将医疗设备XML数据转换为R中的数据帧

Question

我有一个医疗设备生成的XML数据，我正在尝试解析这些数据，但我无论如何也搞不懂它。下面是XML数据的一个示例：

<?xml version="1.0" encoding="UTF-8"?>
<Report Type="CprReport" Version="1.3" Generated="2020-05-06T09:08:47.94976" IncidentID="F0000001" PatientID="DE-IDENTIFIED" SoftwareVersion="11.0.0.1036">
  <DeviceID>BLANK</DeviceID>
  <DeviceType>LP15</DeviceType>
  <CPRAnnotationEdited>false</CPRAnnotationEdited>
  <PowerOn>2020-04-18T20:57:55.00000</PowerOn>
  <DeviceConfiguration>2L355RRB0200UR</DeviceConfiguration>
  <TimeAdjustment>PT1S</TimeAdjustment>
  <CPRStatistics SACVersion="10" CPRPauseThreshold="10" CompressionPauseThreshold="3" MinimumTimeInterval="30" MinimumCompressions="5">
    <OverallStatistic>
      <AverageCompressionRatePerMin>96.3298058454348</AverageCompressionRatePerMin>
      <AverageVentilationRatePerMin>9.34405124270701</AverageVentilationRatePerMin>
      <MedianCompressionRatePerMin>99.8261838893409</MedianCompressionRatePerMin>
      <MedianVentilationRatePerMin>6.51749943203332</MedianVentilationRatePerMin>
      <TotalTimeCompressionsDuringPromptedCprSec>0</TotalTimeCompressionsDuringPromptedCprSec>
      <TotalTimeCompressionsDuringValidSec>1277.72862806776</TotalTimeCompressionsDuringValidSec>
      <TotalTimeCprDuringPromptedCprSec>0</TotalTimeCprDuringPromptedCprSec>
      <TotalTimeCprDuringValidSec>1298.04384154134</TotalTimeCprDuringValidSec>
      <TotalTimePromptedCprSec>0</TotalTimePromptedCprSec>
      <TotalTimeValidSec>1339.14938235198</TotalTimeValidSec>
      <TotalTimeValidSecEx>1339.14938235198</TotalTimeValidSecEx>
    </OverallStatistic>
    <IntervalStatistics>
      <CPRStatisticsItem Interval="1" ResponsibleForCPR="" CPRDurationSec="0" PauseDurationSec="88.355" ReasonForPause="" IntervalComments="" AverageCompressionRatePerMin="-1" AverageVentilationRatePerMin="-1" MedianCompressionRatePerMin="-1" MedianVentilationRatePerMin="-1" TotalTimeCompressionsDuringPromptedCprSec="0" TotalTimeCompressionsDuringValidSec="0.016383236672237" TotalTimeCprDuringPromptedCprSec="0" TotalTimeCprDuringValidSec="0" TotalTimePromptedCprSec="0" TotalTimeValidSec="0.016383236672237" TotalTimeValidSecEx="0.016383236672237"/>
      <CPRStatisticsItem Interval="2" ResponsibleForCPR="" CPRStartTime="2020-04-18T20:59:23.37100" CPREndTime="2020-04-18T21:00:53.69200" CPRDurationSec="90.321" PauseDurationSec="12.337" ReasonForPause="" IntervalComments="" AverageCompressionRatePerMin="95.8528439195659" AverageVentilationRatePerMin="0" MedianCompressionRatePerMin="127.518878980892" MedianVentilationRatePerMin="0" TotalTimeCompressionsDuringPromptedCprSec="0" TotalTimeCompressionsDuringValidSec="80.0812608538943" TotalTimeCprDuringPromptedCprSec="0" TotalTimeCprDuringValidSec="90.3207837740424" TotalTimePromptedCprSec="0" TotalTimeValidSec="102.673744224909" TotalTimeValidSecEx="102.673744224909"/>
      <CPRStatisticsItem Interval="3" ResponsibleForCPR="" CPRStartTime="2020-04-18T21:01:06.04500" CPREndTime="2020-04-18T21:05:05.83000" CPRDurationSec="239.785" PauseDurationSec="18.89" ReasonForPause="" IntervalComments="" AverageCompressionRatePerMin="91.8527379821395" AverageVentilationRatePerMin="0" MedianCompressionRatePerMin="99.4940232081911" MedianVentilationRatePerMin="0" TotalTimeCompressionsDuringPromptedCprSec="0" TotalTimeCompressionsDuringValidSec="239.78505193486" TotalTimeCprDuringPromptedCprSec="0" TotalTimeCprDuringValidSec="239.78505193486" TotalTimePromptedCprSec="0" TotalTimeValidSec="258.691307054622" TotalTimeValidSecEx="258.691307054622"/>
      <CPRStatisticsItem Interval="4" ResponsibleForCPR="" CPRStartTime="2020-04-18T21:05:24.73600" CPREndTime="2020-04-18T21:18:09.50600" CPRDurationSec="764.77" PauseDurationSec="9.322" ReasonForPause="" IntervalComments="" AverageCompressionRatePerMin="97.1202954559885" AverageVentilationRatePerMin="8.60363351605325" MedianCompressionRatePerMin="99.6300586675938" MedianVentilationRatePerMin="8.55159640102828" TotalTimeCompressionsDuringPromptedCprSec="0" TotalTimeCompressionsDuringValidSec="754.693797306596" TotalTimeCprDuringPromptedCprSec="0" TotalTimeCprDuringValidSec="764.769487860022" TotalTimePromptedCprSec="0" TotalTimeValidSec="774.107932763197" TotalTimeValidSecEx="774.107932763197"/>
      <CPRStatisticsItem Interval="5" ResponsibleForCPR="" CPRStartTime="2020-04-18T21:18:18.84400" CPREndTime="2020-04-18T21:21:42.01300" CPRDurationSec="203.169" PauseDurationSec="0.491000000000014" ReasonForPause="" IntervalComments="" AverageCompressionRatePerMin="99.283111575899" AverageVentilationRatePerMin="9.42747647011503" MedianCompressionRatePerMin="99.4707780795654" MedianVentilationRatePerMin="9.45028304169019" TotalTimeCompressionsDuringPromptedCprSec="0" TotalTimeCompressionsDuringValidSec="203.152134735738" TotalTimeCprDuringPromptedCprSec="0" TotalTimeCprDuringValidSec="203.168517972411" TotalTimePromptedCprSec="0" TotalTimeValidSec="203.660015072578" TotalTimeValidSecEx="203.660015072578"/>
    </IntervalStatistics>
  </CPRStatistics>
  <CPRShockPauseStatistics/>
</Report>

