将Infopath .XML表单导入R中的数据框 [英] Import Infopath .XML forms into data frame in R
本文介绍了将Infopath .XML表单导入R中的数据框的处理方法，对大家解决问题具有一定的参考价值，需要的朋友们下面随着小编来一起学习吧！
问题描述
在R中导入Infopath .XML表单并将其转换为数据框的最佳方法是什么?如果我在Excel中打开Infopath .XML文件，则数据框的行和列会正确显示.
What's the best way to import Infopath .XML forms in R, and transform into a dataframe? If I open the Infopath .XML file in Excel, the rows and columns of the data frame appear correctly.
这是我使用XML包在R中尝试过的方法:
Here's what I tried in R using the XML package:
- 使用xmlParse()解析XML文件
- 我使用xmlToDataFrame()尝试将已解析的XML文件转换为数据框
但是，在步骤2中，我收到以下错误消息:
In step 2, however, I receive the following error:
Error in `[<-.data.frame`(`*tmp*`, i, names(nodes[[i]]), value = c("touch your head13011000", :
duplicate subscripts for columns
但是，当我在Excel中打开XML文件时，似乎没有重复的列.如何将XML文件从Infopath转换为R中的数据框?预期的列应为(在Excel中显示):
There do not appear to be duplicate columns, though, when I open the XML file in Excel. How can I transform this XML file from Infopath into a data frame in R? The expected columns should be (as they appear in Excel):
TCID, DateCoded, tcAge, T1_B3, T1_B2, T1_B1, T1_B0, T1_A3, T1_A2, T1_A1, T1_A0, T1_DelayTotal, T2_A3, T2_A2, T2_A1, T2_A, T2_B3, T2_B2, T2_B1, T2_B0, T2_DelayTotal, Coder, notes_t1, note_t2, bachildpres30, baparpres30, bapassptgo, bapassptnogo, bamissgame, P1_B3, P1_B2, P1_B1, P1_B0, P1_A3, P1_A2, P1_A1, P1_A0, P1_DelayTotal, P1_action, P1_go-nogo, P1_score, P1_delay, P1_trial, P1_Ecommand, P1_imitation, P1_restraint, P1_ruleswitch, P1_trials, P1_gotrials, P1_nogotrials, T1_gotrials, T1_nogotrials, T1_trials, T2_gotrials, T2_nogotrials, T2_trials, P1_notplay, T1_trial, T1_go-nogo, T1_score, T1_delay, T1_action, T2_trial, T2_go-nogo, T2_score, T2_delay, T2_action
对于在XML文件中多次出现的变量，我希望它们以长格式出现在数据框中(即，同一变量有多行).我对XML文件没有太多经验，所以非常感谢您的帮助.
For the variables that appear multiple times in the XML file, I'd like them to be in the data frame in long form (i.e., multiple rows for the same variable). I don't have much experience with XML files, so your help is greatly appreciated.
