/s11192-019-03147-3 + + +```{r} +library("BibPlots") + +BibPlots::beamplot(wos_file = "~/PubMed/data/BalciSerdar-B-6401-2011-WOS-OnlyArticles.txt", + do_weight = FALSE) +``` + diff --git a/BibPlots.nb.html b/BibPlots.nb.html new file mode 100644 index 0000000..5b0abe6 --- /dev/null +++ b/BibPlots.nb.html @@ -0,0 +1,1834 @@ + + + + + + + + + + + + + + +BibPlots + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + +
+

BibPlots

+

https://cran.r-project.org/web/packages/BibPlots/BibPlots.pdf

+ +

Haunschild, R., Bornmann, L. & Adams, J. Scientometrics (2019) 120: 925. https://doi.org/10.1007/s11192-019-03147-3 https://link.springer.com/article/10.1007/s11192-019-03147-3

+ + + +

+ + + + +
+ +
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
+ + + +
+ + + + + + + + + + + + + + + + diff --git a/Bibliyometri.Rmd b/Bibliyometri.Rmd new file mode 100644 index 0000000..cb8ceb0 --- /dev/null +++ b/Bibliyometri.Rmd @@ -0,0 +1,89 @@ +--- +title: "Bibliyometri" +output: html_notebook +--- + + +- Web Of Science'dan her zaman tab delimited olarak indir. + + +- Tab delimited dosyaları birleştir. +cat + +https://unix.stackexchange.com/questions/3770/how-to-merge-all-text-files-in-a-directory-into-one +https://apple.stackexchange.com/questions/80611/merging-multiple-csv-files-without-merging-the-header + + + +AU: yazar +AF: yazar açık adları +TI: title, çalışma başlığı +SO: source, dergi ismi +DT: döküman tipleri +DE: yazarın verdiği anahtar sözcük +ID: WOS anahtar sözcükler +AB: abstract varsa +C1: adresler +RP: yazışma adresi +CR: makalenin verdiği referanslar. kayabiliyor. + +NF: bu yayın kaç atıf yapmış +TC: bu yayın kaç atıf almış + +PY: yıl + +WC: web of science categories (daha geniş kapsamlı) +SC: subject categories (dergi kategorisi) + +kategorilerle analiz için citespace kullan + + +UT: alanı boş olmamalı + +UT alanı yoksa, kendin veri oluşturuyorsan tekil WOS: numarası verebilirsin + + +alanlardaki unsurlar WOS'da `;` ile ayrılır. Scopus'da `,` ile ayrılıyor. + + + +``` + WC="Information Science & Library Science" AND AD="Turkey" +``` + +Vosviewer için tab-delimited text olarak kaydetmek lazım. +excel tab-limited olarak kaydedince `"` ekliyor. Bunları silmek lazım. + +metin içinde Türkçe karakterleri değiştirmek lazım. +theseraus ya da regex kullanmak lazım +stop word çıkartmak lazım + + + +Vosviewer yüklemeyi drive ile dene + + + +``` +SO="pathology" AND AD="Turkey" +``` + + +citespace + +data import export +wos tab to wos + + +java -Dfile.encoding=UTF-8 -Duser.country=US -Duser.language=en -Xss5m -jar CiteSpaceV.jar + +java -Dfile.encoding=UTF-8 -Duser.country=US -Duser.language=en -Xms1g -Xmx12g -Xss5m -jar CiteSpaceV.jar + + + + + + + + + diff --git a/Bibliyometri.nb.html b/Bibliyometri.nb.html new file mode 100644 index 0000000..7bb04d3 --- /dev/null +++ b/Bibliyometri.nb.html @@ -0,0 +1,1835 @@ + + + + + + + + + + + + + +Bibliyometri + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + +

https://unix.stackexchange.com/questions/3770/how-to-merge-all-text-files-in-a-directory-into-one https://apple.stackexchange.com/questions/80611/merging-multiple-csv-files-without-merging-the-header

+

AU: yazar AF: yazar açık adları TI: title, çalışma başlığı SO: source, dergi ismi DT: döküman tipleri DE: yazarın verdiği anahtar sözcük ID: WOS anahtar sözcükler AB: abstract varsa C1: adresler RP: yazışma adresi CR: makalenin verdiği referanslar. kayabiliyor.

+

NF: bu yayın kaç atıf yapmış TC: bu yayın kaç atıf almış

+

PY: yıl

+

WC: web of science categories (daha geniş kapsamlı) SC: subject categories (dergi kategorisi)

+

kategorilerle analiz için citespace kullan

+

UT: alanı boş olmamalı

+

UT alanı yoksa, kendin veri oluşturuyorsan tekil WOS: numarası verebilirsin

+

alanlardaki unsurlar WOS’da ; ile ayrılır. Scopus’da , ile ayrılıyor.

+
 WC="Information Science & Library Science" AND AD="Turkey" 
+

Vosviewer için tab-delimited text olarak kaydetmek lazım. excel tab-limited olarak kaydedince " ekliyor. Bunları silmek lazım.

+

metin içinde Türkçe karakterleri değiştirmek lazım. theseraus ya da regex kullanmak lazım stop word çıkartmak lazım

+

Vosviewer yüklemeyi drive ile dene

+
SO="pathology" AND AD="Turkey"
+

citespace

+

data import export wos tab to wos

+

java -Dfile.encoding=UTF-8 -Duser.country=US -Duser.language=en -Xss5m -jar CiteSpaceV.jar

+

java -Dfile.encoding=UTF-8 -Duser.country=US -Duser.language=en -Xms1g -Xmx12g -Xss5m -jar CiteSpaceV.jar

