diff --git a/.DS_Store b/.DS_Store index e25871d..1709ca6 100644 Binary files a/.DS_Store and b/.DS_Store differ diff --git a/BalciS.Rmd b/BalciS.Rmd new file mode 100644 index 0000000..c116a0c --- /dev/null +++ b/BalciS.Rmd @@ -0,0 +1,32 @@ +--- +title: "Data For Balci Serdar" +output: html_notebook +--- + + +```{r extract journal names from all data xml, message=FALSE, warning=FALSE} +myTerm <- rstudioapi::terminalCreate(show = FALSE) +rstudioapi::terminalSend( +myTerm, +"xtract -input data/BalciS.xml -pattern PubmedArticle -sep '\t' -def 'na' -element MedlineCitation/PMID -block ArticleId -if ArticleId@IdType -equals doi -element ArticleId > data/BalciS.csv \n" +) +Sys.sleep(1) +repeat { +Sys.sleep(0.1) +if (rstudioapi::terminalBusy(myTerm) == FALSE) { +print("Code Executed") +break +} +} +``` + + +```{r} +BalciS <- rio::import("data/BalciS.csv") +BalciSdoi <- BalciS$V2 +``` + +```{r} +write(BalciSdoi, "data/BalciSdoi.txt") +``` + diff --git a/BalciS.nb.html b/BalciS.nb.html new file mode 100644 index 0000000..3dbfc12 --- /dev/null +++ b/BalciS.nb.html @@ -0,0 +1,1848 @@ + + + + + + + + + + + + + +Data For Balci Serdar + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + +
myTerm <- rstudioapi::terminalCreate(show = FALSE)
+rstudioapi::terminalSend(
+myTerm,
+"xtract -input data/BalciS.xml -pattern PubmedArticle -sep '\t' -def 'na' -element MedlineCitation/PMID -block ArticleId -if ArticleId@IdType -equals doi -element ArticleId > data/BalciS.csv \n"
+)
+Sys.sleep(1)
+repeat {
+Sys.sleep(0.1)
+if (rstudioapi::terminalBusy(myTerm) == FALSE) {
+print("Code Executed")
+break
+}
+}
+ + +
[1] "Code Executed"
+ + + + + + + + + + +
write((BalciSdoi, "data/BalciSdoi.txt")
+
+ + +
Error: unexpected ',' in "write((BalciSdoi,"
+ + +
NA
+ + + + + +
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
+ + + +
+ + + + + + + + diff --git a/BibliographicStudies.Rmd b/BibliographicStudies.Rmd index 0965486..51d023b 100644 --- a/BibliographicStudies.Rmd +++ b/BibliographicStudies.Rmd @@ -66,6 +66,11 @@ In this analysis we aimed to identify the common research topics Turkish patholo [MeSH Terms Pathology Articles From Turkey](https://sbalci.github.io/pubmed/MeSH_Terms_Pathology_Articles_From_Turkey.html) +--- + + + + --- diff --git a/BibliographicStudies.nb.html b/BibliographicStudies.nb.html index 977336f..54f4cdc 100644 --- a/BibliographicStudies.nb.html +++ b/BibliographicStudies.nb.html @@ -11,7 +11,7 @@ - + Bibliographic Studies @@ -2895,7 +2895,7 @@

Bibliographic Studies

Reproducible Bibliometric Analysis of Pathology Articles Using PubMed, E-direct, WoS, Google Scholar

Serdar Balcı, MD, Pathologist

-

2019-01-11

+

2019-01-13

@@ -2910,7 +2910,7 @@

1 Introduction

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 2019-01-11.

+

This document will be continiously updated and the last update was on 2019-01-13.

@@ -2929,6 +2929,8 @@

2.2 Articles per Journals per Cou

2.3 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

+ +
@@ -2997,7 +2999,7 @@

3 Sources Used For Analysis

4 Feedback

Serdar Balcı, MD, Pathologist would like to hear your feedback: https://goo.gl/forms/YjGZ5DHgtPlR1RnB3

-

This document will be continiously updated and the last update was on 2019-01-11.

+

This document will be continiously updated and the last update was on 2019-01-13.

@@ -1678,7 +1742,6 @@ -