load_data {vaccine}

Load and format data object

Description

This function takes in user-supplied data and returns a data object that can be read in by summary_stats, est_ce, est_med, and other estimation functions. Data is expected to come from a vaccine clinical trial, possibly involving two-phase sampling and possibly including a biomarker of interest.

Usage

load_data(
  time,
  event,
  vacc,
  marker,
  covariates,
  weights,
  ph2,
  strata = NA,
  data,
  covariates_ph2 = FALSE
)

Arguments

time

A character string; the name of the numeric variable representing observed event or censoring times.

event

A character string; the name of the binary variable corresponding to whether the observed time represents an event time (1) or a censoring time (0). Either integer (0/1) or Boolean (T/F) values are allowed.

vacc

A character string; the name of the binary variable denoting whether the individual is in the vaccine group (1) or the placebo group (0). Accepts either integer (0/1) or Boolean (T/F) values.

marker

A character string; the name of the numeric variable of biomarker values.

covariates

A character vector; the names of the covariate columns. Columns values should be either numeric, binary, or factors. Character columns will be converted into factors.

weights

A character string; the name of the numeric variable containing inverse-probability-of-sampling (IPS) weights.

ph2

A character string; the name of the binary variable representing whether the individual is in the phase-two cohort (1) or not (0). Accepts either integer (0/1) or Boolean (T/F) values.

strata

A character string; the name of the variable containing strata identifiers (for two-phase sampling strata).

data

A dataframe containing the vaccine trial data.

covariates_ph2

A boolean; if at least one of the covariates is measured only in the phase-two cohort, set this to TRUE.

Value

An object of class vaccine_dat.

Examples

data(hvtn505)
dat <- load_data(time="HIVwk28preunblfu", event="HIVwk28preunbl", vacc="trt",
                 marker="IgG_V2", covariates=c("age","BMI","bhvrisk"),
                 weights="wt", ph2="casecontrol", data=hvtn505)