+ + +
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
+ + + +
+ + + + + + + + diff --git a/PathologyArticlesFromTurkey.Rmd b/PathologyArticlesFromTurkey.Rmd new file mode 100644 index 0000000..71d1fef --- /dev/null +++ b/PathologyArticlesFromTurkey.Rmd @@ -0,0 +1,168 @@ +--- +title: "Pathology Articles From Turkey" +description: | + Collections and Peeriodicals of selected Pathology Articles From Turkey +author: + - name: Serdar Balcı + url: https://www.serdarbalci.com/ + affiliation: MD Pathologist + affiliation_url: https://sbalci.github.io/ +date: "`r Sys.Date()`" +output: distill::distill_article +--- + +```{r library, include=FALSE} +suppressPackageStartupMessages(library(tidyverse)) +suppressPackageStartupMessages(library(readxl)) +suppressPackageStartupMessages(library(markdown)) +suppressPackageStartupMessages(library(kableExtra)) +suppressPackageStartupMessages(library(tidyRSS)) +``` + + + +```{r setup, include=FALSE} +knitr::opts_chunk$set(echo = FALSE) +``` + + + + + + +--- + +# Pathology Articles From Turkey Peeriodical + +https://peeriodicals.com/peeriodicals/pathology-articles-from-turkey + + +--- + +# RSS Feed From PubMed + +``` +(pathology[Affiliation] OR patoloji[Affiliation]) AND (Turk*[Affiliation] OR Türk*[Affiliation]) +``` + +`r icon::fa("rss")` +[Click Here for the RSS Link](https://eutils.ncbi.nlm.nih.gov/entrez/eutils/erss.cgi?rss_guid=10UQVR81oEgBsJdu9HkJM34nE3gKkc0-VJoAwxWLhi1d2qRs7u) + + + +```{r} +# https://cran.r-project.org/web/packages/tidyRSS/vignettes/tidyrss.html +PAFT_rss1 <- tidyRSS::tidyfeed("https://eutils.ncbi.nlm.nih.gov/entrez/eutils/erss.cgi?rss_guid=10UQVR81oEgBsJdu9HkJM34nE3gKkc0-VJoAwxWLhi1d2qRs7u") +``` + + + +```{r} +PAFT_rss2 <- feedeR::feed.extract("https://eutils.ncbi.nlm.nih.gov/entrez/eutils/erss.cgi?rss_guid=10UQVR81oEgBsJdu9HkJM34nE3gKkc0-VJoAwxWLhi1d2qRs7u") +``` + + + + + + +--- + +# PubMed Collection + + +My NCBI » Collections > Pathology Articles From Turkey + +`(pathology[Affiliation] OR patoloji[Affiliation]) AND (Turk*[Affiliation] OR Türk*[Affiliation])` AND `WOS Journals with Pathology Topic` + +https://www.ncbi.nlm.nih.gov/sites/myncbi/collections/58299810/ + +View my collection, "Pathology Articles From Turkey" from NCBI + + + + +```{r download PAFT data, include=FALSE} +PAFT <- readr::read_csv("https://www.ncbi.nlm.nih.gov/sites/myncbi/collections/58299810/?title=Open%20as%20spreadsheet&") + +``` + + +```{r Prepare Table, eval=FALSE, include=FALSE} +PAFT2 <- PAFT %>% + mutate(Link = paste0("https://www.ncbi.nlm.nih.gov", URL)) %>% + select(Title, Link) %>% + head(n=25) +``` + + +**Style1** + +```{r Print Table, eval=FALSE, include=FALSE, layout="l-body-outset"} +rmarkdown::paged_table(PAFT2) +``` + +**Style2** + +```{r Print Table 2, eval=FALSE, include=FALSE, layout="l-body-outset"} +PAFT2 %>% + gt::gt() +``` + +**Style3** + +```{r Print Table 3, eval=FALSE, include=FALSE, layout="l-body-outset"} +PAFT2 %>% + print.data.frame() +``` + +**Style4** + +```{r Print Table 4, eval=FALSE, include=FALSE, layout="l-screen-inset"} +PAFT2 %>% + knitr::kable() +``` + + + +```{r Print Table Molecular, eval=FALSE, include=FALSE, layout="l-screen-inset"} + +# PancreasPBPathArticles$Title <- kableExtra::cell_spec( +# PancreasPBPathArticles$Title, +# popover = kableExtra::spec_popover( +# content = PancreasPBPathArticles$Journal +# ) +# ) + + +PAFT %>% + filter(Molecular == TRUE) %>% + select(Title, PubMedLink) %>% + kableExtra::kable(escape = FALSE) %>% + kableExtra::kable_styling( + bootstrap_options = c("striped", + "hover", + "condensed", + "responsive"), + fixed_thead = TRUE, + full_width = TRUE + ) %>% + kableExtra::scroll_box(height = "300px") +``` + + + + +## Acknowledgments {.appendix} + +## Footnotes {.appendix} + +## References {.appendix} + +## Document Information {.appendix} + +Last updated on `r Sys.Date()`. + + + + diff --git a/PathologyArticlesFromTurkeyComparedtoAllPublishedArticles.Rmd b/PathologyArticlesFromTurkeyComparedtoAllPublishedArticles.Rmd index 5d993d3..39bf64b 100644 --- a/PathologyArticlesFromTurkeyComparedtoAllPublishedArticles.Rmd +++ b/PathologyArticlesFromTurkeyComparedtoAllPublishedArticles.Rmd @@ -258,7 +258,6 @@ data_hacettepePathology2 <- data_hacettepePathology %>% data_hacettepePathology2 <- data_hacettepePathology2 %>% separate(col = "Affiliation", sep = ";", into = paste0("Affiliation", 1:6925)) - ``` diff --git a/RetractedPathologyArticles/RetractedPathologyArticles.Rmd b/RetractedPathologyArticles/RetractedPathologyArticles.Rmd new file mode 100644 index 0000000..f8833b3 --- /dev/null +++ b/RetractedPathologyArticles/RetractedPathologyArticles.Rmd @@ -0,0 +1,312 @@ +--- +title: "Retracted Pathology Articles in PubMed" +output: html_notebook +--- + +# Aim + +To evaluate the retracted articles in PubMed. + + + +# Materials and Methods + +Data downloaded on 20.10.2019. + +[currentlyindexed_nlmcatalog_result.xml](https://www.ncbi.nlm.nih.gov/portal/utils/file_backend.cgi?Db=nlmcatalog&HistoryId=NCID_1_12059143_130.14.18.48_5555_1571596396_818866540_0MetA0_S_HStore&QueryKey=1&Sort=PubDate&Filter=all&CompleteResultCount=5244&Mode=file&View=xml&p$l=Email&portalSnapshot=%2Fprojects%2Fentrez%2Fpubmed%2FPubMedGroup@1.146&BaseUrl=&PortName=live&RootTag=NLMCatalogRecordSet&DocType=NLMCatalogRecordSet%20PUBLIC%20%22-%2F%2FNLM%2F%2FDTD%20NLMCatalogRecordSet,%201st%20June%202017%2F%2FEN%22%20%22https://www.nlm.nih.gov/databases/dtd/nlmcatalogrecordset_170601.dtd%22&FileName=&ContentType=xml) + + +[Retracted_Publication_sb_OR_Retraction_of_Publication_sb_pubmed_result.xml](https://www.ncbi.nlm.nih.gov/portal/utils/file_backend.cgi?Db=pubmed&HistoryId=NCID_1_12059143_130.14.18.48_5555_1571596396_818866540_0MetA0_S_HStore&QueryKey=18&Sort=&Filter=all&CompleteResultCount=14043&Mode=file&View=xml&p$l=Email&portalSnapshot=%2Fprojects%2Fentrez%2Fpubmed%2FPubMedGroup@1.146&BaseUrl=&PortName=live&RootTag=PubmedArticleSet&DocType=PubmedArticleSet%20PUBLIC%20%22-%2F%2FNLM%2F%2FDTD%20PubMedArticle,%201st%20January%202019%2F%2FEN%22%20%22https://dtd.nlm.nih.gov/ncbi/pubmed/out/pubmed_190101.dtd%22&FileName=&ContentType=xml) + + +[Retracted_Publication_sb_OR_Retraction_of_Publication_sb_timeline.csv](https://www.ncbi.nlm.nih.gov/pubmed?p$l=Email&Mode=download&term=Retracted%20Publication[sb]%20OR%20Retraction%20of%20Publication[sb]&dlid=timeline&filename=timeline.csv&bbid=&p$debugoutput=off) + + + +- Find Retractions Using PubMed and My NCBI! + +https://hslnews.wordpress.com/2013/05/14/retractions/ + +- Comment Correction Type + +https://www.ncbi.nlm.nih.gov/books/NBK3827/#pubmedhelp.Comment_Correction_Type + + + +> Comment Correction Type +> +> The data in these fields are citations to other associated journal publications, e.g., comments or errata. Often these link to the respective citation. Comments/Corrections data can be retrieved by the search term that follows each type: +> +> Comment in: hascommentin +> Comment on: hascommenton +> Corrected and republished in: hascorrectedrepublishedin +> Corrected and republished from: hascorrectedrepublishedfrom +> Dataset use reported in: hasassociatedpublication +> Dataset described in: hasassociateddataset +> Erratum in: haserratumin +> Erratum for: haserratumfor +> Expression of concern in: hasexpressionofconcernin +> Expression of concern for: hasexpressionofconcernfor +> Original Report in: hasoriginalreportin +> Republished in: hasrepublishedin +> Republished from: hasrepublishedfrom +> Retracted and republished in: hasretractedandrepublishedin +> Retracted and republished from: hasretractedandrepublishedfrom +> Retraction in: hasretractionin +> Retraction of: hasretractionof +> Summary for patients in: hassummaryforpatientsin +> Update in: hasupdatein +> Update of: hasupdateof +> + +- Errata, Retractions, and Other Linked Citations in PubMed + +https://www.nlm.nih.gov/bsd/policy/errata.html + + + + + + + +```{r Search PubMed download PMID, eval=FALSE, include=FALSE} +myTerm <- rstudioapi::terminalCreate(show = FALSE) +rstudioapi::terminalSend( + myTerm, + "esearch -db pubmed -query \"(pathology[Affiliation] OR patoloji[Affiliation]) AND (Turkey[Affiliation] OR Türkiye[Affiliation])\" -datetype PDAT -mindate 1800 -maxdate 3000 | \ efetch -format uid > data/pubmed_result_TurkPath_uid.txt \n" +) +Sys.sleep(1) +repeat { + Sys.sleep(0.1) + if (rstudioapi::terminalBusy(myTerm) == FALSE) { + print("Code Executed") + break + } +} +``` + + + +```{r Search local PubMed with downloaded PMID extract data as xml, eval=FALSE, include=FALSE} +myTerm <- rstudioapi::terminalCreate(show = FALSE) +rstudioapi::terminalSend( + myTerm, + "cat data/pubmed_result_TurkPath_uid.txt | \ fetch-pubmed -path /Volumes/Agu2018/PubMed > data/pubmed_result_TurkPath.xml \n" +) +Sys.sleep(1) +repeat { + Sys.sleep(0.1) + if (rstudioapi::terminalBusy(myTerm) == FALSE) { + print("Code Executed") + break + } +} +``` + + + +# Analysis + + +A trend graph of retracted articles derived from Europe PMC #RStats #europepmc {europepmc} 📦 #evergreenreviewgraph #research #bibliography #bibliometrics + + + +```{r europepmc} +library(europepmc) +``` + + +```{r europepmc search} +retractedArticlesPerTotalArticles <- + europepmc::epmc_hits_trend( + query = "(PUB_TYPE:'Retracted Publication' OR PUB_TYPE:'Retraction of Publication')", + period = 1980:2017 + ) + +retractedArticlesPerTotalArticles$Affiliation <- "All" + +retractedArticlesPerTotalArticles_Turkey <- + europepmc::epmc_hits_trend( + query = "(AFF:'Turkey') AND (PUB_TYPE:'Retracted Publication' OR PUB_TYPE:'Retraction of Publication')", + period = 1980:2017 + ) + +retractedArticlesPerTotalArticles_Turkey$Affiliation <- "Turkey" + +retractedArticles <- dplyr::bind_rows( +retractedArticlesPerTotalArticles, +retractedArticlesPerTotalArticles_Turkey) + +``` + + + +```{r graph europepmc search} +library(ggplot2) +ggplot(retractedArticles, + aes(year, + 1000*(query_hits / all_hits), + color = Affiliation) + ) + + geom_point() + + geom_line() + + xlab("Year published") + + ylab("Proportion of Retracted Articles \n data: Europe PMC, 20.10.2019 \n 1000x") +``` + + + + + + + + + + + + +```{r extract year journal name from xml, message=FALSE, warning=FALSE} +myTerm <- rstudioapi::terminalCreate(show = FALSE) +rstudioapi::terminalSend( +myTerm, +"xtract -input data/RetractedPubMed/Retracted_Publication_sb_OR_Retraction_of_Publication_sb_pubmed_result.xml -pattern PubmedArticle -tab \"|\" -sep \";\" -def \"NA\" -element MedlineCitation/PMID ArticleTitle Journal/ISSN ISOAbbreviation PubDate/Year > data/RetractedPubMed/pubmed_result_retracted.csv \n" +) +Sys.sleep(1) +repeat { +Sys.sleep(0.1) +if (rstudioapi::terminalBusy(myTerm) == FALSE) { +print("Code Executed") +break +} +} +``` + + + +```{r read extracted data} +pubmed_result_retracted <- + readr::read_delim( + file = here::here("data", + "RetractedPubMed", + "pubmed_result_retracted.csv"), + delim = "|", + escape_double = FALSE, + col_names = FALSE, + trim_ws = TRUE + ) + +pubmed_result_retracted <- +pubmed_result_retracted %>% + select( + PMID = X1, + title = X2, + journalISSN = X3, + journalName = X4, + year = X5 + ) +``` + + + + + + +```{r extract journal name and topics from xml, message=FALSE, warning=FALSE} +myTerm <- rstudioapi::terminalCreate(show = FALSE) +rstudioapi::terminalSend( +myTerm, +"xtract -input data/currentlyindexed_nlmcatalog_result.xml -pattern NCBICatalogRecord -tab \"|\" -sep \";\" -def \"NA\" -element MedlineTA TitleAlternate BroadJournalHeadingList MeshHeading/DescriptorName ISSN > data/RetractedPubMed/journal_properties.csv \n" +) +Sys.sleep(1) +repeat { +Sys.sleep(0.1) +if (rstudioapi::terminalBusy(myTerm) == FALSE) { +print("Code Executed") +break +} +} +``` + + +```{r read clean journal properties} +journal_properties <- readr::read_delim(here::here("data", "RetractedPubMed" , "journal_properties.csv"), + "|", escape_double = FALSE, col_names = FALSE, + trim_ws = TRUE) + +journal_properties <- journal_properties %>% + select(journal = X1, + topic = X4, + ISSN = X5) + + + +journal_properties <- journal_properties %>% + mutate(journalName = str_split(journal, ";")) %>% + unnest(cols = c(journalName)) %>% + mutate(journalTopic = str_split(topic, ";")) %>% + unnest(cols = c(journalTopic)) %>% + mutate(journalISSN = str_split(ISSN, ";")) %>% + unnest(cols = c(journalISSN)) %>% + select(journalName, + journalTopic, + journalISSN) %>% + unique() + +``` + + + +```{r combine retracted articles with their journal info} +pubmed_result_retracted <- pubmed_result_retracted %>% + left_join(journal_properties, by = c("journalISSN")) +``` + + +```{r find the journal topics in which most retracted articles were} +commonTerms <- c("Medicine", "Science", "Research") + +(pubmed_result_retracted %>% + select(journalTopic, year) %>% + filter(!journalTopic %in% commonTerms) %>% + filter(!is.na(journalTopic)) %>% + group_by(journalTopic) %>% + tally() %>% + arrange(desc(n)) %>% + head(10) %>% + pull(journalTopic) -> mostRetractedTopicsOfJournal) +``` + + + + +This trend graph shows the major topics of the journals that have the most retractions. Data derived from PubMed #RStats #research #bibliography #bibliometrics + + +```{r major topics of the journals that have the most retractions} +pubmed_result_retracted %>% + filter(journalTopic %in% mostRetractedTopicsOfJournal) %>% + filter(year <= 2018 & year >= 1990) %>% + select(journalTopic, year) %>% + group_by(journalTopic, year) %>% + tally() %>% + ggplot( + aes(year, + n, + color = journalTopic + ) + ) + + geom_point() + + geom_line() + + xlab("Year published") + + ylab("Proportion of Retracted Articles \n data: Europe PMC, 20.10.2019") +``` + + + + + + + + + diff --git a/RetractedPathologyArticles/RetractedPathologyArticles.nb.html b/RetractedPathologyArticles/RetractedPathologyArticles.nb.html new file mode 100644 index 0000000..db44e2f --- /dev/null +++ b/RetractedPathologyArticles/RetractedPathologyArticles.nb.html @@ -0,0 +1,2080 @@ + + + + + + + + + + + + + + +Retracted Pathology Articles in PubMed + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + +
+

