anchored_binary.R
In maicplus: Matching Adjusted Indirect Comparison

## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(warning = FALSE, message = FALSE)

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# install.packages("maicplus")
library(maicplus)

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library(dplyr)

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data(centered_ipd_twt)
data(adrs_twt)

centered_colnames <- c("AGE", "AGE_SQUARED", "SEX_MALE", "ECOG0", "SMOKE", "N_PR_THER_MEDIAN")
centered_colnames <- paste0(centered_colnames, "_CENTERED")

weighted_data <- estimate_weights(
  data = centered_ipd_twt,
  centered_colnames = centered_colnames
)

# get dummy binary IPD
pseudo_adrs <- get_pseudo_ipd_binary(
  binary_agd = data.frame(
    ARM = c("B", "C", "B", "C"),
    RESPONSE = c("YES", "YES", "NO", "NO"),
    COUNT = c(280, 120, 200, 200)
  ),
  format = "stacked"
)

result <- maic_anchored(
  weights_object = weighted_data,
  ipd = adrs_twt,
  pseudo_ipd = pseudo_adrs,
  trt_ipd = "A",
  trt_agd = "B",
  trt_common = "C",
  normalize_weight = FALSE,
  endpoint_type = "binary",
  endpoint_name = "Binary Endpoint",
  eff_measure = "OR",
  # binary specific args
  binary_robust_cov_type = "HC3"
)

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result$descriptive

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result$inferential$summary

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result$inferential$fit$model_before
result$inferential$fit$res_AC_unadj
result$inferential$fit$res_AB_unadj

## -----------------------------------------------------------------------------
result$inferential$fit$model_after
result$inferential$fit$res_AC
result$inferential$fit$res_AB

## ----echo = FALSE, eval = FALSE-----------------------------------------------
# # heuristic check
# # merge in adrs with ipd_matched
# 
# ipd <- adrs_twt
# ipd$weights <- weighted_data$data$weights[match(ipd$USUBJID, weighted_data$data$USUBJID)]
# 
# pseudo_ipd <- pseudo_adrs
# pseudo_ipd$weights <- 1
# 
# # Change the reference treatment to C
# ipd$ARM <- stats::relevel(as.factor(ipd$ARM), ref = "C")
# pseudo_ipd$ARM <- stats::relevel(as.factor(pseudo_ipd$ARM), ref = "C")
# 
# binobj_dat <- glm(RESPONSE ~ ARM, ipd, family = binomial(link = "logit"))
# binobj_dat_adj <- suppressWarnings(glm(RESPONSE ~ ARM, ipd, weights = weights, family = binomial(link = "logit")))
# binobj_agd <- glm(RESPONSE ~ ARM, pseudo_ipd, family = binomial(link = "logit"))
# 
# bin_robust_cov <- sandwich::vcovHC(binobj_dat_adj, type = "HC3")
# bin_robust_coef <- lmtest::coeftest(binobj_dat_adj, vcov. = bin_robust_cov)
# bin_robust_ci <- lmtest::coefci(binobj_dat_adj, vcov. = bin_robust_cov)
# 
# exp(summary(binobj_dat)$coef[2, "Estimate"])
# exp(summary(binobj_dat_adj)$coef[2, "Estimate"])
# 
# bin_robust_ci
# exp(bin_robust_ci)
# 
# res_AC <- res_BC <- list()
# res_AC$est <- bin_robust_coef[2, "Estimate"]
# res_AC$se <- bin_robust_coef[2, "Std. Error"]
# 
# res_BC$est <- summary(binobj_agd)$coefficients[2, "Estimate"]
# res_BC$se <- summary(binobj_agd)$coefficients[2, "Std. Error"]
# 
# res_AB <- bucher(res_AC, res_BC, conf_lv = 0.95)
# print(res_AB, exponentiate = TRUE)

## -----------------------------------------------------------------------------
weighted_data2 <- estimate_weights(
  data = centered_ipd_twt,
  centered_colnames = centered_colnames,
  n_boot_iteration = 100,
  set_seed_boot = 1234
)

result_boot <- maic_anchored(
  weights_object = weighted_data2,
  ipd = adrs_twt,
  pseudo_ipd = pseudo_adrs,
  trt_ipd = "A",
  trt_agd = "B",
  trt_common = "C",
  normalize_weight = FALSE,
  endpoint_type = "binary",
  endpoint_name = "Binary Endpoint",
  eff_measure = "OR",
  boot_ci_type = "perc",
  # binary specific args
  binary_robust_cov_type = "HC3"
)

result_boot$inferential$fit$boot_res_AB