process.all.data: Fully process data

In ISARICDataPlatform/CovidClinicalDataProcessor: Data Import and Processing for ISARIC COVID-19 Hospital Data

Fully process data

Description

Fully process data

Usage

process.all.data(
  demog.file.name,
  microb.file.name = NA,
  symptoms.file.name = NA,
  pregnancy.file.name = NA,
  ICU.file.name = NA,
  treatment.file.name = NA,
  vit_sign.file.name = NA,
  outcome.file.name = NA,
  laboratory.file.name = NA,
  minimum.comorb = 100,
  minimum.sympt = 100,
  minimum.treatments = 1000,
  dtplyr.step = FALSE
)

Arguments

demog.file.name	Path of the demographics data file (CDISC format)
microb.file.name	Path of the demographics data file (CDISC format)
symptoms.file.name	Path of the symptoms data file (CDISC format, optional)
pregnancy.file.name	Path of the RP data file (CDISC format, optional)
ICU.file.name	Path of the healthcare encounters data file (CDISC format, optional)
treatment.file.name	Path of the intervention data file (CDISC format, optional)
vit_sign.file.name	Path of the VS data file (CDISC format, optional)
outcome.file.name	Path of the dispositions data file (CDISC format, optional)
laboratory.file.name	Path of the LB data file (CDISC format, optional)
minimum.treatments	The minimum number of instances of a treatment required for inclusion as a column
dtplyr.step	Return the output as dtplyr_step to avoid unnecessary future calls to as_tibble or as.data.table

Value

Formatted outcome data as a tibble or dtplyr_step

ISARICDataPlatform/CovidClinicalDataProcessor documentation built on March 22, 2022, 7:51 p.m.