Aim

+

To evaluate the retracted articles in PubMed.

+
+
+

Materials and Methods

+

Data downloaded on 20.10.2019.

+

currentlyindexed_nlmcatalog_result.xml

+

Retracted_Publication_sb_OR_Retraction_of_Publication_sb_pubmed_result.xml

+

Retracted_Publication_sb_OR_Retraction_of_Publication_sb_timeline.csv

+ +

https://hslnews.wordpress.com/2013/05/14/retractions/

+ +

https://www.ncbi.nlm.nih.gov/books/NBK3827/#pubmedhelp.Comment_Correction_Type

+
+

Comment Correction Type

+

The data in these fields are citations to other associated journal publications, e.g., comments or errata. Often these link to the respective citation. Comments/Corrections data can be retrieved by the search term that follows each type:

+
Comment in: hascommentin
+Comment on: hascommenton
+Corrected and republished in: hascorrectedrepublishedin
+Corrected and republished from: hascorrectedrepublishedfrom
+Dataset use reported in: hasassociatedpublication
+Dataset described in: hasassociateddataset
+Erratum in: haserratumin
+Erratum for: haserratumfor
+Expression of concern in: hasexpressionofconcernin
+Expression of concern for: hasexpressionofconcernfor
+Original Report in: hasoriginalreportin
+Republished in: hasrepublishedin
+Republished from: hasrepublishedfrom
+Retracted and republished in: hasretractedandrepublishedin
+Retracted and republished from: hasretractedandrepublishedfrom
+Retraction in: hasretractionin
+Retraction of: hasretractionof
+Summary for patients in: hassummaryforpatientsin
+Update in: hasupdatein
+Update of: hasupdateof
+
+ +

https://www.nlm.nih.gov/bsd/policy/errata.html

+ + + + + + + +
+
+

Analysis

+

A trend graph of retracted articles derived from Europe PMC #RStats #europepmc {europepmc} 📦 #evergreenreviewgraph #research #bibliography #bibliometrics

