calibrate_TTE {debiasedTrialEmulation} | R Documentation |
Negative Control Calibration for Target Trial Emulation
Description
Performs calibration with negative control outcomes to further reduce confounding bias in Target Trial Emulation results.
Usage
calibrate_TTE(tte_obj = NULL, custom_results = NULL, custom_nco_results = NULL)
Arguments
tte_obj |
Optional. An object of class "TTE" from the TTE_pipeline function. If provided, the function will use the negative control results from this object. Either this or both custom_results and custom_nco_results must be provided. |
custom_results |
Optional. A data frame containing the primary outcome results if no TTE object is available. Must contain columns 'names_outcome', 'logEst', and 'seLogEst'. |
custom_nco_results |
Optional. A data frame containing the negative control outcome results if no TTE object is available. Must contain columns 'names_outcome', 'logEst', and 'seLogEst'. |
Value
An object of class "dTTE" containing both the TTE results and calibration results
Examples
library("dplyr")
data(demo_data)
# First run TTE pipeline
xvars <- c("eth_cat", "age_cat", "sex", "cohort_entry_month",
"obese", "pmca_index", "n_ed", "n_inpatient",
"n_tests", "imm_date_diff_grp", "medical_1", "medical_2",
"medical_3", "medical_4", "medical_5")
yvars1 <- colnames(demo_data %>% select(starts_with("visits_")))
ncovars1 <- colnames(demo_data %>% select(starts_with("nco_visits_")))
tte_result <- TTE_pipeline(demo_data, xvars=xvars, yvars=yvars1, ncovars=ncovars1,
ps_type="Matching", outcome_measure="RR")
# Then calibrate results
dtte_result <- calibrate_TTE(tte_obj = tte_result)
# Alternatively, provide custom results
df_results <- data.frame(
names_outcome = c("outcome1", "outcome2"),
logEst = c(0.1, -0.2),
seLogEst = c(0.05, 0.08)
)
df_nco_results <- data.frame(
names_outcome = c("nco1", "nco2", "nco3"),
logEst = c(0.02, -0.03, 0.01),
seLogEst = c(0.03, 0.04, 0.02)
)
dtte_result <- calibrate_TTE(custom_results = df_results, custom_nco_results = df_nco_results)
[Package debiasedTrialEmulation version 0.1.0 Index]