some other samples of PubMed searches
RISmed another RISmed example easyPubmed for business nah, this one
if(!require(easyPubMed)){
install.packages("easyPubMed") }## Loading required package: easyPubMed## Warning: package 'easyPubMed' was built under R version 3.5.2library(easyPubMed)
library(tidyverse)## ── Attaching packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse 1.2.1 ──## ✔ ggplot2 3.2.1 ✔ purrr 0.3.2
## ✔ tibble 2.1.3 ✔ dplyr 0.8.3
## ✔ tidyr 1.0.0 ✔ stringr 1.4.0
## ✔ readr 1.3.1 ✔ forcats 0.4.0## Warning: package 'ggplot2' was built under R version 3.5.2## Warning: package 'tibble' was built under R version 3.5.2## Warning: package 'tidyr' was built under R version 3.5.2## Warning: package 'purrr' was built under R version 3.5.2## Warning: package 'dplyr' was built under R version 3.5.2## Warning: package 'forcats' was built under R version 3.5.2## ── Conflicts ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse_conflicts() ──
## ✖ dplyr::filter() masks stats::filter()
## ✖ dplyr::lag() masks stats::lag()library(XML)## Warning: package 'XML' was built under R version 3.5.2new_PM_query <- "(APEX1[TI] OR OGG1[TI]) AND (2010[PDAT]:2013[PDAT])"
out.B <- batch_pubmed_download(pubmed_query_string = new_PM_query, dest_file_prefix = "apex1_sample")## [1] "PubMed data batch 1 / 1 downloaded..."# Retrieve the full name of the XML file downloaded in the previous step
new_PM_file <- out.B[1]
new_PM_df <- table_articles_byAuth(pubmed_data = new_PM_file, included_authors = "first", max_chars = 0)## Processing PubMed data .................................................. done!# Alternatively, the output of a fetch_pubmed_data() could have been used# Printing a sample of the resulting data frame
new_PM_df$address <- substr(new_PM_df$address, 1, 28)
new_PM_df$jabbrv <- substr(new_PM_df$jabbrv, 1, 9)
print(new_PM_df[1:10, c("pmid", "year", "jabbrv", "lastname", "address")]) ## pmid year jabbrv lastname address
## 1 24190502 2015 Arch. Tox Bach Grup de Mutagènesi, Departam
## 2 24186001 2014 Tumour Bi Yan Department of Clinical Labor
## 3 24175791 2014 Asian Pac Li Cancer Center, Daping Hospit
## 4 24121118 2014 Mech. Age Lillenes Centre for Molecular Biology
## 5 24101388 2014 J. Physio Antushevich The Kielanowski Institute of
## 6 24075420 2014 DNA Repai Gu State Key Laboratory of Repr
## 7 23999824 2014 Tumour Bi Chen Department of Hepatobiliary
## 8 23959014 2014 Biol. Res Alanazi Genome Research Chair, Depar
## 9 23909557 2014 Genet Tes Wang Department of Oncology, Shan
## 10 23892003 2014 Exp. Cell Yan State Key Laboratory of Repr