+ + + +
library(europepmc)
+ + + + + + +
retractedArticlesPerTotalArticles <- 
+    europepmc::epmc_hits_trend(
+    query = "(PUB_TYPE:'Retracted Publication' OR PUB_TYPE:'Retraction of Publication')",
+    period = 1980:2017
+    )
+
+retractedArticlesPerTotalArticles$Affiliation <- "All"
+
+retractedArticlesPerTotalArticles_Turkey <- 
+    europepmc::epmc_hits_trend(
+    query = "(AFF:'Turkey') AND (PUB_TYPE:'Retracted Publication' OR PUB_TYPE:'Retraction of Publication')",
+    period = 1980:2017
+    )
+
+retractedArticlesPerTotalArticles_Turkey$Affiliation <- "Turkey"
+
+retractedArticles <- dplyr::bind_rows(
+retractedArticlesPerTotalArticles,
+retractedArticlesPerTotalArticles_Turkey)
+
+ + + + + + +
library(ggplot2)
+ggplot(retractedArticles, 
+       aes(year, 
+           1000*(query_hits / all_hits),
+           color = Affiliation)
+       ) + 
+  geom_point() + 
+  geom_line() +
+  xlab("Year published") + 
+  ylab("Proportion of Retracted Articles \n data: Europe PMC, 20.10.2019 \n 1000x")
+ + + + + + +
myTerm <- rstudioapi::terminalCreate(show = FALSE)
+rstudioapi::terminalSend(
+myTerm,
+"xtract -input data/RetractedPubMed/Retracted_Publication_sb_OR_Retraction_of_Publication_sb_pubmed_result.xml -pattern PubmedArticle -tab \"|\" -sep \";\" -def \"NA\" -element MedlineCitation/PMID ArticleTitle Journal/ISSN ISOAbbreviation PubDate/Year > data/RetractedPubMed/pubmed_result_retracted.csv \n"
+)
+Sys.sleep(1)
+repeat {
+Sys.sleep(0.1)
+if (rstudioapi::terminalBusy(myTerm) == FALSE) {
+print("Code Executed")
+break
+}
+}
+ + + + + + +
pubmed_result_retracted <-
+    readr::read_delim(
+        file = here::here("data",
+                          "RetractedPubMed",
+                          "pubmed_result_retracted.csv"),
+        delim = "|",
+        escape_double = FALSE,
+        col_names = FALSE,
+        trim_ws = TRUE
+    )
+ + +
Parsed with column specification:
+cols(
+  X1 = col_double(),
+  X2 = col_character(),
+  X3 = col_character(),
+  X4 = col_character(),
+  X5 = col_double()
+)
+ + +
pubmed_result_retracted <- 
+pubmed_result_retracted %>%
+    select(
+        PMID = X1,
+        title = X2,
+        journalISSN = X3, 
+        journalName = X4,
+        year = X5
+    )
+ + + + + + +
myTerm <- rstudioapi::terminalCreate(show = FALSE)
+rstudioapi::terminalSend(
+myTerm,
+"xtract -input data/currentlyindexed_nlmcatalog_result.xml -pattern NCBICatalogRecord -tab \"|\" -sep \";\" -def \"NA\" -element MedlineTA TitleAlternate BroadJournalHeadingList MeshHeading/DescriptorName ISSN > data/RetractedPubMed/journal_properties.csv \n"
+)
+Sys.sleep(1)
+repeat {
+Sys.sleep(0.1)
+if (rstudioapi::terminalBusy(myTerm) == FALSE) {
+print("Code Executed")
+break
+}
+}
+ + +
[1] "Code Executed"
+ + + + + + +
journal_properties <- readr::read_delim(here::here("data", "RetractedPubMed" , "journal_properties.csv"), 
+    "|", escape_double = FALSE, col_names = FALSE, 
+    trim_ws = TRUE)
+
+journal_properties <- journal_properties %>% 
+    select(journal = X1,
+           topic = X4,
+           ISSN = X5)
+
+
+
+journal_properties <- journal_properties %>% 
+    mutate(journalName = str_split(journal, ";")) %>%
+  unnest(cols = c(journalName)) %>% 
+    mutate(journalTopic = str_split(topic, ";")) %>%
+  unnest(cols = c(journalTopic)) %>% 
+    mutate(journalISSN = str_split(ISSN, ";")) %>%
+  unnest(cols = c(journalISSN)) %>% 
+    select(journalName,
+           journalTopic,
+           journalISSN) %>% 
+    unique()
+
+ + + + + + +
+ +
+ + + + + + +
+ +
+ + + +

This trend graph shows the major topics of the journals that have the most retractions. Data derived from PubMed #RStats #research #bibliography #bibliometrics

+ + + +
pubmed_result_retracted %>% 
+    filter(journalTopic %in% mostRetractedTopicsOfJournal) %>% 
+    filter(year <= 2018 & year >= 1990) %>% 
+    select(journalTopic, year) %>% 
+    group_by(journalTopic, year) %>% 
+    tally() %>% 
+    ggplot( 
+       aes(year, 
+           n,
+           color = journalTopic
+           )
+       ) + 
+  geom_point() + 
+  geom_line() +
+  xlab("Year published") + 
+  ylab("Proportion of Retracted Articles \n data: Europe PMC, 20.10.2019")
+ + +

+ + + + +
+ +
---
title: "Retracted Pathology Articles in PubMed"
output: html_notebook
---

# Aim

To evaluate the retracted articles in PubMed.



# Materials and Methods

Data downloaded on 20.10.2019.

[currentlyindexed_nlmcatalog_result.xml](https://www.ncbi.nlm.nih.gov/portal/utils/file_backend.cgi?Db=nlmcatalog&HistoryId=NCID_1_12059143_130.14.18.48_5555_1571596396_818866540_0MetA0_S_HStore&QueryKey=1&Sort=PubDate&Filter=all&CompleteResultCount=5244&Mode=file&View=xml&p$l=Email&portalSnapshot=%2Fprojects%2Fentrez%2Fpubmed%2FPubMedGroup@1.146&BaseUrl=&PortName=live&RootTag=NLMCatalogRecordSet&DocType=NLMCatalogRecordSet%20PUBLIC%20%22-%2F%2FNLM%2F%2FDTD%20NLMCatalogRecordSet,%201st%20June%202017%2F%2FEN%22%20%22https://www.nlm.nih.gov/databases/dtd/nlmcatalogrecordset_170601.dtd%22&FileName=&ContentType=xml)


[Retracted_Publication_sb_OR_Retraction_of_Publication_sb_pubmed_result.xml](https://www.ncbi.nlm.nih.gov/portal/utils/file_backend.cgi?Db=pubmed&HistoryId=NCID_1_12059143_130.14.18.48_5555_1571596396_818866540_0MetA0_S_HStore&QueryKey=18&Sort=&Filter=all&CompleteResultCount=14043&Mode=file&View=xml&p$l=Email&portalSnapshot=%2Fprojects%2Fentrez%2Fpubmed%2FPubMedGroup@1.146&BaseUrl=&PortName=live&RootTag=PubmedArticleSet&DocType=PubmedArticleSet%20PUBLIC%20%22-%2F%2FNLM%2F%2FDTD%20PubMedArticle,%201st%20January%202019%2F%2FEN%22%20%22https://dtd.nlm.nih.gov/ncbi/pubmed/out/pubmed_190101.dtd%22&FileName=&ContentType=xml)


[Retracted_Publication_sb_OR_Retraction_of_Publication_sb_timeline.csv](https://www.ncbi.nlm.nih.gov/pubmed?p$l=Email&Mode=download&term=Retracted%20Publication[sb]%20OR%20Retraction%20of%20Publication[sb]&dlid=timeline&filename=timeline.csv&bbid=&p$debugoutput=off)



- Find Retractions Using PubMed and My NCBI!

https://hslnews.wordpress.com/2013/05/14/retractions/

- Comment Correction Type

https://www.ncbi.nlm.nih.gov/books/NBK3827/#pubmedhelp.Comment_Correction_Type



> Comment Correction Type
> 
> The data in these fields are citations to other associated journal publications, e.g., comments or errata. Often these link to the respective citation. Comments/Corrections data can be retrieved by the search term that follows each type:
> 
>     Comment in: hascommentin
>     Comment on: hascommenton
>     Corrected and republished in: hascorrectedrepublishedin
>     Corrected and republished from: hascorrectedrepublishedfrom
>     Dataset use reported in: hasassociatedpublication
>     Dataset described in: hasassociateddataset
>     Erratum in: haserratumin
>     Erratum for: haserratumfor
>     Expression of concern in: hasexpressionofconcernin
>     Expression of concern for: hasexpressionofconcernfor
>     Original Report in: hasoriginalreportin
>     Republished in: hasrepublishedin
>     Republished from: hasrepublishedfrom
>     Retracted and republished in: hasretractedandrepublishedin
>     Retracted and republished from: hasretractedandrepublishedfrom
>     Retraction in: hasretractionin
>     Retraction of: hasretractionof
>     Summary for patients in: hassummaryforpatientsin
>     Update in: hasupdatein
>     Update of: hasupdateof
> 

