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_14-JournalWatchPBPath.Rmd
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_14-JournalWatchPBPath.Rmd
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---
title: "PBPath Journal Watch"
subtitle: "Recent Articles from PubMed"
author: "Serdar Balcı, MD, Pathologist"
date: '`r # format(Sys.Date())`'
output:
html_notebook:
code_folding: hide
highlight: kate
number_sections: yes
theme: cerulean
toc: yes
toc_float: yes
fig_caption: yes
html_document:
df_print: kable
number_sections: yes
toc: yes
---
# Analysis of Recent Pancreas Related Articles
Pancreas Journals
https://www.ncbi.nlm.nih.gov/nlmcatalog/?term=pancreas
Pathology Journals
Member List
DOI Link
PubMed Link
Journal Link
Altmetric API
Dimensions API
USCAP abstracts vs publication
Member list vs worldmap
```{r load required packages}
# load required packages
library(tidyverse)
library(knitr)
library(rstudioapi)
```
```{r setup, include=FALSE}
knitr::opts_chunk$set(message=FALSE, warning=FALSE, tidy = TRUE)
```
```r
myTerm <- rstudioapi::terminalCreate(show = FALSE)
rstudioapi::terminalSend(myTerm, "esearch -db pubmed -query 'pancreas[Title/Abstract]) AND pathology' -datetype EDAT -min 2018/05/01 -max 3000 | \
efetch -format xml | \
xtract -pattern PubmedArticle -element MedlineCitation/PMID \
-block ArticleId -if ArticleId@IdType -equals doi -element ArticleId &> myquery.txt")
Sys.sleep(1)
repeat{
Sys.sleep(0.1)
if(rstudioapi::terminalBusy(myTerm) == FALSE){
print("Code Executed")
break
}
}
```
```r
readLines("myquery.txt")
```
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 $","" ,ISSNList) # to remove last OR
```
Data is retrieved from PubMed via E-direct.
PubMed collection from National Library of Medicine (https://www.ncbi.nlm.nih.gov/pubmed/), has the most comprehensive information about peer reviewed articles in medicine.
The API (https://dataguide.nlm.nih.gov/) is available for getting and fetching data from the server.
The query for PubMed is generated as "ISSN List AND keywords" like done in [advanced search of PubMed](https://www.ncbi.nlm.nih.gov/pubmed/advanced).
```{r Generate Search Formula For Pathology Journals AND Countries}
# Generate Search Formula For Pathology Journals AND Countries
searchformulaTR <- paste("'",ISSNList,"'", " AND ", "Turkey[Affiliation]")
searchformulaDE <- paste("'",ISSNList,"'", " AND ", "Germany[Affiliation]")
searchformulaJP <- paste("'",ISSNList,"'", " AND ", "Japan[Affiliation]")
```
From the fetched data articles are grouped by country and keywords.
```{r Articles per countries per year}
# Articles per countries per year
tableTR <- table(YearPubmed(fetchTurkey)) %>%
as_tibble() %>%
rename(Turkey = n, Year = Var1)
tableDE <- table(YearPubmed(fetchGermany)) %>%
as_tibble() %>%
rename(Germany = n, Year = Var1)
tableJP <- table(YearPubmed(fetchJapan)) %>%
as_tibble() %>%
rename(Japan = n, Year = Var1)
# Join Tables
articles_per_year_table <- list(
tableTR,
tableDE,
tableJP
) %>%
reduce(left_join, by = "Year", .id = "id")
```
```{r Prepare table for output}
# Prepare table for output
articles_per_year <- articles_per_year_table %>%
gather(Country, n, 2:4)
articles_per_year$Country <- factor(articles_per_year$Country,
levels =c("Japan", "Germany", "Turkey"))
```
**Result:**
```{r Print the Table of Articles per year per country, echo=FALSE}
# Print the Table of Articles per year, per country
knitr::kable(articles_per_year_table, caption = "Table of Articles per year, per country")
```
mapgraph
And the figure below shows this data in a line graph.
---
# 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()`.
---
# Back to Main Menu
[Main Page for Bibliographic Analysis](https://sbalci.github.io/pubmed/BibliographicStudies.html)