PubMed data extraction

[SChander]

Hi everyone,

I am trying to get PubMed publication of Cardiology from 2000- 2021 with author name and gender. I am trying to get via easyPubMed package but not succeeded yet. Will appreciate your help.

[williaml]

Hi, have you had a look at the vignette? The author name is there. Not sure if you'll get gender.

https://cran.r-project.org/web/packages/easyPubMed/vignettes/getting_started_with_easyPubMed.html

[SChander]

Thank you William,

I am able to run following codes and R shows me total 3583 papers published in 10 years. However, will accessing the ID and name of authors it shows me only 100 responses. And do you know how can we sort out "randomized controlled trials (RCT)" from them? Following are the codes I am using for it.

library(easyPubMed)
qr1 <- get_pubmed_ids("gastrointestinal[TI] AND 2000[PDAT] : 2021[PDAT")
print(qr1$Count)

btch1 <- fetch_pubmed_data(pubmed_id_list = qr1, retstart = 0, retmax = 3583)
btch1 <- table_articles_byAuth(btch1, included_authors = 'last', max_chars = 0)
btch1[, c("pmid", "lastname", "firstname")]

Thanks

[SChander]

Hello Everyone,

I am trying to get query of all pubmed papers in a particular field and it shows me total 3558 papers. However, will accessing ID and name of authors it shows me an error and doesn't output any response. Following are the codes I using for it: Any help will be truly appreciated.

Thanks

library(easyPubMed)
qr1 <- get_pubmed_ids("gastro[TI] AND 2000[PDAT] : 2021[PDAT")
print(qr1$Count)

btch1 <- fetch_pubmed_data(pubmed_id_list = qr1, retstart = 0, retmax = 3583)
btch1 <- table_articles_byAuth(btch1, included_authors = 'last', max_chars = 0)
btch1[, c("pmid", "lastname", "firstname")]

btch4 <- fetch_pubmed_data(pubmed_id_list = qr1, retstart = 3583)
btch4 <- table_articles_byAuth(btch4, included_authors = 'last', max_chars = 0)
btch4[, c("pmid", "lastname", "firstname")]