update 3

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)
+```
+

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 
+
+
+
+
+
+
+
+
+

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)
+```
+
+
+
+<!-- Open all links in new tab-->  
+<!-- <base target="_blank"/>   -->
+
+---
+
+# 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/
+
+<a href="https://www.ncbi.nlm.nih.gov/sites/myncbi/serdar.balci.1/collections/58299810/public/">View my collection, "Pathology Articles From Turkey" from NCBI</a>
+
+
+
+
+```{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()`.
+
+
+
+

PathologyArticlesFromTurkeyComparedtoAllPublishedArticles.Rmd

@@ -258,7 +258,6 @@ data_hacettepePathology2 <- data_hacettepePathology %>%
 data_hacettepePathology2 <-  data_hacettepePathology2 %>% 
   separate(col = "Affiliation", sep = ";", into = paste0("Affiliation", 1:6925))
 
-
 ```