preprocess.data {bets.covid19}

Prepare data frame for analysis

Description

Prepare data frame for analysis

Usage

preprocess.data(
  data,
  infected_in = c("Wuhan", "Outside"),
  symptom_impute = FALSE
)

Arguments

data

A data frame

infected_in

Either "Wuhan" or "Outside"

symptom_impute

Whether to use initial medical visit and confirmation to impute missing symptom onset.

Details

A summary of the procedures:

1. Convert all dates to number of days since 1-Dec-2019.

2. Separates data into those returned from Wuhan and those infected outside of wuhan.

3. Restrict to cases with a known symptom onset date.

4. Parse column 'Infected' into two columns: Infected_first and Infected_last.

5. For all cases, set Infected_first to 1 if it is missing.

6. For outside cases, set Infected_last to be no later than symptom onset.

7. For Wuhan-exported cases, set Infected_last to no later than symptom onset and end of Wuhan stay.

Value

A data frame

Author(s)

Nianqiao Ju <[e-mail]>, Qingyuan Zhao <[e-mail]>

Examples

data(covid19_data)
head(data <- preprocess.data(covid19_data))

 ## This is how the wuhan_exported data frame is created
data <- subset(data, Symptom < Inf)
data <- subset(data, Arrived <= 54)
data$Location <- do.call(rbind, strsplit(as.character(data$Case), "-"))[, 1]
wuhan_exported <- data.frame(Location = data$Location,
                             B = data$Begin_Wuhan,
                             E = data$End_Wuhan,
                             S = data$Symptom)
## devtools::use_data(wuhan_exported)