recover grid and semantic

.gitignore

@@ -13,3 +13,6 @@ CitNetExplorer
 CiteSpaceV
 Pediatric-Surgery
 p values regular expression
+AIDA-Booklet-V2.2.pdf
+vosviewer.jnlp
+grid-2018-11-14-

ArticlesPerJournalsPerCountry-.Rmd

@@ -0,0 +1,197 @@
+---
+title: "Bibliographic Studies"
+subtitle: "Articles per journals per country"
+author: "Serdar Balcı, MD, Pathologist"
+date: '`r format(Sys.Date())`'
+output: 
+  html_notebook: 
+    code_folding: hide
+    fig_caption: yes
+    highlight: kate
+    number_sections: yes
+    theme: cerulean
+    toc: yes
+    toc_float: yes
+  html_document: 
+    code_folding: hide
+    df_print: kable
+    keep_md: yes
+    number_sections: yes
+    theme: cerulean
+    toc: yes
+    toc_float: yes
+    highlight: kate
+---
+
+If you want to see the code used in the analysis please click the code button on the right upper corner or throughout the page.
+
+---
+
+# Analysis
+
+```{r setup, include=FALSE}
+knitr::opts_chunk$set(message=FALSE, warning=FALSE, tidy = TRUE)
+```
+
+## Articles per journals per country
+
+**Aim:**
+
+In the [previous analysis](https://sbalci.github.io/pubmed/CountryBasedComparison.html) we have observed that Japanese researchers have much more articles than German and Turkish researchers.
+
+Here we will look at the distribution of articles per journals per country. 
+
+
+**Methods:**
+
+```{r load required packages}
+# load required packages
+library(tidyverse)
+library(RISmed)
+```
+
+Pathology Journal ISSN List was retrieved from [In Cites Clarivate](https://jcr.incites.thomsonreuters.com/), and Journal Data Filtered as follows: `JCR Year: 2016 Selected Editions: SCIE,SSCI Selected Categories: 'PATHOLOGY' Selected Category Scheme: WoS`
+
+```{r Get ISSN List from data downloaded from WoS}
+# Get ISSN List from data downloaded from WoS
+ISSNList <- JournalHomeGrid <- read_csv("data/JournalHomeGrid.csv", 
+                                        skip = 1) %>% 
+    select(ISSN) %>% 
+    filter(!is.na(ISSN)) %>% 
+    t() %>% 
+    paste("OR ", collapse = "") # add OR between ISSN List
+
+ISSNList <- gsub(" OR $","" ,ISSNList) # to remove last OR
+```
+
+Data is retrieved from PubMed via RISmed package.
+PubMed collection from National Library of Medicine (https://www.ncbi.nlm.nih.gov/pubmed/), has the most comprehensive information about peer reviewed articles in medicine.
+The API (https://dataguide.nlm.nih.gov/), and R packages are available for getting and fetching data from the server.
+
+The search formula for PubMed is generated as "ISSN List AND Country[Affiliation]" like done in [advanced search of PubMed](https://www.ncbi.nlm.nih.gov/pubmed/advanced).
+
+```{r Generate Search Formula For Pathology Journals AND Countries}
+# Generate Search Formula For Pathology Journals AND Countries
+searchformulaTR <- paste("'",ISSNList,"'", " AND ", "Turkey[Affiliation]")
+searchformulaDE <- paste("'",ISSNList,"'", " AND ", "Germany[Affiliation]")
+searchformulaJP <- paste("'",ISSNList,"'", " AND ", "Japan[Affiliation]")
+```
+
+Articles from Japan, German and Turkey are retrieved limiting the search with pathology journals, affiliation and last 10 years.
+
+```{r Search PubMed, Get and Fetch}
+# Search PubMed, Get and Fetch
+TurkeyArticles <- EUtilsSummary(searchformulaTR, type = 'esearch', db = 'pubmed', mindate = 2007, maxdate = 2017, retmax = 10000)
+fetchTurkey <- EUtilsGet(TurkeyArticles)
+
+GermanyArticles <- EUtilsSummary(searchformulaDE, type = 'esearch', db = 'pubmed', mindate = 2007, maxdate = 2017, retmax = 10000)
+fetchGermany <- EUtilsGet(GermanyArticles)
+
+JapanArticles <- EUtilsSummary(searchformulaJP, type = 'esearch', db = 'pubmed', mindate = 2007, maxdate = 2017, retmax = 10000)