- Errata, Retractions, and Other Linked Citations in PubMed

https://www.nlm.nih.gov/bsd/policy/errata.html


<!-- Not used -->
<!-- ## Data retriveal from PubMed using EDirect  -->

<!-- Article PMID downloaded as `txt`. -->

```{r Search PubMed download PMID, eval=FALSE, include=FALSE}
myTerm <- rstudioapi::terminalCreate(show = FALSE)
rstudioapi::terminalSend(
    myTerm,
    "esearch -db pubmed -query \"(pathology[Affiliation] OR patoloji[Affiliation]) AND (Turkey[Affiliation] OR Türkiye[Affiliation])\" -datetype PDAT -mindate 1800 -maxdate 3000 | \ efetch -format uid > data/pubmed_result_TurkPath_uid.txt \n"
)
Sys.sleep(1)
repeat {
    Sys.sleep(0.1)
    if (rstudioapi::terminalBusy(myTerm) == FALSE) {
        print("Code Executed")
        break
    }
}
```



```{r Search local PubMed with downloaded PMID extract data as xml, eval=FALSE, include=FALSE}
myTerm <- rstudioapi::terminalCreate(show = FALSE)
rstudioapi::terminalSend(
    myTerm,
    "cat data/pubmed_result_TurkPath_uid.txt | \ fetch-pubmed -path /Volumes/Agu2018/PubMed > data/pubmed_result_TurkPath.xml \n"
)
Sys.sleep(1)
repeat {
    Sys.sleep(0.1)
    if (rstudioapi::terminalBusy(myTerm) == FALSE) {
        print("Code Executed")
        break
    }
}
```



# Analysis


A trend graph of retracted articles derived from Europe PMC #RStats #europepmc {europepmc} 📦 #evergreenreviewgraph #research #bibliography #bibliometrics



```{r europepmc}
library(europepmc)
```


```{r europepmc search}
retractedArticlesPerTotalArticles <- 
    europepmc::epmc_hits_trend(
    query = "(PUB_TYPE:'Retracted Publication' OR PUB_TYPE:'Retraction of Publication')",
    period = 1980:2017
    )

retractedArticlesPerTotalArticles$Affiliation <- "All"

retractedArticlesPerTotalArticles_Turkey <- 
    europepmc::epmc_hits_trend(
    query = "(AFF:'Turkey') AND (PUB_TYPE:'Retracted Publication' OR PUB_TYPE:'Retraction of Publication')",
    period = 1980:2017
    )

retractedArticlesPerTotalArticles_Turkey$Affiliation <- "Turkey"

retractedArticles <- dplyr::bind_rows(
retractedArticlesPerTotalArticles,
retractedArticlesPerTotalArticles_Turkey)

```



```{r graph europepmc search}
library(ggplot2)
ggplot(retractedArticles, 
       aes(year, 
           1000*(query_hits / all_hits),
           color = Affiliation)
       ) + 
  geom_point() + 
  geom_line() +
  xlab("Year published") + 
  ylab("Proportion of Retracted Articles \n data: Europe PMC, 20.10.2019 \n 1000x")
```












```{r extract year journal name from xml, message=FALSE, warning=FALSE}
myTerm <- rstudioapi::terminalCreate(show = FALSE)
rstudioapi::terminalSend(
myTerm,
"xtract -input data/RetractedPubMed/Retracted_Publication_sb_OR_Retraction_of_Publication_sb_pubmed_result.xml -pattern PubmedArticle -tab \"|\" -sep \";\" -def \"NA\" -element MedlineCitation/PMID ArticleTitle Journal/ISSN ISOAbbreviation PubDate/Year > data/RetractedPubMed/pubmed_result_retracted.csv \n"
)
Sys.sleep(1)
repeat {
Sys.sleep(0.1)
if (rstudioapi::terminalBusy(myTerm) == FALSE) {
print("Code Executed")
break
}
}
```



```{r read extracted data}
pubmed_result_retracted <-
    readr::read_delim(
        file = here::here("data",
                          "RetractedPubMed",
                          "pubmed_result_retracted.csv"),
        delim = "|",
        escape_double = FALSE,
        col_names = FALSE,
        trim_ws = TRUE
    )

pubmed_result_retracted <- 
pubmed_result_retracted %>%
    select(
        PMID = X1,
        title = X2,
        journalISSN = X3, 
        journalName = X4,
        year = X5
    )
```






```{r extract journal name and topics from xml, message=FALSE, warning=FALSE}
myTerm <- rstudioapi::terminalCreate(show = FALSE)
rstudioapi::terminalSend(
myTerm,
"xtract -input data/currentlyindexed_nlmcatalog_result.xml -pattern NCBICatalogRecord -tab \"|\" -sep \";\" -def \"NA\" -element MedlineTA TitleAlternate BroadJournalHeadingList MeshHeading/DescriptorName ISSN > data/RetractedPubMed/journal_properties.csv \n"
)
Sys.sleep(1)
repeat {
Sys.sleep(0.1)
if (rstudioapi::terminalBusy(myTerm) == FALSE) {
print("Code Executed")
break
}
}
```


```{r read clean journal properties}
journal_properties <- readr::read_delim(here::here("data", "RetractedPubMed" , "journal_properties.csv"), 
    "|", escape_double = FALSE, col_names = FALSE, 
    trim_ws = TRUE)

journal_properties <- journal_properties %>% 
    select(journal = X1,
           topic = X4,
           ISSN = X5)



journal_properties <- journal_properties %>% 
    mutate(journalName = str_split(journal, ";")) %>%
  unnest(cols = c(journalName)) %>% 
    mutate(journalTopic = str_split(topic, ";")) %>%
  unnest(cols = c(journalTopic)) %>% 
    mutate(journalISSN = str_split(ISSN, ";")) %>%
  unnest(cols = c(journalISSN)) %>% 
    select(journalName,
           journalTopic,
           journalISSN) %>% 
    unique()

```



```{r combine retracted articles with their journal info}
pubmed_result_retracted <- pubmed_result_retracted %>% 
    left_join(journal_properties, by = c("journalISSN"))
```


```{r find the journal topics in which most retracted articles were}
commonTerms <- c("Medicine", "Science", "Research")

(pubmed_result_retracted %>% 
    select(journalTopic, year) %>% 
    filter(!journalTopic %in% commonTerms) %>% 
            filter(!is.na(journalTopic)) %>% 
    group_by(journalTopic) %>% 
    tally() %>% 
    arrange(desc(n)) %>% 
    head(10) %>% 
    pull(journalTopic) -> mostRetractedTopicsOfJournal)
```




This trend graph shows the major topics of the journals that have the most retractions. Data derived from PubMed #RStats  #research #bibliography #bibliometrics


```{r major topics of the journals that have the most retractions}
pubmed_result_retracted %>% 
    filter(journalTopic %in% mostRetractedTopicsOfJournal) %>% 
    filter(year <= 2018 & year >= 1990) %>% 
    select(journalTopic, year) %>% 
    group_by(journalTopic, year) %>% 
    tally() %>% 
    ggplot( 
       aes(year, 
           n,
           color = journalTopic
           )
       ) + 
  geom_point() + 
  geom_line() +
  xlab("Year published") + 
  ylab("Proportion of Retracted Articles \n data: Europe PMC, 20.10.2019")
```











