The goal of HL7.R is to enable wrangling of HL7 2.3.1/2.4 in R. This package was driven by the need of HL7 wrangling for NCIMS tasks (a notifiable conditions database for a state health authority). HL7 messages are just flattened list objects, and as such can be imported into R as a nested list.
Information on HL7 specifications were sourced from:
# install.packages("devtools")
devtools::install_github("Shaunson26/HL7.R")#> Loading required package: usethis
#> ℹ Loading HL7.R
#> HL7.R - for help see vignette('Getting-started', package = 'HL7.R') or vignette('package = 'HL7.R') for other examples
The first problem this package solves is parsing of HL7 messages into a
nested list. The function parse_hl7_message() will parse a HL7 file
into a list. This works for both single messages and batch messages. For
each parsed message, the function will try it’s best at naming all the
elements. This is simple for the top level elements (HL7 segments), but
a bit more cumbersome within the list elements (HL7 segment fields). By
convention, fields are referenced by number (“The fourth field in MSH is
the sending facility”), but having names can make things a bit more
readable at times. Repeated segments within a message are numbered in
the output list e.g. OBX.1 OBX.2 (using the Set ID value).
Notes
- All values should be imported as text, and any conversion needs to be done downstream e.g with datetimes
- A
filenameattribute is attached with the list object
Use parse_hl7_message() on a file path.
hl7_file <- system.file(package = 'HL7.R', 'extdata/hl7-2.3.1.hl7')
hl7_list <- parse_hl7_message(hl7_file)
names(hl7_list)
#> [1] "MSH" "PID" "PV1" "OBR" "OBX.1" "OBX.2" "OBX.3" "OBX.4"
# First 5 fields of these segments
hl7_list$MSH[1:5]
#> $EncodingCharacters
#> [1] "^~\\&"
#>
#> $SendingApplication
#> [1] "22-70047081"
#>
#> $SendingFacility
#> [1] "AN EXAMPLE LAB"
#>
#> $ReceivingApplication
#> [1] "NDD"
#>
#> $ReceivingFacility
#> [1] "NSW HEALTH"
hl7_list$PID[1:5]
#> $SetID
#> [1] ""
#>
#> $PatientID
#> [1] ""
#>
#> $PatientIdentifierList
#> [1] "AN EXAMPLE LAB"
#>
#> $AlternatePatientIDPID
#> [1] ""
#>
#> $PatientName
#> $PatientName$familyName
#> [1] "SIMPSON"
#>
#> $PatientName$givenName
#> [1] "HOMER"# File from where data parsed
attr(hl7_list, 'filename')
#> [1] "hl7-2.3.1.hl7"Traditionally indexes are used, but using named elements can help readability.
with(hl7_list,
data.frame(
first_name = PID[[5]][[2]],
last_name = PID[[5]][[1]],
suburb = PID[[11]][[3]]
)
)
#> first_name last_name suburb
#> 1 HOMER SIMPSON SPRINGFIELD
with(hl7_list,
data.frame(
first_name = PID$PatientName$givenName,
last_name = PID$PatientName$familyName,
suburb = PID$PatientAddress$city
)
)
#> first_name last_name suburb
#> 1 HOMER SIMPSON SPRINGFIELDparse_hl7_message() will check for batch headers and parse
appropriately. The result is a list of parsed messages.
hl7_file <- system.file(package = 'HL7.R', 'extdata/fake-covid-batch.hl7')
hl7_list <- parse_hl7_message(hl7_file)
#> Found 2 messages within file
# unnamed list of length of the number of messages
length(hl7_list)
#> [1] 2
names(hl7_list)
#> NULL
# a single message lives within the list elements now
names(hl7_list[[1]])
#> [1] "MSH" "PID" "OBX.1"
# accessing things
hl7_list[[1]]$PID$PatientName
#> $familyName
#> [1] "Homer"
#>
#> $givenName
#> [1] "Simpson"
hl7_list[[2]]$PID$PatientName
#> $familyName
#> [1] "Ned"
#>
#> $givenName
#> [1] "Flanders"Cycle through each file and use parse_hl7_message()
# Two HL7 files starting with 'fake' are distributed with this package,
hl7_files <-
system.file(package = 'HL7.R', 'extdata') %>%
list.files(pattern = 'fake-covid-\\d.hl7$', full.names = T)
basename(hl7_files)
#> [1] "fake-covid-1.hl7" "fake-covid-2.hl7"
# Parse into list
hl7_list <- lapply(hl7_files, parse_hl7_message)
length(hl7_list)
#> [1] 2
# Equivalent result to a parsed batch HL7
hl7_list[[1]]$PID$PatientName
#> $familyName
#> [1] "Homer"
#>
#> $givenName
#> [1] "Simpson"
hl7_list[[2]]$PID$PatientName
#> $familyName
#> [1] "Ned"
#>
#> $givenName
#> [1] "Flanders"
# el = list element in each loop
lapply(hl7_list, function(el){
with(el,
data.frame(
first_name = PID$PatientName$givenName,
last_name = PID$PatientName$familyName,
suburb = PID$PatientAddress$city,
lab = MSH$SendingFacility,
test = OBX.1$ObservationIdentifier$text,
result = OBX.1$ObservationValue[[2]]
)
)
}) %>%
do.call(rbind.data.frame, .)
#> first_name last_name suburb lab test result
#> 1 Simpson Homer Springfield Dr Hibbert Medical nCoV-2019 PCR Postive
#> 2 Flanders Ned Springfield Nick Riviera Appartment nCoV-2019 PCR NegativeThe second problem this package solves is converting any arbitrary piece
of data into a HL7 message. This is conducted by piecing together
segments such as the message header (MSH), Patient identification
(PID) and Observation/Results (OBX). This package provides segment
functions e.g. MSH(), PID(), with named parameters that will build a
text segment ready for piecing together using the function
build_hl7().
Notes
- There a default blank values for all the fields in a segment function,
and they will be included in the final output as shown below up until
the last observed value i.e. trailing blanks are trimmed see the
parameter
.trimin most functions - There are helper functions
*Components()for nested fields. As these are helpers, you can safely skip if you can correctly create the required value - Dates/Datetimes can be converted using
datetime_to_hl7_datetime()
example_hl7_build <-
build_hl7(
MSH(SendingFacility = 'A lab', ReceivingFacility = 'NSW Health', VersionID = '2.3.1'),
PID(PatientID = '1234',
PatientName = PatientNameComponents(familyName = 'Ross',
givenName = 'Bob'),
PatientAddress = PatientAddressComponents(streetAddress = '123 Fake Street',
city = 'Springfield',
zipPostcode = '90120')),
OBX(SetID = 1,
ValueType = 'CE',
ObservationIdentifier = ObservationIdentifierComponents(identifier = 'NSW_LOINC-376',
text = 'nCoV-2019 PCR',
nameOfCodingSystem = 'LN'),
ObservationValue = variedComponents('260415000^Not Detected^SNOMED-CT'))
)example_hl7_build
#> MSH|^~\&||A lab||NSW Health||||||2.3.1
#> PID||1234|||Ross^Bob||||||123 Fake Street^^Springfield^^90120
#> OBX|1|CE|NSW_LOINC-376^nCoV-2019 PCR^LN||260415000^Not Detected^SNOMED-CTConversion of Date and Datetimes
datetime_to_hl7_datetime(Sys.time())
#> [1] "20230117160223".trim will trim trailing blank fields. It is TRUE by default
MSH(SendingFacility = 'NSW HEALTH', VersionID = '2.3.1')
#> MSH|^~\&||NSW HEALTH||||||||2.3.1
MSH(SendingFacility = 'NSW HEALTH', VersionID = '2.3.1', .trim = FALSE)
#> MSH|^~\&||NSW HEALTH||||||||2.3.1||||||||
PatientAddressComponents(streetAddress = '123 Fake Street')
#> [1] "123 Fake Street"
PatientAddressComponents(streetAddress = '123 Fake Street', .trim = FALSE)
#> [1] "123 Fake Street^^^^^"Often we have the task of translating a line list into HL7 messages. A simple example is show below:
- loop through the rows using
lapply - convert the row into a list for easy reference e.g.
d$firstname
# A 2 row line list with fake data is distributed with this package
some_line_list <- read.csv(system.file(package = 'HL7.R', 'extdata/fake-covid-n2.csv'))
some_line_list
#> firstname lastname street suburb test_id text_text result_code result_text facility
#> 1 Homer Simpson 742 Evergreen Terrace Springfield ncov19 nCoV-2019 PCR P Postive Dr Hibbert Medical
#> 2 Ned Flanders 744 Evergreen Terrace Springfield ncov19 nCoV-2019 PCR N Negative Nick Riviera Appartmenthl7_build_list <-
lapply(1:nrow(some_line_list), function(row){
# d = data element (the row, as a list)
d <- as.list(some_line_list[row,])
build_hl7(
MSH(SendingFacility = d$facility, ReceivingFacility = 'NSW Health', VersionID = '2.3.1'),
PID(PatientID = '1',
PatientName = PatientNameComponents(familyName = d$firstname,
givenName = d$lastname),
PatientAddress = PatientAddressComponents(streetAddress = d$street,
city = d$suburb)),
OBX(SetID = 1,
ValueType = 'CE',
ObservationIdentifier = ObservationIdentifierComponents(identifier = d$test_id,
text = d$text_text,
nameOfCodingSystem = 'LN'),
ObservationValue = variedComponents(d$result_code, d$result_text))
)
})hl7_build_list
#> [[1]]
#> MSH|^~\&||Dr Hibbert Medical||NSW Health||||||2.3.1
#> PID||1|||Homer^Simpson||||||742 Evergreen Terrace^^Springfield
#> OBX|1|CE|ncov19^nCoV-2019 PCR^LN||P^Postive
#>
#> [[2]]
#> MSH|^~\&||Nick Riviera Appartment||NSW Health||||||2.3.1
#> PID||1|||Ned^Flanders||||||744 Evergreen Terrace^^Springfield
#> OBX|1|CE|ncov19^nCoV-2019 PCR^LN||N^Negative# for filenames 001, 002, etc if necessary
n_leading_zero <- sprintf('%%0%sd', nchar(length(hl7_build_list)))
# Output somewhere
# * note this was used to make fake-covid-*.hl7 used above
for(i in seq_along(hl7_build_list)){
i_leading_zero = sprintf(fmt = n_leading_zero, i)
filename = sprintf('Some-filename-%s.hl7', i_leading_zero)
path = file.path('some/path', filename)
writeLines(hl7_build_list[[i]], con = path)
}Clone repo, open HL7.R.Rproj and use devtools
library(devtools)
load_all()
#> ℹ Loading HL7.R
#> HL7.R - for help see vignette('Getting-started', package = 'HL7.R') or vignette('package = 'HL7.R') for other examplesSomeone built the package and has given you the file - be aware if they
built using source or binary. Generally, tar.gz = source, zip =
binary
install.packages('HL7.R.xxx.tar.gz', repos = NULL, type = 'source')
install.packages('HL7.R.xxx.zip', repos = NULL)A local package repo may exist. Again, be aware if they built using
source or binary. Look for ./bin and ./src in the DRAT folder.
library(drat)
drat::addRepo("workgroup", 'file:drive:/path/to/drat')
install.packages('HL7.R', repos = options()$repos[2]) # assuming binary
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