tests/testthat/test-sensitivity_analysis_BinCont_copula.R

In Surrogate: Evaluation of Surrogate Endpoints in Clinical Trials

test_that("sensitivity_analysis_BinCont_copula() works in a simplified setting",
          {
            copula_family = "clayton"
            marginal_surrogate = "normal"
            data("Schizo_BinCont")
            na = is.na(Schizo_BinCont$CGI_Bin) | is.na(Schizo_BinCont$PANSS)
            X = Schizo_BinCont$PANSS[!na]
            Y = Schizo_BinCont$CGI_Bin[!na]
            Treat = Schizo_BinCont$Treat[!na]
            Treat = ifelse(Treat == 1, 1, 0)
            data = data.frame(X,
                              Y,
                              Treat)
            fitted_model = fit_copula_model_BinCont(data, copula_family, marginal_surrogate, twostep = FALSE)

            n_sim = 2
            set.seed(1)
            sens_results = sensitivity_analysis_BinCont_copula(
              fitted_model,
              n_sim,
              cond_ind = TRUE,
              lower = c(-1,-1,-1,-1),
              upper = c(1, 1, 1, 1),
              n_prec = 1e3
            )
            expect_equal(
              sens_results[,1],
              c(0.43244243, 0.30876395),
              tolerance = 1e-3
            )
          })

test_that("sensitivity_analysis_BinCont_copula() works in a simplified setting with limits in the sensitivity analysis",
          {
            copula_family = "clayton"
            marginal_surrogate = "normal"
            data("Schizo_BinCont")
            na = is.na(Schizo_BinCont$CGI_Bin) | is.na(Schizo_BinCont$PANSS)
            X = Schizo_BinCont$PANSS[!na]
            Y = Schizo_BinCont$CGI_Bin[!na]
            Treat = Schizo_BinCont$Treat[!na]
            Treat = ifelse(Treat == 1, 1, 0)
            data = data.frame(X,
                              Y,
                              Treat)
            fitted_model = fit_copula_model_BinCont(data, copula_family, marginal_surrogate, twostep = FALSE)

            n_sim = 2
            set.seed(1)
            sens_results = sensitivity_analysis_BinCont_copula(
              fitted_model,
              n_sim,
              cond_ind = TRUE,
              lower = c(0, 0, 0, 0),
              upper = c(0.95, 0.95, 0.95, 0.95),
              n_prec = 1e3
            )
            expect_equal(
              sens_results[,1],
              c(0.41079208, 0.3107483),
              tolerance = 1e-3
            )
          })