import_data: Import REDCap data

In jpasquier/mscovid: Multi-state analysis of covid19 hospitalizations (canton de VD)

Description

Import a formatted Excel REDCap datafile containing the following variables:

• no_unique = anonymized identifier

• sex = patient's gender (M/F)

• age = patient's age (years)

• arrivee_hopital = date of hospitalization

• debut_soins_intensif = date of admission in ICU

• fin_soins_intensifs = intensive care discharge date

• sortie_hopital = discharge date from hospital

• deces = death indicator (0/1)

The four date variable must be in date format in Excel. A censoring date could be defined. If such a date is not given, it is guessed based on the data.

Usage

import_data(path, ..., censoring_date = NULL)

Arguments

path	path to data file
...	other parameter passed to readxl::read_xlsx
censoring_date	date used for censoring (optional, format: %Y-%m-%d)

Value

a dataframe containing the following variables

• id = anonymized identifier

• sex = patient's gender (factor M/F)

• age = patient's age (years)

• hos_in = date of hospitalization

• icu_in = date of admission in ICU

• icu_out = intensive care discharge date

• hos_out = discharge date from hospital

• death = death indicator (logical true/false)

The censoring date is returned as an attributes (censoring_date)

jpasquier/mscovid documentation built on March 31, 2021, 4:42 a.m.