XML 个节点到 R 数据框，所有更高级别的节点属性作为列

Question

我有一个 XML 文件，格式如下：

<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
    <fishmeter>
      <mission cruise="2019114" station="344" platform="4174">
        <fishstation serialno="7">
          <platform>4174</platform>
          <nation>58</nation>
          <latitudestart>60.746062433333336</latitudestart>
          <longitudestart>2.6755209333333334</longitudestart>
          <latitudeend>60.75632006666667</latitudeend>
          <longitudeend>2.64776135</longitudeend>
          <catchsample species="172414" samplenumber="1" noname="makrell" aphia="127023">
            <conservation>1</conservation>
            <producttype>1</producttype>
            <weight>10.195</weight>
            <count>0</count>
            <lengthsampleweight>0</lengthsampleweight>
            <sampleproducttype>1</sampleproducttype>
            <lengthmeasurement>E</lengthmeasurement>
            <specimensamplecount>36</specimensamplecount>
            <individual specimenno="1">
              <lengthunit>2</lengthunit>
              <length>0.36</length>
              <individualproducttype>1</individualproducttype>
            </individual>
            <individual specimenno="2">
              <lengthunit>2</lengthunit>
              <length>0.36</length>
              <individualproducttype>1</individualproducttype>
            </individual>
            <individual specimenno="3">
              <lengthunit>2</lengthunit>
              <length>0.315</length>
              <individualproducttype>1</individualproducttype>
            </individual>
            <individual specimenno="4">
              <lengthunit>2</lengthunit>
              <length>0.315</length>
              <individualproducttype>1</individualproducttype>
            </individual>
          </catchsample>
          <catchsample species="167044" samplenumber="1" noname="knurr" aphia="150637">
            <conservation>1</conservation>
            <producttype>1</producttype>
            <weight>2.52</weight>
            <count>0</count>
            <lengthsampleweight>0</lengthsampleweight>
            <sampleproducttype>1</sampleproducttype>
            <lengthmeasurement>E</lengthmeasurement>
            <specimensamplecount>10</specimensamplecount>
            <individual specimenno="1">
              <lengthunit>2</lengthunit>
              <length>0.28</length>
              <individualproducttype>1</individualproducttype>
            </individual>
            <individual specimenno="2">
              <lengthunit>2</lengthunit>
              <length>0.285</length>
              <individualproducttype>1</individualproducttype>
            </individual>
            <individual specimenno="3">
              <lengthunit>2</lengthunit>
              <length>0.37</length>
              <individualproducttype>1</individualproducttype>
            </individual>
            <individual specimenno="4">
              <lengthunit>2</lengthunit>
              <length>0.315</length>
              <individualproducttype>1</individualproducttype>
            </individual>
            <individual specimenno="5">
              <lengthunit>2</lengthunit>
              <length>0.32</length>
              <individualproducttype>1</individualproducttype>
            </individual>
            <individual specimenno="6">
              <lengthunit>2</lengthunit>
              <length>0.38</length>
              <individualproducttype>1</individualproducttype>
            </individual>
            <individual specimenno="7">
              <lengthunit>2</lengthunit>
              <length>0.39</length>
              <individualproducttype>1</individualproducttype>
            </individual>
            <individual specimenno="8">
              <lengthunit>2</lengthunit>
              <length>0.305</length>
              <individualproducttype>1</individualproducttype>
            </individual>
            <individual specimenno="9">
              <lengthunit>2</lengthunit>
              <length>0.24</length>
              <individualproducttype>1</individualproducttype>
            </individual>
            <individual specimenno="10">
              <lengthunit>2</lengthunit>
              <length>0.36</length>
              <individualproducttype>1</individualproducttype>
            </individual>
          </catchsample>
        </fishstation>
      </mission>
    </fishmeter>

我正在尝试将 individual 节点作为行提取到数据框中，将信息从父 catchsample 和祖父 fishstation 节点中保留在附加列中，以便生成数据框包含以下列：

cruise, station, platform, serialno, platform, nation, latitudestart, longitudestart, latitudeend, longitudeend, species, samplenumber, noname, aphia, conservation, producttype, weight, count, lengthsampleweight, sampleproducttype, lengthmeasurement, specimensamplecount, specimenno, lengthunit, length, individualproducttype

根据 R XML - combining parent and child nodes into data frame 的回答，我设法将 individual 节点数据提取到数据框中，但是，不是来自更高级别节点的相关信息。

  fish<- read_xml('test.xml') %>% 
      xml_find_all('//individual') %>% 
      map_dfr(~flatten(c(xml_attrs(.x), 
                         map(xml_children(.x), 
                             ~set_names(as.list(xml_text(.x)), xml_name(.x)))))) %>%
      type_convert()

# A tibble: 14 x 4
   specimenno lengthunit length individualproducttype
        <dbl>      <dbl>  <dbl>                 <dbl>
 1          1          2  0.36                      1
 2          2          2  0.36                      1
 3          3          2  0.315                     1
 4          4          2  0.315                     1
 5          1          2  0.28                      1
 6          2          2  0.285                     1
 7          3          2  0.37                      1
 8          4          2  0.315                     1
 9          5          2  0.32                      1
10          6          2  0.38                      1
11          7          2  0.39                      1
12          8          2  0.305                     1
13          9          2  0.24                      1
14         10          2  0.36                      1

Answer 1

你可以这样做：

library(xml2)
library(purrr)
library(readr)
library(rvest)
library(tibble)

individuals <- read_xml('test.xml') %>% 
  xml_find_all('//individual')

to_add <- function(individual, xpath) individual %>% 
  html_nodes(xpath = xpath) %>% 
  {list(html_text(.), html_name(.))} %>% 
  {setNames(object = .[[1]], nm = .[[2]])}

get_data <- function(individual){
  
  out <- c(
    individual %>% html_attrs(),
    individual %>% html_nodes(xpath = "..") %>% html_attrs() %>% unlist,
    individual %>% html_nodes(xpath = "../..") %>% html_attrs() %>% unlist,
    individual %>% html_nodes(xpath = "../../..") %>% html_attrs() %>% unlist
  )
  
  xpathes <- c("../../*[not(descendant::*)]", "../*[not(descendant::*)]", "*")
  
  c(sapply(xpathes, to_add, individual = individual, USE.NAMES = FALSE) %>% unlist, out)
}

然后：

lapply(individuals, get_data) %>% 
  do.call(what = cbind) %>% 
  as.tibble

XML 个节点到 R 数据框，所有更高级别的节点属性作为列

XML nodes to R data frame with all higher-level node attributes as columns

xml

r

xml2

tidyverse