下面是当我使用xmlParse时在R中解析的XML文件的样子:
Below is what the parsed XML file looks like in R when I use xmlParse:
<my:myFields lang="en-us" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:w="http://schemas.microsoft.com/office/word/2003/wordml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:v="urn:schemas-microsoft-com:vml" xmlns:wx="http://schemas.microsoft.com/office/word/2003/auxHint" xmlns:aml="http://schemas.microsoft.com/aml/2001/core" xmlns:w10="urn:schemas-microsoft-com:office:word" xmlns:st="urn:schemas-microsoft-com:office:smarttags" xmlns:xhtml="http://www.w3.org/1999/xhtml" xmlns:my="http://schemas.microsoft.com/office/infopath/2003/myXSD/2009-07-01T18:12:59" xmlns:xd="http://schemas.microsoft.com/office/infopath/2003">
<my:SPSS>
<my:TCID>10</my:TCID>
<my:DateCoded>2013-04-01</my:DateCoded>
<my:tcAge>30</my:tcAge>
<my:T1_B3>6</my:T1_B3>
<my:T1_B2>0</my:T1_B2>
<my:T1_B1>0</my:T1_B1>
<my:T1_B0>0</my:T1_B0>
<my:T1_A3>0</my:T1_A3>
<my:T1_A2>0</my:T1_A2>
<my:T1_A1>1</my:T1_A1>
<my:T1_A0>5</my:T1_A0>
<my:T1_DelayTotal>1</my:T1_DelayTotal>
<my:T2_A3 nil="true"/>
<my:T2_A2 nil="true"/>
<my:T2_A1 nil="true"/>
<my:T2_A0 nil="true"/>
<my:T2_B3 nil="true"/>
<my:T2_B2 nil="true"/>
<my:T2_B1 nil="true"/>
<my:T2_B0 nil="true"/>
<my:T2_DelayTotal nil="true"/>
<my:Coder>Name</my:Coder>
</my:SPSS>
<my:notes_t1/>
<my:note_t2/>
<my:bachildpres30>0</my:bachildpres30>
<my:baparpres30>0</my:baparpres30>
<my:bapassptgo>1</my:bapassptgo>
<my:bapassptnogo>0</my:bapassptnogo>
<my:bamissgame>0</my:bamissgame>
<my:P1_B3>4</my:P1_B3>
<my:P1_B2>0</my:P1_B2>
<my:P1_B1>0</my:P1_B1>
<my:P1_B0>1</my:P1_B0>
<my:P1_A3>0</my:P1_A3>
<my:P1_A2>0</my:P1_A2>
<my:P1_A1>1</my:P1_A1>
<my:P1_A0>3</my:P1_A0>
<my:P1_DelayTotal>0</my:P1_DelayTotal>
<my:group2>
<my:group3>
<my:P1_action>touch your head</my:P1_action>
<my:P1_go-nogo>1</my:P1_go-nogo>
<my:P1_score>3</my:P1_score>
<my:P1_delay>0</my:P1_delay>
<my:P1_trial>1</my:P1_trial>
<my:P1_Ecommand>1</my:P1_Ecommand>
<my:P1_imitation>0</my:P1_imitation>
<my:P1_restraint>0</my:P1_restraint>
<my:P1_ruleswitch>0</my:P1_ruleswitch>
</my:group3>
<my:group3>
<my:P1_action>touch your nose</my:P1_action>
<my:P1_go-nogo>1</my:P1_go-nogo>
<my:P1_score>3</my:P1_score>
<my:P1_delay>0</my:P1_delay>
<my:P1_trial>2</my:P1_trial>
<my:P1_Ecommand>1</my:P1_Ecommand>
<my:P1_imitation>0</my:P1_imitation>
<my:P1_restraint>0</my:P1_restraint>
<my:P1_ruleswitch>0</my:P1_ruleswitch>
</my:group3>
<my:group3>
<my:P1_action>touch your tummy</my:P1_action>
<my:P1_go-nogo>1</my:P1_go-nogo>
<my:P1_score>3</my:P1_score>
<my:P1_delay>0</my:P1_delay>
<my:P1_trial>3</my:P1_trial>
<my:P1_Ecommand>1</my:P1_Ecommand>
<my:P1_imitation>0</my:P1_imitation>
<my:P1_restraint>0</my:P1_restraint>
<my:P1_ruleswitch>0</my:P1_ruleswitch>
</my:group3>
<my:group3>
<my:P1_action>touch your head</my:P1_action>
<my:P1_go-nogo>1</my:P1_go-nogo>
