install.packages("easyPubMed")

library(easyPubMed)

library(dplyr)

library(parallel)

library(foreach)

library(doParallel)

get_pubmed <- function(query = my_query){

? # ncbi_key = '6c656032d3e950f2b15656d687fd4eeb8008'

? my_query <- get_pubmed_ids(my_query)

? my_query$Count

? # Fetch data

? my_abstracts_xml <- fetch_pubmed_data(my_query)??

? # Store Pubmed Records as elements of a list

? all_xml <- articles_to_list(my_abstracts_xml)

? # Windows systems may not support the following code.

??

? # Start a cluster with 3 cores

? cl <- makeCluster(4)

? registerDoParallel(cl)

??

? # Perform operation (use foreach)

? # The .combine argument guides result aggregation

? fullDF <- tryCatch(

? ? {foreach(x=1:length(all_xml),?

? ? ? ? ? ? ?.packages = 'easyPubMed',

? ? ? ? ? ? ?.combine = rbind) %dopar% article_to_df(pubmedArticle = all_xml[[x]],?

? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?autofill = T,?

? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?max_chars = -1,?

? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?getKeywords = T,?

? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?getAuthors = T)},?

? ? error = function(e) {NULL},

? ? finally = {stopCluster(cl)})

? fullDF <- fullDF %>%?

? ? as_tibble()

? return(fullDF)

}

##根據(jù)期刊/關(guān)鍵詞查找：

my_query<-"(Idiopathic pulmonary fibrosis[TIAB]) AND ((2022[Date - Publication] : 2022[Date - Publication]))"

qr1<-get_pubmed_ids(my_query)

##my_query<-"(Journal of Hepatology[Journal]) AND ((2022[Date - Publication] : 2022[Date - Publication]))"

##qr1<-get_pubmed_ids(my_query)

result<-fetch_pubmed_data(qr1,encoding = "ASCII")

result<-table_articles_byAuth(result,included_authors = "last",max_chars = 500)

write.csv(result,file="D:\\MDR database\\result.csv",row.names = F)