+fetchJapan <- EUtilsGet(JapanArticles)
+```
+
+The retrieved information was compiled in a table.
+
+```{r}
+
+ISSNTR <- table(ISSN(fetchTurkey)) %>% 
+    as_tibble() %>% 
+    rename(Turkey = n, Journal = Var1)
+
+ISSNDE <- table(ISSN(fetchGermany)) %>% 
+    as_tibble() %>% 
+    rename(Germany = n, Journal = Var1)
+
+ISSNJP <- table(ISSN(fetchJapan)) %>% 
+    as_tibble() %>% 
+    rename(Japan = n, Journal = Var1)
+
+articles_per_journal <- list(
+    ISSNTR,
+    ISSNDE,
+    ISSNJP
+) %>%
+    reduce(left_join, by = "Journal", .id = "id") %>% 
+    gather(Country, n, 2:4)
+
+articles_per_journal$Country <- factor(articles_per_journal$Country,
+                                       levels =c("Japan", "Germany", "Turkey"))
+
+```
+
+
+
+**Result:**
+
+In this graph x-axis is the list of journals with decreasing impact factor, and y-axis is the number of articles published in that journal. The colors and shapes are showing the country of affiliation. We see that in one journal articles from Japan is more than 800.  
+
+```{r}
+ggplot(data = articles_per_journal, aes(x = Journal, y = n, group = Country,
+                                     colour = Country, shape = Country,
+                                     levels = Country
+)) +
+    geom_point() +
+    labs(x = "Journals with decreasing impact factor", y = "Number of Articles") +
+    ggtitle("Pathology Articles Per Journal") + 
+    theme(plot.title = element_text(hjust = 0.5),
+          axis.text.x=element_blank())
+
+```
+
+
+**Comment:**
+
+It is seen that one of the journals [ISSN: 1440-1827](https://onlinelibrary.wiley.com/page/journal/14401827/homepage/productinformation.html) has more than 800 articles from Japan. This journal is also from Japan. Here we wonder if there is an editorial preference for articles from their home country. 
+
+We sometimes observe this situation if there is a conference in that country, and the conference abstracts are indexed. 
+
+This may also be a clue that if a country has a journal listed in indexes, than it is more easy for the researchers in that country to publish their results.
+
+
+**Future Work:**
+
+Whether this observation is a unique situation, or there is a tendency in the journals to publish article from their country of origin, merits further investigation. 
+
+
+
+---
+
+
+# Feedback
+
+[Serdar Balcı, MD, Pathologist](https://github.com/sbalci) would like to hear your feedback: https://goo.gl/forms/YjGZ5DHgtPlR1RnB3
+
+This document will be continiously updated and the last update was on `r Sys.Date()`.
+
+---
+
+<script id="dsq-count-scr" src="//https-sbalci-github-io.disqus.com/count.js" async></script>
+
+<div id="disqus_thread"></div>
+<script>
+
+/**
+*  RECOMMENDED CONFIGURATION VARIABLES: EDIT AND UNCOMMENT THE SECTION BELOW TO INSERT DYNAMIC VALUES FROM YOUR PLATFORM OR CMS.
+*  LEARN WHY DEFINING THESE VARIABLES IS IMPORTANT: https://disqus.com/admin/universalcode/#configuration-variables*/
+/*
+var disqus_config = function () {
+this.page.url = PAGE_URL;  // Replace PAGE_URL with your page's canonical URL variable
+this.page.identifier = PAGE_IDENTIFIER; // Replace PAGE_IDENTIFIER with your page's unique identifier variable
+};
+*/
+(function() { // DON'T EDIT BELOW THIS LINE
+var d = document, s = d.createElement('script');
+s.src = 'https://https-sbalci-github-io.disqus.com/embed.js';
+s.setAttribute('data-timestamp', +new Date());
+(d.head || d.body).appendChild(s);
+})();
+</script>
+<noscript>Please enable JavaScript to view the <a href="https://disqus.com/?ref_noscript">comments powered by Disqus.</a></noscript>
+
+
+---
+
+# Back to Main Menu
+
+[Main Page for Bibliographic Analysis](https://sbalci.github.io/pubmed/BibliographicStudies.html)

