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Compute conditional cumulative incidences from fitted Cox models

Source: R/compute_psi_dx.R
predict_from_model_0.Rd

These functions compute the conditional day- and covariate-specific cumulative incidence for each row of newdata.

  • predict_from_model_0() computes \(\psi_0(t_0; d, x) = 1 - S_0(d+t_0 \mid x)/S_0(d+\tau \mid x)\) by calling predict(fit_0, newdata, type = "survival") at eval_times d + t0 and d + tau.

predict_from_model_1() computes \(\psi_1(t_0; d, x) = 1 - S_1(t_0 \mid d, x)/S_1(\tau \mid d, x)\) by calling predict(fit_1, newdata, type = "survival")at eval_timest0andtau`.

Usage

predict_from_model_0(fit_0, exposure_time, t0, tau, newdata)

predict_from_model_1(fit_1, exposure_time, t0, tau, newdata)

Value

The newdata data frame with three additional columns:

  • predict_from_model_0(): surv_0_d_plus_tau, surv_0_d_plus_t0, and psi_0_dx

  • predict_from_model_1(): surv_1_tau, surv_1_t0, and psi_1_dx

Examples

# Fit hazard model under no vaccine
fit_0 <- fit_model_0(
  data = simdata,
  outcome_time = "Y",
  outcome_status = "event",
  exposure = "V",
  exposure_time = "D_obs",
  covariates = covariates
 )
#> Error: object 'covariates' not found

# Fit hazard model under vaccine
fit_1 <- fit_model_1(
  data = simdata,
  outcome_time = "Y",
  outcome_status = "event",
  exposure = "V",
  exposure_time = "D_obs",
  tau = tau
 )
#> Error in fit_model_1(data = simdata, outcome_time = "Y", outcome_status = "event",     exposure = "V", exposure_time = "D_obs", tau = tau): argument "covariates" is missing, with no default


# Define dataset for prediction,
# e.g. vaccinated indiviudals at risk tau days after vaccination
newdata <- simdata[simdata$V == 1 & (simdata$Y - simdata$D_obs) > 14,]

# Predict from hazard model under no vaccine
predict_from_model_0(
    fit_0,
    exposure_time = "D_obs",
    t0 = 90,
    tau = 14,
    newdata = newdata
)
#> Error: object 'fit_0' not found

# Predict from hazard model under vaccine
predict_from_model_1(
  fit_1,
  exposure_time = "D_obs",
  t0 = 90,
  tau = 14,
  newdata = newdata
)
#> Error in predict_from_model_1(fit_1, exposure_time = "D_obs", t0 = 90,     tau = 14, newdata = newdata): could not find function "predict_from_model_1"