updated on 2018-12-19 21:48:28

.gitignore

@@ -8,3 +8,7 @@ pathologyarticles
 packrat/src/
 data/
 Neurosurgery-Articles
+VOSviewer
+CitNetExplorer
+CiteSpaceV
+Pediatric-Surgery

BibliographicStudies.Rmd

@@ -91,6 +91,20 @@ In this analysis we aimed to identify the common research topics Turkish patholo
 <!-- ## 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

BibliographicStudies.nb.html

@@ -11,7 +11,7 @@
 
 <meta name="author" content="Serdar Balcı, MD, Pathologist" />
 
-<meta name="date" content="2018-10-16" />
+<meta name="date" content="2018-11-13" />
 
 <title>Bibliographic Studies</title>
 
@@ -2832,7 +2832,7 @@
 <h1 class="title toc-ignore">Bibliographic Studies</h1>
 <h3 class="subtitle"><em>Reproducible Bibliometric Analysis of Pathology Articles Using PubMed, E-direct, WoS, Google Scholar</em></h3>
 <h4 class="author"><em>Serdar Balcı, MD, Pathologist</em></h4>
-<h4 class="date"><em>2018-10-16</em></h4>
+<h4 class="date"><em>2018-11-13</em></h4>
 
 </div>
 
@@ -2847,7 +2847,7 @@ <h1><span class="header-section-number">1</span> Introduction</h1>
 <hr />
 <p>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.</p>
 <p>I would like to hear your feedback: <a href="https://goo.gl/forms/YjGZ5DHgtPlR1RnB3" class="uri">https://goo.gl/forms/YjGZ5DHgtPlR1RnB3</a></p>
-<p>This document will be continiously updated and the last update was on 2018-10-16.</p>
+<p>This document will be continiously updated and the last update was on 2018-11-13.</p>
 <hr />
 </div>
 <div id="analysis" class="section level1">
@@ -2878,6 +2878,12 @@ <h2><span class="header-section-number">2.3</span> Most Common MeSH Terms and Ke
 <hr />
 <!-- ## correction pathology articles -->
 <hr />
+<!-- ## p values in pathology articles a text analysis of pubmed articles using regular expression -->
+<hr />
+<!-- ## ulakbim patoloji TR dizin -->
+<hr />
+<!-- ## europepmc paketi ile endometriozis analizi -->
+<hr />
 </div>
 </div>
 <div id="sources-used-for-analysis" class="section level1">
@@ -2888,12 +2894,12 @@ <h1><span class="header-section-number">3</span> Sources Used For Analysis</h1>
 <div id="feedback" class="section level1">
 <h1><span class="header-section-number">4</span> Feedback</h1>
 <p><a href="https://github.com/sbalci">Serdar Balcı, MD, Pathologist</a> would like to hear your feedback: <a href="https://goo.gl/forms/YjGZ5DHgtPlR1RnB3" class="uri">https://goo.gl/forms/YjGZ5DHgtPlR1RnB3</a></p>
-<p>This document will be continiously updated and the last update was on 2018-10-16.</p>
+<p>This document will be continiously updated and the last update was on 2018-11-13.</p>
 <hr />
 <!-- rnb-text-end -->
 </div>
 
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+<div id="rmd-source-code">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</div>
 
 
 </div>

PathologyArticlesFromTurkeyComparedtoAllPublishedArticles.Rmd

@@ -0,0 +1,39 @@
+---
+title: "Pathology Articles From Turkey Compared to All Published Articles"
+output: html_notebook
+---
+
+# europepmc
+
+https://cran.r-project.org/web/packages/europepmc/index.html
+
+https://cran.r-project.org/web/packages/europepmc/vignettes/evergreenreviewgraphs.html
+
+
+```{r}
+library(europepmc)
+```
+
+
+```{r}
+articlesPerTotalArticles <- europepmc::epmc_hits_trend(query = "(AFF:'Turkey') AND ((AFF:'pathology') OR (AFF:'Pathology'))", period = 1980:2017)
+
+articlesPerTotalArticles
+```
+
+
+
+A trend graph of articles of #pathologist from #Turkey derived from Europe PMC #RStats #europepmc #evergreenreviewgraph #pathology  #research #bibliography
+
+
+```{r}
+library(ggplot2)
+ggplot(articlesPerTotalArticles, aes(year, query_hits / all_hits)) + 
+  geom_point() + 
+  geom_line() +
+  xlab("Year published") + 
+  ylab("Proportion of Pathology articles \n from Turkey in Europe PMC")
+```
+
+
+

Sources.Rmd

@@ -57,6 +57,13 @@ and
 [Google Scholar](https://scholar.google.com).
 
 
+
+https://www.scopus.com/sources
+
+
+
+
+
 https://dtd.nlm.nih.gov/ncbi/pubmed/out/doc/2018/
 
 

crossref.bib

@@ -0,0 +1,26 @@
+@article{Br_ggmann_2016,
+	doi = {10.1186/s12905-016-0336-0},
+	url = {https://doi.org/10.1186%2Fs12905-016-0336-0},
+	year = 2016,
+	month = {sep},
+	publisher = {Springer Nature},
+	volume = {16},
+	number = {1},
+	author = {Dörthe Brüggmann and Alexandra Elizabeth-Martinez and Doris Klingelhöfer and David Quarcoo and Jenny M. Jaque and David A. Groneberg},
+	title = {Endometriosis and its global research architecture: an in-depth density-equalizing mapping analysis},
+	journal = {{BMC} Women{\textquotesingle}s Health}
+}
+
+@article{Br_ggmann_2016,
+	doi = {10.1186/s12905-016-0336-0},
+	url = {https://doi.org/10.1186%2Fs12905-016-0336-0},
+	year = 2016,
+	month = {sep},
+	publisher = {Springer Nature},
+	volume = {16},
+	number = {1},
+	author = {Dörthe Brüggmann and Alexandra Elizabeth-Martinez and Doris Klingelhöfer and David Quarcoo and Jenny M. Jaque and David A. Groneberg},
+	title = {Endometriosis and its global research architecture: an in-depth density-equalizing mapping analysis},
+	journal = {{BMC} Women{\textquotesingle}s Health}
+}
+

endometriosis.Rmd

@@ -0,0 +1,39 @@
+---
+title: "endometriosis"
+output: html_notebook
+---
+
+```{r}
+library(europepmc)
+```
+
+
+```{r}
+endometriosis_articlesPerTotalArticles <- europepmc::epmc_hits_trend(query = "endometriosis", period = 1980:2017)
+
+endometriosis_articlesPerTotalArticles
+View(endometriosis_articlesPerTotalArticles)
+```
+
+
+```{r}
+library(ggplot2)
+ggplot(endometriosis_articlesPerTotalArticles, aes(year, query_hits / all_hits)) + 
+  geom_point() + 
+  geom_line() +
+  xlab("Year published") + 
+  ylab("Proportion of Endometriois \n articles in Europe PMC")
+```
+
+
+
+
+https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5031306/
+
+
+```{r}
+knitcitations::citep("10.1186/s12905-016-0336-0")
+```
+
+
+

p values regular expression

@@ -0,0 +1,2 @@
+p values in pathology articles
+regular expression

ulakbim patoloji

@@ -0,0 +1,2 @@
+ulakbim patoloji
+TR dizin