In PietaSchofield/sentinelreadr: Read RSNTL Files And Convert XML To Data Tables

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

library(tidyverse)
library(sentinelreadr)
library(logr)
logfile <- file.path(Sys.getenv("HOME"),paste0("sentinelreadr_",gsub("([ ]|:|-)","_",Sys.time())))
lf <- logr::log_open(logfile)

Introduction

This is a small package that simplifies the extraction of the data that is stored in xml inside RSNTL file. At the present there are three main function

read_rsntl() which extract the xml elements from the RSNTL file and creates a list of xml documents
testdetails_xml_to_table() coverts the testdetails section of the file into a data.table
clinical_xml_to_table() that converts the clinical data elements into data.tables

input_filename <- system.file("extdata","2013_B_07-01-2021_13-49-43.RSNTL",package="sentinelreadr")
xml <- read_rsntl(input_filename,chkDMV=T)

The test data section can be decoded to a tibble. Because the xml object returned buy the read_rstnl() funtion is a list of lists it is best to use the lapply function to the various items in the xml object

is(xml)
summary(xml)
lapply(xml,is)

patient <- lapply(xml$test_details,testdetails_xml_to_table,trans=T)
DT::datatable(patient[[1]])

The summary shows that there are two datasets in this file

data <- lapply(xml$clinical_data,clinical_xml_to_table)
DT::datatable(data[[1]])

However it appears they are the same data

DT::datatable(data[[2]])

This data is plotable

library(ggplot2)
gg <- ggplot(data[[2]],aes(x=Time,y=Systolic)) + geom_point(colour="blue") 
plot(gg)

Reading the other files

input_filename <- system.file("extdata","2014_B_07-01-2021_13-49-44.RSNTL",package="sentinelreadr")
xml <- read_rsntl(input_filename,chkDMV=T)

Get test details

patient <- lapply(xml$test_details,testdetails_xml_to_table)
DT::datatable(patient[[1]])

Get data details

data <- lapply(xml$clinical_data,clinical_xml_to_table)
DT::datatable(data[[1]])

Read file 3

input_filename <- system.file("extdata","2011_B_07-01-2021_13-49-41.RSNTL",package="sentinelreadr")
xml <- read_rsntl(input_filename,chkDMV=T)

Get test details file 3

patient <- lapply(xml$test_details,testdetails_xml_to_table)
DT::datatable(patient[[1]])

Get data details 3

data <- lapply(xml$clinical_data,clinical_xml_to_table)
DT::datatable(data[[1]])

Errors

Check that files that are corrupt complete but return a NULL xml

input_filename <- system.file("extdata","2014_B_07-01-2021_error_1.RSNTL",package="sentinelreadr")
xml <- read_rsntl(input_filename,chkDMV=T)
is.null(xml)

input_filename <- system.file("extdata","2014_B_07-01-2021_error_2.RSNTL",package="sentinelreadr")
xml <- read_rsntl(input_filename,chkDMV=T)
is.null(xml)

Process Directory

Use the process_files function to process all .RSNTL files in a directory to create a table of patient details and a table with all the reading from all the files with a column that links them to the patient id

# The directory of RSNTL files
directory <- system.file("extdata",package="sentinelreadr")

# A file to hold the patient table
patienttable <- file.path(Sys.getenv("HOME"),"patient.csv")

# A file to hold the reading table
resultstable <- file.path(Sys.getenv("HOME"),"results.csv")

# A file to hold the reading table

results <- process_files(directory, pattablefile=patienttable, restablefile=resultstable,
                         silent=F,db=F)
lapply(results,nrow)
logr::log_close()