<my:P1_score>0</my:P1_score>
<my:P1_delay>0</my:P1_delay>
<my:P1_trial>4</my:P1_trial>
<my:P1_Ecommand>0</my:P1_Ecommand>
<my:P1_imitation>0</my:P1_imitation>
<my:P1_restraint>0</my:P1_restraint>
<my:P1_ruleswitch>0</my:P1_ruleswitch>
</my:group3>
<my:group3>
<my:P1_action>touch your head</my:P1_action>
<my:P1_go-nogo>1</my:P1_go-nogo>
<my:P1_score>3</my:P1_score>
<my:P1_delay>0</my:P1_delay>
<my:P1_trial>5</my:P1_trial>
<my:P1_Ecommand>0</my:P1_Ecommand>
<my:P1_imitation>0</my:P1_imitation>
<my:P1_restraint>0</my:P1_restraint>
<my:P1_ruleswitch>0</my:P1_ruleswitch>
</my:group3>
<my:group3>
<my:P1_action>touch your nose</my:P1_action>
<my:P1_go-nogo>1</my:P1_go-nogo>
<my:P1_score>3</my:P1_score>
<my:P1_delay>0</my:P1_delay>
<my:P1_trial>6</my:P1_trial>
<my:P1_Ecommand>0</my:P1_Ecommand>
<my:P1_imitation>0</my:P1_imitation>
<my:P1_restraint>0</my:P1_restraint>
<my:P1_ruleswitch>0</my:P1_ruleswitch>
</my:group3>
<my:group3>
<my:P1_action>clap your hands</my:P1_action>
<my:P1_go-nogo>1</my:P1_go-nogo>
<my:P1_score>3</my:P1_score>
<my:P1_delay>0</my:P1_delay>
<my:P1_trial>7</my:P1_trial>
<my:P1_Ecommand>0</my:P1_Ecommand>
<my:P1_imitation>0</my:P1_imitation>
<my:P1_restraint>0</my:P1_restraint>
<my:P1_ruleswitch>0</my:P1_ruleswitch>
</my:group3>
<my:group3>
<my:P1_action>touch your nose</my:P1_action>
<my:P1_go-nogo>0</my:P1_go-nogo>
<my:P1_score>0</my:P1_score>
<my:P1_delay>0</my:P1_delay>
<my:P1_trial>8</my:P1_trial>
<my:P1_Ecommand>0</my:P1_Ecommand>
<my:P1_imitation>0</my:P1_imitation>
<my:P1_restraint>0</my:P1_restraint>
<my:P1_ruleswitch>0</my:P1_ruleswitch>
</my:group3>
<my:group3>
<my:P1_action>touch your ears</my:P1_action>
<my:P1_go-nogo>0</my:P1_go-nogo>
<my:P1_score>0</my:P1_score>
<my:P1_delay>0</my:P1_delay>
<my:P1_trial>9</my:P1_trial>
<my:P1_Ecommand>0</my:P1_Ecommand>
<my:P1_imitation>0</my:P1_imitation>
<my:P1_restraint>0</my:P1_restraint>
<my:P1_ruleswitch>0</my:P1_ruleswitch>
</my:group3>
<my:group3>
<my:P1_action>touch your tummy</my:P1_action>
<my:P1_go-nogo>0</my:P1_go-nogo>
<my:P1_score>0</my:P1_score>
<my:P1_delay>0</my:P1_delay>
<my:P1_trial>10</my:P1_trial>
<my:P1_Ecommand>0</my:P1_Ecommand>
<my:P1_imitation>0</my:P1_imitation>
<my:P1_restraint>0</my:P1_restraint>
<my:P1_ruleswitch>0</my:P1_ruleswitch>
</my:group3>
<my:group3>
<my:P1_action>touch your eyes</my:P1_action>
<my:P1_go-nogo>0</my:P1_go-nogo>
<my:P1_score>1</my:P1_score>
<my:P1_delay>0</my:P1_delay>
<my:P1_trial>11</my:P1_trial>
<my:P1_Ecommand>0</my:P1_Ecommand>
<my:P1_imitation>0</my:P1_imitation>
<my:P1_restraint>1</my:P1_restraint>
<my:P1_ruleswitch>0</my:P1_ruleswitch>
</my:group3>
<my:group3>
<my:P1_action>touch your eyes</my:P1_action>
<my:P1_go-nogo>1</my:P1_go-nogo>
<my:P1_score>3</my:P1_score>
<my:P1_delay>0</my:P1_delay>
<my:P1_trial>12</my:P1_trial>
<my:P1_Ecommand>0</my:P1_Ecommand>
<my:P1_imitation>0</my:P1_imitation>