+ + + +
+ + + + + + + + + + + + + + + + diff --git a/RetractedPathologyArticles/Retracted_Articles_Europe_PMC.png b/RetractedPathologyArticles/Retracted_Articles_Europe_PMC.png new file mode 100644 index 0000000..e7a08b1 Binary files /dev/null and b/RetractedPathologyArticles/Retracted_Articles_Europe_PMC.png differ diff --git a/RetractedPathologyArticles/Topics_journals_most_retractions.png b/RetractedPathologyArticles/Topics_journals_most_retractions.png new file mode 100644 index 0000000..cac06d7 Binary files /dev/null and b/RetractedPathologyArticles/Topics_journals_most_retractions.png differ diff --git a/RetractedPathologyArticles/retracted pathology articles b/RetractedPathologyArticles/retracted pathology articles new file mode 100644 index 0000000..143e41a --- /dev/null +++ b/RetractedPathologyArticles/retracted pathology articles @@ -0,0 +1,12 @@ +retracted pathology articles + + +Retraction Watch Database User Guide + +https://retractionwatch.com/retraction-watch-database-user-guide/ + + +National Library of Medicine (NLM) and Retracted Publications + + +https://www.ncbi.nlm.nih.gov/pubmedhealth/PMHT0027066/ \ No newline at end of file diff --git a/Vosviewer.Rmd b/Vosviewer.Rmd index f201b90..9fb6838 100644 --- a/Vosviewer.Rmd +++ b/Vosviewer.Rmd @@ -1,10 +1,8 @@ --- -title: "Vosviewer" +title: "VOSviewer" output: html_notebook --- - - --- # VOSVIEWER @@ -18,3 +16,175 @@ https://seinecle.github.io/vosviewer-tutorials/ --- + +```{bash} +cd ~/PubMed/PedCer3JournalWOS/WOS_rawdata/ +cat *.txt > ~/PubMed/PedCer3JournalWOS/WOS_combined/combinedWOS.txt + +``` + +``` +1. VosViewer haritalarını etkileşimli hale getirmek için aşağıdaki linkte sarı ile işaretli yerlere sunucuya attığınız map ve network dosyalarının adresini yazmanız gerekiyor. +http://www.vosviewer.com/vosviewer.php?map=http://yunus.hacettepe.edu.tr/~ztaskin/Hacettepe_MedLife/map_coauthor.txt&network=http://yunus.hacettepe.edu.tr/~ztaskin/Hacettepe_MedLife/network_coauthor.txt +2. VosViewer’ı buradan: http://www.vosviewer.com/ / CiteSpace’i de şuradan http://cluster.ischool.drexel.edu/~cchen/citespace/download/ indirebilirsiniz. +3. Bir klasöreki çok sayıda txt dosyasını tek seferde birleştirmek için: + - Terminal ekranını açın (Başlat > Çalıştır > cmd) + - cd koduyla txt dosyalarının yer aldığı klasöre gidin. (cd .. bir üst klasöre gider / cd (dosya adı) yazdığınız dosya adına) + - Ardından şu kodu çalıştırın > for %f in (*.txt) do type "%f" >> output.txt + - Veriyi excel’de açın. Fazla etiketleri silin. Her dosyanın ilk satırı fazla olacak çünkü. Bazen dönüştürmede duplike de yapabiliyor. Duplikeleri bul ve sil yapabilirsiniz emin olmak için. +4. CiteSpace’i çalıştıramazsanız aşağıdaki iki kodu terminal ekranından çalıştırmayı deneyebilirsiniz. +- java -Dfile.encoding=UTF-8 -Duser.country=US -Duser.language=en -Xss5m -jar CiteSpaceV.jar +- java -Dfile.encoding=UTF-8 -Duser.country=US -Duser.language=en -Xms1g -Xmx12g -Xss5m -jar CiteSpaceV.jar +5. DORA deklarasyonunu buradan https://sfdora.org/read/tr/ Leiden Manifesto’yu buradan http://www.leidenmanifesto.org/ okuyabilirsiniz. +6. PubMed sorgularını VosViewer’da çalıştırmak için send to > file > Medline > Create file patikasını kullanarak veriyi indirebilirsiniz. Sorunsuz çalışıyor. +``` + + + +``` +/Users/serdarbalciold/PubMed/PedCer3JournalWOS/WOS_combined/combinedWOS2.txt +VOSviewer'da çalıştırıldı. +co-occurance, author keywords, full counting, thesaurus +/Users/serdarbalciold/PubMed/PedCer3JournalWOS/thesaurus_PedCer.txt +min number of occurenece keyword: 5 +569/12377 keywords meet >5 treshold +all keywords included in the map +/Users/serdarbalciold/PubMed/PedCer3JournalWOS/export_selected_keywords.txt +``` + + + + + + +```{r} +library(data.table) +# library(bibliometrix) +``` + + +```{r} +keywords_PedCer3JournalVOSviewer <- fread( + here::here("PedCer3JournalWOS/export_selected_keywords.txt"), sep = "\t") +View(keywords_PedCer3JournalVOSviewer) + +map_PedCer3JournalVOSviewer <- fread( + here::here("PedCer3JournalWOS/map_keywords.txt"), sep = "\t") +View(map_PedCer3JournalVOSviewer) + +network_PedCer3JournalVOSviewer <- fread( + here::here("PedCer3JournalWOS/network_keywords.txt"), sep = "\t") +View(network_PedCer3JournalVOSviewer) + +# /Users/serdarbalciold/PubMed/PedCer3JournalWOS/keyword.gml +# /Users/serdarbalciold/PubMed/PedCer3JournalWOS/keyword_pajek_network.net +# /Users/serdarbalciold/PubMed/PedCer3JournalWOS/network_pajek_partition.clu +# /Users/serdarbalciold/PubMed/PedCer3JournalWOS/keyword_pajek_vector.vec + + + +``` + + + + + +```{r} +# biblio <- readLines("~/PubMed/PedCer3JournalWOS/WOS_rawdata/Kitap1.txt") +# biblio_df_df <- bibliometrix::convert2df(file = biblio, dbsource = "isi", format = "bibtex") + +PedCer3Journal <- readr::read_delim(file = "~/PubMed/PedCer3JournalWOS/WOS_combined/combinedWOS2.txt", + delim = "\t") + +library(tidyverse) + +PedCer3JournalID <- PedCer3Journal %>% + rowid_to_column() %>% + select(documentID = rowid, + DOI = DI, + WOS = UT, + PMID = PM) + +``` + + +```{r} +# keywordID +# keywords_PedCer3JournalVOSviewer$id + +# keywordNAME +# keywords_PedCer3JournalVOSviewer$keyword + +keywordsPedCer3Journal <- + keywords_PedCer3JournalVOSviewer %>% + select(keywordID = id, + keywordNAME = keyword) + + +# keywordID +# map_PedCer3JournalVOSviewer$id + +# keywordNAME +# map_PedCer3JournalVOSviewer$label + +mapPedCer3Journal <- map_PedCer3JournalVOSviewer %>% + select(keywordID = id, + keywordNAME = label, + cluster = cluster) + +# documentID +# network_PedCer3JournalVOSviewer$V1 + +# documentID +# network_PedCer3JournalVOSviewer$V2 + +``` + + +```{r} +combined_PedCer3Journal <- PedCer3JournalID %>% + full_join(occurancePedCer3Journal, by = "documentID") %>% + full_join(mapPedCer3Journal, by = "keywordID") +``` + + + +``` +I am afraid there is no easy solution for this. In the final step in the ‘Create Map’ wizard, a list of keywords is presented. By right-clicking on this list, it is possible to export the document-keyword relations to a text file. In addition, by saving your keyword map in a VOSviewer map file (using the ‘Save’ button on the ’File’ tab), the relations between keywords and clusters can be obtained. By combining the information from the two files, it is possible to find out which documents belong to which clusters. However, this requires some data analysis to be performed outside VOSviewer. Unfortunately, no easier solution is available at the moment. +``` + +``` +If you have multiple Web of Science files (in tab-delimited format), it may be best to merge the files into a single file. The first line in this file will be a header line. The second line will be document 1, the third line will be document 2, and so on. +``` + + +```{r} +combined_PedCer3Journal %>% + filter(cluster == 1) %>% + janitor::tabyl(keywordNAME, cluster) %>% + janitor::adorn_pct_formatting(rounding = 'half up', digits = 1) %>% + knitr::kable() + +``` + + + +- import WOS data into R + +https://github.com/jessicabeyer/wosr + +https://cran.r-project.org/web/packages/wosr/wosr.pdf + +https://github.com/alberto-martin/read.wos.R + +https://cran.rstudio.com/web/packages/bibliometrix/vignettes/bibliometrix-vignette.html + +convert2df(file, dbsource = "isi", format = "plaintext") + + + + + + + + diff --git a/Vosviewer.nb.html b/Vosviewer.nb.html index 04e750f..5ca0d1b 100644 --- a/Vosviewer.nb.html +++ b/Vosviewer.nb.html @@ -7,11 +7,12 @@ + -Vosviewer +VOSviewer - - + + + + + +
+ + + @@ -1771,10 +1759,402 @@