BibliographicStudies-.Rmd

@@ -0,0 +1,147 @@
+---
+title: "Bibliographic Studies"
+subtitle: "Reproducible Bibliometric Analysis of Pathology Articles Using PubMed, E-direct, WoS, Google Scholar"
+author: "Serdar Balcı, MD, Pathologist"
+date: '`r format(Sys.Date())`'
+output: 
+  html_document: 
+    code_folding: hide
+    df_print: kable
+    highlight: kate
+    keep_md: yes
+    number_sections: yes
+    theme: cerulean
+    toc: yes
+    toc_float: yes
+  html_notebook: 
+    code_folding: hide
+    fig_caption: yes
+    highlight: kate
+    number_sections: yes
+    theme: cerulean
+    toc: yes
+    toc_depth: 5
+    toc_float: yes
+---
+
+# Introduction
+
+It is a very common bibliometric study type to retrospectively analyse the number of peer reviewed articles written from a country to view the amount of contribution made in a specific scientific discipline.
+
+These studies require too much effort, since the data is generally behind paywalls and restrictions.
+
+I have previously contributed to a research to identify the Articles from Turkey Published in Pathology Journals Indexed in International Indexes; which is published here: [Turk Patoloji Derg. 2010, 26(2):107-113 doi: 10.5146/tjpath.2010.01006](http://www.turkjpath.org/summary_en.php3?id=1423) 
+
+This study had required manual investigation of many excel files, which was time consuming; also redoing and updating the data and results require a similar amount of effort.
+
+
+---
+
+If you want to see the code used in the analysis please click the code button on the right upper corner or throughout the page. 
+
+I would like to hear your feedback: https://goo.gl/forms/YjGZ5DHgtPlR1RnB3
+
+This document will be continiously updated and the last update was on `r Sys.Date()`.
+
+---
+
+
+# Analysis
+
+---
+
+## Country Based Comparison
+
+To see the analysis comparing number of pathology articles from Turkey, German and Japan see this analysis: [Country Based Comparison](https://sbalci.github.io/pubmed/CountryBasedComparison.html)
+
+---
+
+## Articles per Journals per Country
+
+In this analysis we aimed to compare number articles per journals per country. We tried to identify if articles from a country is published in certain journals: [Articles Per Journals Per Country](https://sbalci.github.io/pubmed/ArticlesPerJournalsPerCountry.html)
+
+## Most Common MeSH Terms and Keywords used in Pathology Articles from Turkey
+
+In this analysis we aimed to identify the common research topics Turkish pathologists are interested. We extracted most common MeSH terms and keywords from PubMed articles using EDirect:
+[MeSH Terms Pathology Articles From Turkey](https://sbalci.github.io/pubmed/MeSH_Terms_Pathology_Articles_From_Turkey.html)
+
+
+---
+
+<!-- ## Journals Published Articles From Turkey   -->
+
+---
+
+<!-- ## SEER Research Per Countries / Who is doing SEER Research? -->
+
+---
+
+<!-- ## Semantic Scholar -->
+
+---
+
+<!-- ## neutrophil lymph ratio -->
+
+---
+
+<!-- ## retracted pathology articles -->
+
+---
+
+<!-- ## correction pathology articles -->
+
+
+---
+
+<!-- ## p values in pathology articles a text analysis of pubmed articles using regular expression -->
+
+
+---
+
+<!-- ## ulakbim patoloji TR dizin -->
+
+---
+
+<!-- ## europepmc paketi ile endometriozis analizi -->
+
+
+---
+
+# Sources Used For Analysis
+
+Here are the sources used in these analysis: [Sources Used For Analysis](https://sbalci.github.io/pubmed/Sources.html)
+
+---
+
+# Feedback
+
+[Serdar Balcı, MD, Pathologist](https://github.com/sbalci) would like to hear your feedback: https://goo.gl/forms/YjGZ5DHgtPlR1RnB3
+
+This document will be continiously updated and the last update was on `r Sys.Date()`.
+
+---
+
+<script id="dsq-count-scr" src="//https-sbalci-github-io.disqus.com/count.js" async></script>
+
+<div id="disqus_thread"></div>
+<script>
+
+/**
+*  RECOMMENDED CONFIGURATION VARIABLES: EDIT AND UNCOMMENT THE SECTION BELOW TO INSERT DYNAMIC VALUES FROM YOUR PLATFORM OR CMS.
+*  LEARN WHY DEFINING THESE VARIABLES IS IMPORTANT: https://disqus.com/admin/universalcode/#configuration-variables*/
+/*
+var disqus_config = function () {
+this.page.url = PAGE_URL;  // Replace PAGE_URL with your page's canonical URL variable
+this.page.identifier = PAGE_IDENTIFIER; // Replace PAGE_IDENTIFIER with your page's unique identifier variable
+};
+*/
+(function() { // DON'T EDIT BELOW THIS LINE
+var d = document, s = d.createElement('script');
+s.src = 'https://https-sbalci-github-io.disqus.com/embed.js';
+s.setAttribute('data-timestamp', +new Date());
+(d.head || d.body).appendChild(s);
+})();
+</script>
+<noscript>Please enable JavaScript to view the <a href="https://disqus.com/?ref_noscript">comments powered by Disqus.</a></noscript>
+
+---