Question

哦，伙计。我很难从我的代码中删除for循环，因为我发现它们非常直观，我首先学习了C ++。下面，我正在获取搜索的ID（在这种情况下为copd），并使用该ID检索其完整的XML文件，并从中将其位置保存到向量中。我不知道如何加快速度，大约需要5分钟才能运行700个ID，而大多数搜索都有70,000多个ID。感谢您提供任何指导。

library(rentrez)
library(XML)

# number of articles for term copd
count <- entrez_search(db = "pubmed", term = "copd")$count

# set max to count
id <- entrez_search(db = "pubmed", term = "copd", retmax = count)$ids

# empty vector that will soon contain locations
location <- character()

# get all location data 
for (i in 1:count)
{
  # get ID of each search
  test <- entrez_fetch(db = "pubmed", id = id[i], rettype = "XML")

  # convert to XML
  test_list <- XML::xmlToList(test)

  # retrieve location
  location <- c(location, test_list$PubmedArticle$MedlineCitation$Article$AuthorList$Author$AffiliationInfo$Affiliation)
}

Answer 1

这可能会给你一个开始 - 似乎可以一次拉下多个。

library(rentrez)
library(xml2)

# number of articles for term copd
count <- entrez_search(db = "pubmed", term = "copd")$count

# set max to count
id_search <- entrez_search(db = "pubmed", term = "copd", retmax = count, use_history = T)

# get all
document <- entrez_fetch(db = "pubmed", rettype = "XML", web_history = id_search$web_history)

document_list <- as_list(read_xml(document))

问题是这仍然很耗时，因为有大量文件。它还很好奇，当我尝试过这篇文章时，它会返回10,000篇文章 - 你可以立即回复的内容可能会受到限制。

然后，您可以使用purrr包之类的内容开始提取所需的信息。

在R中矢量化for-loop

1 个答案: