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getData: add fread support, refactor code, expand roxygen #27

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getData: add fread support, refactor code, expand roxygen #27

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@ck37 ck37 commented Sep 24, 2021

Hello,

Here is a PR to refactor the functions in getData.R and getData_nodocker.R. My primary motivation was to support data.table's fread() csv import function to speed up CSV imports for large files. While I was doing that I tried to refactor the code to remove duplication and add roxygen for the man pages. Happy to modify if any changes are preferred.

Here is some testing code that I tried on BIDMC data (7.2 million rows):

# Takes 27 seconds with read.csv
system.time({
LocalPatientObservations = FourCePhase2.1Data::getLocalPatientObservations()
})

# 5-6 seconds with fread
system.time({
LocalPatientObservations = FourCePhase2.1Data::getLocalPatientObservations(fread = TRUE)
})

# Change to fread by default.
options(`4ce.fread` = TRUE)
# Confirm that it worked:
getOption("4ce.fread")

# Now uses fread without specifying in function call.
system.time({
LocalPatientObservations = FourCePhase2.1Data::getLocalPatientObservations()
})

Cheers,
Chris

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