R: Convert dataframe to include survival (Surv) objects

makeSurvDF

R Documentation

Convert dataframe to include survival (Surv) objects

Description

Within a dataframe, paired numeric fields that use a "_lo" and "_hi" suffix naming convention (e.g., "conc_lo" "conc_hi") are combined into a single Surv object (e.g., "conc") using the "interval2" option provided by through the survival::Surv(conc_lo, conc_hi, type = "interval2") syntax.

Usage

makeSurvDF(df, suf_lo = "_lo", suf_hi = "_hi")

Arguments

`df`	name of data frame
`suf_lo`	Column name suffix for "lo" values. Default = "_lo"
`suf_hi`	Column name suffix for "hi" values. Default = "_hi"

Details

Converting fields to Surv objects works with field pairs that have a "_lo" and "_hi" suffix naming convention. The numeric value for "_hi" must be greater than or equal to the "_lo" value. Source data that violate this requirement are set to NA with a summary report outputted to the console.

The user can specify their own values for the lo/hi suffixes or use the defaults.

Value

dataframe with Surv fields

Examples

df <- dataCensored[1:20,]
colnames(df)
df1 <- unSurvDF(df)
colnames(df1)
# Default values
df2 <- makeSurvDF(df1)
colnames(df2)
# User values
df3 <- unSurvDF(df, "_LOW", "_HIGH")
colnames(df3)
df4 <- makeSurvDF(df3, "_LOW", "_HIGH")
colnames(df4)