<my:P1_restraint>0</my:P1_restraint>
<my:P1_ruleswitch>0</my:P1_ruleswitch>
</my:group3>
</my:group2>
<my:P1_trials>9</my:P1_trials>
<my:P1_gotrials>5</my:P1_gotrials>
<my:P1_nogotrials>4</my:P1_nogotrials>
<my:T1_gotrials>6</my:T1_gotrials>
<my:T1_nogotrials>6</my:T1_nogotrials>
<my:T1_trials>12</my:T1_trials>
<my:T2_gotrials>0</my:T2_gotrials>
<my:T2_nogotrials>0</my:T2_nogotrials>
<my:T2_trials>0</my:T2_trials>
<my:P1_notplay/>
<my:group4>
<my:group5>
<my:T1_trial>1</my:T1_trial>
<my:T1_go-nogo>1</my:T1_go-nogo>
<my:T1_score>3</my:T1_score>
<my:T1_delay>1</my:T1_delay>
<my:T1_action>Touch your tongue</my:T1_action>
</my:group5>
<my:group5>
<my:T1_trial>2</my:T1_trial>
<my:T1_go-nogo>1</my:T1_go-nogo>
<my:T1_score>3</my:T1_score>
<my:T1_delay>0</my:T1_delay>
<my:T1_action>Touch your teeth</my:T1_action>
</my:group5>
<my:group5>
<my:T1_trial>3</my:T1_trial>
<my:T1_go-nogo>0</my:T1_go-nogo>
<my:T1_score>0</my:T1_score>
<my:T1_delay>0</my:T1_delay>
<my:T1_action>Touch your ear</my:T1_action>
</my:group5>
<my:group5>
<my:T1_trial>4</my:T1_trial>
<my:T1_go-nogo>1</my:T1_go-nogo>
<my:T1_score>3</my:T1_score>
<my:T1_delay>0</my:T1_delay>
<my:T1_action>Clap your hands</my:T1_action>
</my:group5>
<my:group5>
<my:T1_trial>5</my:T1_trial>
<my:T1_go-nogo>0</my:T1_go-nogo>
<my:T1_score>0</my:T1_score>
<my:T1_delay>0</my:T1_delay>
<my:T1_action>Clap your hands</my:T1_action>
</my:group5>
<my:group5>
<my:T1_trial>6</my:T1_trial>
<my:T1_go-nogo>0</my:T1_go-nogo>
<my:T1_score>0</my:T1_score>
<my:T1_delay>0</my:T1_delay>
<my:T1_action>Touch your eyes</my:T1_action>
</my:group5>
<my:group5>
<my:T1_trial>7</my:T1_trial>
<my:T1_go-nogo>0</my:T1_go-nogo>
<my:T1_score>0</my:T1_score>
<my:T1_delay>0</my:T1_delay>
<my:T1_action>Touch your feet</my:T1_action>
</my:group5>
<my:group5>
<my:T1_trial>8</my:T1_trial>
<my:T1_go-nogo>1</my:T1_go-nogo>
<my:T1_score>3</my:T1_score>
<my:T1_delay>0</my:T1_delay>
<my:T1_action>Touch your nose</my:T1_action>
</my:group5>
<my:group5>
<my:T1_trial>9</my:T1_trial>
<my:T1_go-nogo>0</my:T1_go-nogo>
<my:T1_score>1</my:T1_score>
<my:T1_delay>0</my:T1_delay>
<my:T1_action>Touch your nose</my:T1_action>
</my:group5>
<my:group5>
<my:T1_trial>10</my:T1_trial>
<my:T1_go-nogo>1</my:T1_go-nogo>
<my:T1_score>3</my:T1_score>
<my:T1_delay>0</my:T1_delay>
<my:T1_action>Touch your tummy</my:T1_action>
</my:group5>
<my:group5>
<my:T1_trial>11</my:T1_trial>
<my:T1_go-nogo>0</my:T1_go-nogo>
<my:T1_score>0</my:T1_score>
<my:T1_delay>0</my:T1_delay>
<my:T1_action>Wave your hand</my:T1_action>
</my:group5>
<my:group5>
<my:T1_trial>12</my:T1_trial>
<my:T1_go-nogo>1</my:T1_go-nogo>
<my:T1_score>3</my:T1_score>
<my:T1_delay>0</my:T1_delay>
<my:T1_action>Touch your head</my:T1_action>
</my:group5>
</my:group4>
<my:group6>
<my:group7>
<my:T2_trial>1</my:T2_trial>
<my:T2_go-nogo>0</my:T2_go-nogo>
<my:T2_score/>
