从 R 统计中的 XML 文件创建数据集 [英] Creating a dataset from an XML file in R statistics
问题描述
我正在尝试下载期刊文章记录的 XML 文件，并创建一个数据集，以便在 R 中进一步询问.我对 XML 完全陌生，而且在 R 方面还是新手.我使用来自 2 个来源的一些代码拼凑了一些代码:GoogleScholarXScraper和提取记录来自 pubMed
I am trying to download an XML file of journal article records and create a dataset for further interrogation in R. I'm completely new to XML and quite novice at R. I cobbled together some code using bits of code from 2 sources: GoogleScholarXScraper and Extracting records from pubMed
library(RCurl)
library(XML)
library(stringr)
#Search terms
SearchString<-"cancer+small+cell+non+lung+survival+plastic"
mySearch<-str_c("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=",SearchString,"&usehistory=y",sep="",collapse=NULL)
#Seach
pub.esearch<-getURL(mySearch)
#Extract QueryKey and WebEnv
pub.esearch<-xmlTreeParse(pub.esearch,asText=TRUE)
key<-as.numeric(xmlValue(pub.esearch[["doc"]][["eSearchResult"]][["QueryKey"]]))
env<-xmlValue(pub.esearch[["doc"]][["eSearchResult"]][["WebEnv"]])
#Fetch Records
myFetch<-str_c("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&WebEnv=",env,"&retmode=xml&query_key=",key)
pub.efetch<-getURL(myFetch)
myxml<-xmlTreeParse(pub.efetch,asText=TRUE,useInternalNodes=TRUE)
#Create dataset of article characteristics #This doesn't work
pub.data<-NULL
pub.data<-data.frame(
journal <- xpathSApply(myxml,"//PubmedArticle/MedlineCitation/MedlineJournalInfo/MedlineTA", xmlValue),
abstract<- xpathSApply(myxml,"//PubmedArticle/MedlineCitation/Article/Abstract/AbstractText",xmlValue),
affiliation<-xpathSApply(myxml,"//PubmedArticle/MedlineCitation/Article/Affiliation", xmlValue),
year<-xpathSApply(myxml,"//PubmedArticle/MedlineCitation/Article/Journal/JournalIssue/PubDate/Year", xmlValue)
,stringsAsFactors=FALSE)
我似乎遇到的主要问题是我返回的 XML 文件的结构不完全统一.例如，一些引用的节点结构是这样的:
The main problem I seem to have is that my returned XML file is not completely uniformly structured. For example, some references have a node structure like this:
- <Abstract>
<AbstractText>The Wilms' tumor gene... </AbstractText>
虽然有些标签是这样的
- <Abstract>
<AbstractText Label="BACKGROUND & AIMS" NlmCategory="OBJECTIVE">Some background text.</AbstractText>
<AbstractText Label="METHODS" NlmCategory="METHODS"> Some text on methods.</AbstractText>
当我提取 'AbstactText' 时，我希望能取回 24 行数据(我今天运行这个合成搜索时有 24 条记录)，但 xpathSApply 将 'AbstactText' 中的所有标签作为我的数据帧的单个元素返回.有没有办法在此实例中折叠 XML 结构/忽略标签?有没有办法让 xpathSApply 在路径末尾找不到任何东西时返回NA"?我知道 xmlToDataFrame，这听起来应该符合要求，但是每当我尝试使用它时，它似乎都没有给我任何明智的选择.
When I extract the 'AbstactText' I am hoping to get 24 rows of data back (there are 24 records when I run this made up search today), but xpathSApply returns all labels within 'AbstactText' as individual elements of my dataframe. Is there a way to collapse the XML structure in this instance/Ignore the labels? Is there a way to make xpathSApply return 'NA' when nothing is found at end of a path? I am aware of xmlToDataFrame, which sounds like it should fit the bill, but whenever I try to use this it doesn't seem to give me anything sensible.
感谢您的帮助
推荐答案
我不确定你想要哪个:
xpathSApply(myxml,"//*/AbstractText[@Label]")
将获得带有标签的节点(保留所有属性等).
will get the nodes with labels (keeping all attributes etc).
xpathSApply(myxml,"//*/AbstractText[not(@Label)]",xmlValue)
将获得没有标签的节点.
will get the nodes without labels.
test<-xpathApply(myxml,"//*/Abstract",xmlValue)
> length(test)
[1] 24
可以给你你想要的
用 NA 填充隶属关系、年份等
to get affiliation, year etc padded with NA's
dumfun<-function(x,xstr){
res<-xpathSApply(x,xstr,xmlValue)
if(length(res)==0){
out<-NA
}else{
out<-res
}
out
}
xpathSApply(myxml,"//*/Article",dumfun,xstr='./Affiliation')
xpathSApply(myxml,"//*/Article",dumfun,xstr='./Journal/JournalIssue/PubDate/Year')
这篇关于从 R 统计中的 XML 文件创建数据集的文章就介绍到这了，希望我们推荐的答案对大家有所帮助，也希望大家多多支持IT屋！