我希望从<OverallStatistics>和<IntervalStatistics>生成两个数据帧。

我正在使用XML包解析数据，下面是我到目前为止所做的工作：

df <- xmlParse(file = "file.xml", useInternalNodes = TRUE)

df_1 <- xmlToDataFrame(df, nodes = getNodeSet(df, "//CPRStatistics"))

这就是我被卡住的地方。

Answer 1

通常，package xml2更容易使用，尽管package XML至少会尝试在合理的情况下创建数据帧。

从<OverallStatistic>获取的节点集更容易做成数据帧：

library(XML)
df <- xmlParse(file = "file.xml", useInternalNodes = TRUE)
overall <- xmlToDataFrame(df, nodes = getNodeSet(df, "//OverallStatistic"))

此数据框中只有一行：

overall
#>   AverageCompressionRatePerMin AverageVentilationRatePerMin
#> 1             96.3298058454348             9.34405124270701
#>   MedianCompressionRatePerMin MedianVentilationRatePerMin
#> 1            99.8261838893409            6.51749943203332
#>   TotalTimeCompressionsDuringPromptedCprSec TotalTimeCompressionsDuringValidSec
#> 1                                         0                    1277.72862806776
#>   TotalTimeCprDuringPromptedCprSec TotalTimeCprDuringValidSec TotalTimePromptedCprSec
#> 1                                0           1298.04384154134                       0
#>   TotalTimeValidSec TotalTimeValidSecEx
#> 1  1339.14938235198    1339.14938235198

第二个节点<IntervalStatistics>更难解析，因为值存储在属性中，而不是作为文本节点。这需要您找到所有的<CPRStatisticsItem>节点，将它们的所有属性剥离到一个列表中，然后将它们一起rbind到一个数据框中。在本例中，由于数据框有如此多的列，为了便于打印到屏幕，我将其转换为tibble而不是数据框：

dplyr::as_tibble(do.call(rbind, lapply(getNodeSet(df, "//CPRStatisticsItem")[-1], xmlAttrs)))
#> # A tibble: 4 x 19
#>   Interval ResponsibleForC~ CPRStartTime CPREndTime CPRDurationSec PauseDurationSec
#>   <chr>    <chr>            <chr>        <chr>      <chr>          <chr>           
#> 1 2        ""               2020-04-18T~ 2020-04-1~ 90.321         12.337          
#> 2 3        ""               2020-04-18T~ 2020-04-1~ 239.785        18.89           
#> 3 4        ""               2020-04-18T~ 2020-04-1~ 764.77         9.322           
#> 4 5        ""               2020-04-18T~ 2020-04-1~ 203.169        0.4910000000000~
#> # ... with 13 more variables: ReasonForPause <chr>, IntervalComments <chr>,
#> #   AverageCompressionRatePerMin <chr>, AverageVentilationRatePerMin <chr>,
#> #   MedianCompressionRatePerMin <chr>, MedianVentilationRatePerMin <chr>,
#> #   TotalTimeCompressionsDuringPromptedCprSec <chr>,
#> #   TotalTimeCompressionsDuringValidSec <chr>,
#> #   TotalTimeCprDuringPromptedCprSec <chr>, TotalTimeCprDuringValidSec <chr>,
#> #   TotalTimePromptedCprSec <chr>, TotalTimeValidSec <chr>, TotalTimeValidSecEx <chr>