<my:T2_delay>0</my:T2_delay>
<my:T2_action>Touch your tongue</my:T2_action>
</my:group7>
<my:group7>
<my:T2_trial>2</my:T2_trial>
<my:T2_go-nogo>0</my:T2_go-nogo>
<my:T2_score/>
<my:T2_delay>0</my:T2_delay>
<my:T2_action>Touch your teeth</my:T2_action>
</my:group7>
<my:group7>
<my:T2_trial>3</my:T2_trial>
<my:T2_go-nogo>1</my:T2_go-nogo>
<my:T2_score/>
<my:T2_delay>0</my:T2_delay>
<my:T2_action>Touch your ear</my:T2_action>
</my:group7>
<my:group7>
<my:T2_trial>4</my:T2_trial>
<my:T2_go-nogo>0</my:T2_go-nogo>
<my:T2_score/>
<my:T2_delay>0</my:T2_delay>
<my:T2_action>Clap your hands</my:T2_action>
</my:group7>
<my:group7>
<my:T2_trial>5</my:T2_trial>
<my:T2_go-nogo>1</my:T2_go-nogo>
<my:T2_score/>
<my:T2_delay>0</my:T2_delay>
<my:T2_action>Clap your hands</my:T2_action>
</my:group7>
<my:group7>
<my:T2_trial>6</my:T2_trial>
<my:T2_go-nogo>1</my:T2_go-nogo>
<my:T2_score/>
<my:T2_delay>0</my:T2_delay>
<my:T2_action>Touch your eyes</my:T2_action>
</my:group7>
<my:group7>
<my:T2_trial>7</my:T2_trial>
<my:T2_go-nogo>1</my:T2_go-nogo>
<my:T2_score/>
<my:T2_delay>0</my:T2_delay>
<my:T2_action>Touch your feet</my:T2_action>
</my:group7>
<my:group7>
<my:T2_trial>8</my:T2_trial>
<my:T2_go-nogo>0</my:T2_go-nogo>
<my:T2_score/>
<my:T2_delay>0</my:T2_delay>
<my:T2_action>Touch your nose</my:T2_action>
</my:group7>
<my:group7>
<my:T2_trial>9</my:T2_trial>
<my:T2_go-nogo>1</my:T2_go-nogo>
<my:T2_score/>
<my:T2_delay>0</my:T2_delay>
<my:T2_action>Touch your nose</my:T2_action>
</my:group7>
<my:group7>
<my:T2_trial>10</my:T2_trial>
<my:T2_go-nogo>0</my:T2_go-nogo>
<my:T2_score/>
<my:T2_delay>0</my:T2_delay>
<my:T2_action>Touch your tummy</my:T2_action>
</my:group7>
<my:group7>
<my:T2_trial>11</my:T2_trial>
<my:T2_go-nogo>1</my:T2_go-nogo>
<my:T2_score/>
<my:T2_delay>0</my:T2_delay>
<my:T2_action>Wave your hand</my:T2_action>
</my:group7>
<my:group7>
<my:T2_trial>12</my:T2_trial>
<my:T2_go-nogo>0</my:T2_go-nogo>
<my:T2_score/>
<my:T2_delay>0</my:T2_delay>
<my:T2_action>Touch your head</my:T2_action>
</my:group7>
</my:group6>
</my:myFields>
推荐答案
根据我的经验，xmlToDataFrame仅在XML已经以非常一致的方式进行结构化时才起作用.您正在使用的数据以多种不同的方式进行结构化:
In my experience, xmlToDataFrame only works when the XML is already structured in a very consistent way. The data you are working with is structured in many different ways:
# Assuming you've already read your data into a character vector called `xml_file
xml_file <- xmlParse(xml_file)
xml_file <- xmlToList(xml_file)
stack(sapply(xml_file, length))
values ind
1 22 SPSS
2 0 notes_t1
3 0 note_t2
4 1 bachildpres30
5 1 baparpres30
6 1 bapassptgo
7 1 bapassptnogo
8 1 bamissgame
9 1 P1_B3
10 1 P1_B2
11 1 P1_B1
12 1 P1_B0
13 1 P1_A3
14 1 P1_A2
15 1 P1_A1
16 1 P1_A0
17 1 P1_DelayTotal
18 12 group2
19 1 P1_trials
20 1 P1_gotrials
21 1 P1_nogotrials
22 1 T1_gotrials
23 1 T1_nogotrials
24 1 T1_trials
25 1 T2_gotrials
26 1 T2_nogotrials
27 1 T2_trials
28 0 P1_notplay
29 12 group4
30 12 group6
31 1 .attrs
因此，您的大多数节点都包含一个值.一些是空的. "SPSS"节点包含22个值，所有值均具有不同的名称，"group2"，"group4"和"group6"均包含12个节点，每个节点包含多个值，但其值在节点之间相似.当我查看导入文件时Excel的功能时，它将12个节点的组件彼此堆叠在一起，然后将所有22个"SPSS"组件与所有单值节点串在一起，并重复该字符串用于堆叠12个节点的组件所产生的行数，然后将这两部分绑定成列.
So most of your nodes contain a single value. A few are empty. The "SPSS" node contains 22 values, all with different names, and "group2", "group4", and "group6" all contain 12 nodes, each of which contains multiple values, but whose values are similar across nodes. When I looked at what Excel did when I imported the file, it stacked the 12-node components on top of each other, then strung all 22 of the "SPSS" components together with all of the single-value nodes and repeated that string for as many rows as had been created from stacking the 12-node components, and then bound the two pieces together in columns.
为此，请从12个节点的块中分离出长字符串:
To do that, separate out the long string from the 12-node chunks:
xml_file_singles <- xml_file[sapply(xml_file, length) != 12]
xml_file_singles[sapply(xml_file_singles, length) == 0] <- NA
xml_file_singles <- unlist(xml_file_singles)
xml_file_multiples <- xml_file[sapply(xml_file, length) == 12]
现在获取12个节点的块并将每个块转换为数据帧:
Now take the 12-node chunks and turn each chunk into a data frame:
xml_file_multiples <- lapply(1:length(xml_file_multiples), function(i) {
x <- lapply(xml_file_multiples[[i]], function(y) {
data.frame(as.list(unlist(y)), stringsAsFactors = FALSE)})
x <- do.call("rbind", x)
cbind("group" = names(xml_file_multiples)[i], x)
})
现在使用plyr包的rbind.fill函数将所有新数据帧放在一起:
Now use the plyr package's rbind.fill function to put all the new data frames together:
require(plyr)
xml_file_multiples <- do.call("rbind.fill", xml_file_multiples)
现在cbind将您的长字符串值绑定到绑定的数据帧:
Now cbind your long string of values to your bound dataframes:
xml_final <- cbind(as.list(xml_file_singles), xml_file_multiples,
stringsAsFactors = FALSE)
这种方法，就像Excel一样，引入了很多NA，因为不同的12节点块的列名都略有不同.如果您在致电rbind.fill之前完成了此操作:
This approach, like Excel's, introduces a whole lot of NAs, because the column names for your different 12-node chunks all differ slightly. If you did this before calling rbind.fill:
xml_file_multiples <- lapply(1:length(xml_file_multiples), function(i) {
x <- lapply(xml_file_multiples[[i]], function(y) {
data.frame(as.list(unlist(y)), stringsAsFactors = FALSE)})
x <- do.call("rbind", x)
x <- cbind("group" = names(xml_file_multiples)[i], x)
colnames(x) <- gsub("^\\w\\d_", "", colnames(x))
x
})
您将生成较少的NA，因为您将生成较少的冗余列，但是随后您将不得不依靠组"列中的值来跟踪哪些行最初出现在哪个节点中.
You would generate fewer NA's because you would generate fewer redundant columns, but then you would have to rely on the values in the "group" column to keep track of which rows had originally appeared in which node.
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