VOSVIEWER TUTORIALS Documentation for Vosviewer in multiple languages

https://seinecle.github.io/vosviewer-tutorials/


+ + +
cd ~/PubMed/PedCer3JournalWOS/WOS_rawdata/ 
+cat *.txt > ~/PubMed/PedCer3JournalWOS/WOS_combined/combinedWOS.txt
+
+ + + +
1. VosViewer haritalarını etkileşimli hale getirmek için aşağıdaki linkte sarı ile işaretli yerlere sunucuya attığınız map ve network dosyalarının adresini yazmanız gerekiyor.
+http://www.vosviewer.com/vosviewer.php?map=http://yunus.hacettepe.edu.tr/~ztaskin/Hacettepe_MedLife/map_coauthor.txt&network=http://yunus.hacettepe.edu.tr/~ztaskin/Hacettepe_MedLife/network_coauthor.txt
+2. VosViewer’ı buradan: http://www.vosviewer.com/ / CiteSpace’i de şuradan http://cluster.ischool.drexel.edu/~cchen/citespace/download/ indirebilirsiniz.
+3. Bir klasöreki çok sayıda txt dosyasını tek seferde birleştirmek için:
+                - Terminal ekranını açın (Başlat > Çalıştır > cmd)
+                - cd koduyla txt dosyalarının yer aldığı klasöre gidin. (cd .. bir üst klasöre gider / cd (dosya adı) yazdığınız dosya adına)
+                - Ardından şu kodu çalıştırın > for %f in (*.txt) do type "%f" >> output.txt
+                - Veriyi excel’de açın. Fazla etiketleri silin. Her dosyanın ilk satırı fazla olacak çünkü. Bazen dönüştürmede duplike de yapabiliyor. Duplikeleri bul ve sil yapabilirsiniz emin olmak için.
+4. CiteSpace’i çalıştıramazsanız aşağıdaki iki kodu terminal ekranından çalıştırmayı deneyebilirsiniz.
+- java -Dfile.encoding=UTF-8 -Duser.country=US -Duser.language=en -Xss5m -jar CiteSpaceV.jar
+- java -Dfile.encoding=UTF-8 -Duser.country=US -Duser.language=en -Xms1g -Xmx12g -Xss5m -jar CiteSpaceV.jar
+5. DORA deklarasyonunu buradan https://sfdora.org/read/tr/ Leiden Manifesto’yu buradan http://www.leidenmanifesto.org/ okuyabilirsiniz.
+6. PubMed sorgularını VosViewer’da çalıştırmak için send to > file > Medline > Create file patikasını kullanarak veriyi indirebilirsiniz. Sorunsuz çalışıyor.
+
/Users/serdarbalciold/PubMed/PedCer3JournalWOS/WOS_combined/combinedWOS2.txt 
+VOSviewer'da çalıştırıldı.
+co-occurance, author keywords, full counting, thesaurus
+/Users/serdarbalciold/PubMed/PedCer3JournalWOS/thesaurus_PedCer.txt
+min number of occurenece keyword: 5
+569/12377 keywords meet >5 treshold
+all keywords included in the map
+/Users/serdarbalciold/PubMed/PedCer3JournalWOS/export_selected_keywords.txt
+ + + +
library(data.table)
+ + +
Registered S3 method overwritten by 'data.table':
+  method           from
+  print.data.table     
+data.table 1.12.2 using 2 threads (see ?getDTthreads).  Latest news: r-datatable.com
+ + +
# library(bibliometrix)
+ + + + + + +
keywords_PedCer3JournalVOSviewer <- fread(
+    here::here("PedCer3JournalWOS/export_selected_keywords.txt"), sep = "\t")
+View(keywords_PedCer3JournalVOSviewer)
+
+map_PedCer3JournalVOSviewer <- fread(
+    here::here("PedCer3JournalWOS/map_keywords.txt"), sep = "\t")
+View(map_PedCer3JournalVOSviewer)
+
+network_PedCer3JournalVOSviewer <- fread(
+    here::here("PedCer3JournalWOS/network_keywords.txt"), sep = "\t")
+View(network_PedCer3JournalVOSviewer)
+
+# /Users/serdarbalciold/PubMed/PedCer3JournalWOS/keyword.gml
+# /Users/serdarbalciold/PubMed/PedCer3JournalWOS/keyword_pajek_network.net
+# /Users/serdarbalciold/PubMed/PedCer3JournalWOS/network_pajek_partition.clu
+# /Users/serdarbalciold/PubMed/PedCer3JournalWOS/keyword_pajek_vector.vec
+
+ + + + + + +
# biblio <- readLines("~/PubMed/PedCer3JournalWOS/WOS_rawdata/Kitap1.txt")
+# biblio_df_df <- bibliometrix::convert2df(file = biblio, dbsource = "isi", format = "bibtex")
+
+PedCer3Journal <- readr::read_delim(file = "~/PubMed/PedCer3JournalWOS/WOS_combined/combinedWOS2.txt",
+                          delim = "\t")
+ + +
Parsed with column specification:
+cols(
+  .default = col_character()
+)
+See spec(...) for full column specifications.
+ + +
library(tidyverse)
+ + +
── Attaching packages ──────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse 1.2.1 ──
+✔ ggplot2 3.2.1           ✔ purrr   0.3.2      
+✔ tibble  2.1.3           ✔ dplyr   0.8.3      
+✔ tidyr   0.8.99.9000     ✔ stringr 1.4.0      
+✔ readr   1.3.1           ✔ forcats 0.4.0      
+── Conflicts ─────────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse_conflicts() ──
+✖ dplyr::between()   masks data.table::between()
+✖ dplyr::filter()    masks stats::filter()
+✖ dplyr::first()     masks data.table::first()
+✖ dplyr::lag()       masks stats::lag()
+✖ dplyr::last()      masks data.table::last()
+✖ purrr::transpose() masks data.table::transpose()
+ + +
PedCer3JournalID <- PedCer3Journal %>% 
+    rowid_to_column() %>% 
+    select(documentID = rowid,
+           DOI = DI,
+           WOS = UT,
+           PMID = PM)
+
+ + + + + + +
# keywordID
+# keywords_PedCer3JournalVOSviewer$id
+
+# keywordNAME
+# keywords_PedCer3JournalVOSviewer$keyword
+
+keywordsPedCer3Journal <- 
+    keywords_PedCer3JournalVOSviewer %>% 
+    select(keywordID = id,
+           keywordNAME = keyword)
+
+
+# keywordID
+# map_PedCer3JournalVOSviewer$id
+
+# keywordNAME
+# map_PedCer3JournalVOSviewer$label
+
+mapPedCer3Journal <- map_PedCer3JournalVOSviewer %>% 
+    select(keywordID = id,
+           keywordNAME = label,
+           cluster = cluster)
+
+# documentID
+# network_PedCer3JournalVOSviewer$V1
+
+# documentID
+# network_PedCer3JournalVOSviewer$V2
+
+ + + + + + +
combined_PedCer3Journal <- PedCer3JournalID %>% 
+    full_join(occurancePedCer3Journal, by = "documentID") %>% 
+    full_join(mapPedCer3Journal, by = "keywordID")
+ + + +
I am afraid there is no easy solution for this. In the final step in the ‘Create Map’ wizard, a list of keywords is presented. By right-clicking on this list, it is possible to export the document-keyword relations to a text file. In addition, by saving your keyword map in a VOSviewer map file (using the ‘Save’ button on the ’File’ tab), the relations between keywords and clusters can be obtained. By combining the information from the two files, it is possible to find out which documents belong to which clusters. However, this requires some data analysis to be performed outside VOSviewer. Unfortunately, no easier solution is available at the moment.
+
If you have multiple Web of Science files (in tab-delimited format), it may be best to merge the files into a single file. The first line in this file will be a header line. The second line will be document 1, the third line will be document 2, and so on.
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
keywordNAME1
asymptomatic500.0%
bowel resection100.0%
colectomy100.0%
colitis100.0%
colon interposition100.0%
colonic atresia100.0%
colostomy100.0%
continence100.0%
emergency4500.0%
enhanced recovery after surgery100.0%
enterostomy100.0%
esophageal lengthening100.0%
esophageal replacement100.0%
extremely low birth weight100.0%
familial adenomatous polyposis100.0%
feeding100.0%
gastric pull-up100.0%
gastric transposition100.0%
gastric tube100.0%
growth100.0%
hypoxia100.0%
inflammatory bowel disease100.0%
ıleostomy100.0%
ınflammatory bowel disease100.0%
ıntestinal malrotation100.0%
ıntestinal perforation100.0%
ıschemia100.0%
jejunostomy100.0%
kids’ ınpatient database100.0%
laparotomy100.0%
length of stay100.0%
long gap esophageal atresia100.0%
malrotation100.0%
nec100.0%
neonatal100.0%
nıcu100.0%
nutrition100.0%
operative technique100.0%
ostomy600.0%
pilonidal disease100.0%
premature100.0%
primary anastomosis100.0%
primary repair100.0%
resection100.0%
restorative proctocolectomy100.0%
small bowel100.0%
spontaneous intestinal perforation100.0%
stricture100.0%
ulcerative colitis100.0%
very low birth weight100.0%
volvulus100.0%
+ + + + + + + +

https://github.com/jessicabeyer/wosr

+

https://cran.r-project.org/web/packages/wosr/wosr.pdf

+

https://github.com/alberto-martin/read.wos.R

+

https://cran.rstudio.com/web/packages/bibliometrix/vignettes/bibliometrix-vignette.html

+

convert2df(file, dbsource = “isi”, format = “plaintext”)

+
-
LS0tCnRpdGxlOiAiVm9zdmlld2VyIgpvdXRwdXQ6IGh0bWxfbm90ZWJvb2sKLS0tCgoKCi0tLQoKIyBWT1NWSUVXRVIKCiMjIFZPU1ZJRVdFUiBUVVRPUklBTFMgRG9jdW1lbnRhdGlvbiBmb3IgVm9zdmlld2VyIGluIG11bHRpcGxlIGxhbmd1YWdlcwoKaHR0cHM6Ly9naXRodWIuY29tL3NlaW5lY2xlL1Zvc3ZpZXdlci10dXRvcmlhbHMKCmh0dHBzOi8vc2VpbmVjbGUuZ2l0aHViLmlvL3Zvc3ZpZXdlci10dXRvcmlhbHMvCgoKLS0tCgo=
+
---
title: "VOSviewer"
output: html_notebook
---

---

# VOSVIEWER

## VOSVIEWER TUTORIALS Documentation for Vosviewer in multiple languages

https://github.com/seinecle/Vosviewer-tutorials

https://seinecle.github.io/vosviewer-tutorials/


---


```{bash}
cd ~/PubMed/PedCer3JournalWOS/WOS_rawdata/ 
cat *.txt > ~/PubMed/PedCer3JournalWOS/WOS_combined/combinedWOS.txt

```

```
1. VosViewer haritalarını etkileşimli hale getirmek için aşağıdaki linkte sarı ile işaretli yerlere sunucuya attığınız map ve network dosyalarının adresini yazmanız gerekiyor.
http://www.vosviewer.com/vosviewer.php?map=http://yunus.hacettepe.edu.tr/~ztaskin/Hacettepe_MedLife/map_coauthor.txt&network=http://yunus.hacettepe.edu.tr/~ztaskin/Hacettepe_MedLife/network_coauthor.txt
2. VosViewer’ı buradan: http://www.vosviewer.com/ / CiteSpace’i de şuradan http://cluster.ischool.drexel.edu/~cchen/citespace/download/ indirebilirsiniz.
3. Bir klasöreki çok sayıda txt dosyasını tek seferde birleştirmek için:
                - Terminal ekranını açın (Başlat > Çalıştır > cmd)
                - cd koduyla txt dosyalarının yer aldığı klasöre gidin. (cd .. bir üst klasöre gider / cd (dosya adı) yazdığınız dosya adına)
                - Ardından şu kodu çalıştırın > for %f in (*.txt) do type "%f" >> output.txt
                - Veriyi excel’de açın. Fazla etiketleri silin. Her dosyanın ilk satırı fazla olacak çünkü. Bazen dönüştürmede duplike de yapabiliyor. Duplikeleri bul ve sil yapabilirsiniz emin olmak için.
4. CiteSpace’i çalıştıramazsanız aşağıdaki iki kodu terminal ekranından çalıştırmayı deneyebilirsiniz.
- java -Dfile.encoding=UTF-8 -Duser.country=US -Duser.language=en -Xss5m -jar CiteSpaceV.jar
- java -Dfile.encoding=UTF-8 -Duser.country=US -Duser.language=en -Xms1g -Xmx12g -Xss5m -jar CiteSpaceV.jar
5. DORA deklarasyonunu buradan https://sfdora.org/read/tr/ Leiden Manifesto’yu buradan http://www.leidenmanifesto.org/ okuyabilirsiniz.
6. PubMed sorgularını VosViewer’da çalıştırmak için send to > file > Medline > Create file patikasını kullanarak veriyi indirebilirsiniz. Sorunsuz çalışıyor.
```



```
/Users/serdarbalciold/PubMed/PedCer3JournalWOS/WOS_combined/combinedWOS2.txt 
VOSviewer'da çalıştırıldı.
co-occurance, author keywords, full counting, thesaurus
/Users/serdarbalciold/PubMed/PedCer3JournalWOS/thesaurus_PedCer.txt
min number of occurenece keyword: 5
569/12377 keywords meet >5 treshold
all keywords included in the map
/Users/serdarbalciold/PubMed/PedCer3JournalWOS/export_selected_keywords.txt
```






```{r}
library(data.table)
# library(bibliometrix)
```


```{r}
keywords_PedCer3JournalVOSviewer <- fread(
    here::here("PedCer3JournalWOS/export_selected_keywords.txt"), sep = "\t")
View(keywords_PedCer3JournalVOSviewer)

map_PedCer3JournalVOSviewer <- fread(
    here::here("PedCer3JournalWOS/map_keywords.txt"), sep = "\t")
View(map_PedCer3JournalVOSviewer)

network_PedCer3JournalVOSviewer <- fread(
    here::here("PedCer3JournalWOS/network_keywords.txt"), sep = "\t")
View(network_PedCer3JournalVOSviewer)

# /Users/serdarbalciold/PubMed/PedCer3JournalWOS/keyword.gml
# /Users/serdarbalciold/PubMed/PedCer3JournalWOS/keyword_pajek_network.net
# /Users/serdarbalciold/PubMed/PedCer3JournalWOS/network_pajek_partition.clu
# /Users/serdarbalciold/PubMed/PedCer3JournalWOS/keyword_pajek_vector.vec



```





```{r}
# biblio <- readLines("~/PubMed/PedCer3JournalWOS/WOS_rawdata/Kitap1.txt")
# biblio_df_df <- bibliometrix::convert2df(file = biblio, dbsource = "isi", format = "bibtex")

PedCer3Journal <- readr::read_delim(file = "~/PubMed/PedCer3JournalWOS/WOS_combined/combinedWOS2.txt",
                          delim = "\t")

library(tidyverse)

PedCer3JournalID <- PedCer3Journal %>% 
    rowid_to_column() %>% 
    select(documentID = rowid,
           DOI = DI,
           WOS = UT,
           PMID = PM)

```


```{r}
# keywordID
# keywords_PedCer3JournalVOSviewer$id

# keywordNAME
# keywords_PedCer3JournalVOSviewer$keyword

keywordsPedCer3Journal <- 
    keywords_PedCer3JournalVOSviewer %>% 
    select(keywordID = id,
           keywordNAME = keyword)


# keywordID
# map_PedCer3JournalVOSviewer$id

# keywordNAME
# map_PedCer3JournalVOSviewer$label

mapPedCer3Journal <- map_PedCer3JournalVOSviewer %>% 
    select(keywordID = id,
           keywordNAME = label,
           cluster = cluster)

# documentID
# network_PedCer3JournalVOSviewer$V1

# documentID
# network_PedCer3JournalVOSviewer$V2

```


```{r}
combined_PedCer3Journal <- PedCer3JournalID %>% 
    full_join(occurancePedCer3Journal, by = "documentID") %>% 
    full_join(mapPedCer3Journal, by = "keywordID")
```



```
I am afraid there is no easy solution for this. In the final step in the ‘Create Map’ wizard, a list of keywords is presented. By right-clicking on this list, it is possible to export the document-keyword relations to a text file. In addition, by saving your keyword map in a VOSviewer map file (using the ‘Save’ button on the ’File’ tab), the relations between keywords and clusters can be obtained. By combining the information from the two files, it is possible to find out which documents belong to which clusters. However, this requires some data analysis to be performed outside VOSviewer. Unfortunately, no easier solution is available at the moment.
```

```
If you have multiple Web of Science files (in tab-delimited format), it may be best to merge the files into a single file. The first line in this file will be a header line. The second line will be document 1, the third line will be document 2, and so on.
```


```{r}
combined_PedCer3Journal %>% 
    filter(cluster == 1) %>% 
    janitor::tabyl(keywordNAME, cluster) %>%
  janitor::adorn_pct_formatting(rounding = 'half up', digits = 1) %>%
  knitr::kable()
    
```



- import WOS data into R

https://github.com/jessicabeyer/wosr

https://cran.r-project.org/web/packages/wosr/wosr.pdf

https://github.com/alberto-martin/read.wos.R

https://cran.rstudio.com/web/packages/bibliometrix/vignettes/bibliometrix-vignette.html

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









@@ -1804,6 +2184,29 @@

VOSVIEWER TUTORIALS Documentation for Vosviewer in multiple languages

+ + + + + + + +