tests/testthat/test-single_dichotomous_mcmc.R

In ToxicR: Analyzing Toxicology Dose-Response Data

context("Single Dichotomous Models MCMC")


test_that("Probit", {
     set.seed(5981)
     mData <- build_single_dichotomous_dataset()
     c = single_dichotomous_fit(mData[,1],mData[,2],mData[,3],model_type = "probit", fit_type = "mcmc")
     validate_model(c,  "Model:  Probit" ,  c(-1.22897249357605, 0.946667348047251) ,  c(BMD = 13.7570231637969, BMDL = 11.0421600688424, BMDU = 17.634673852233) )
})

test_that("Log Probit", {
     set.seed(5981)
     mData <- build_single_dichotomous_dataset2()
     c = single_dichotomous_fit(mData[,1],mData[,2],mData[,3],model_type = "log-probit", fit_type = "mcmc")
     validate_model(c,  "Model:  Log-Probit" ,  c(-2.5767039674999, -0.363921570939808, 0.585986511476555) ,  c(BMD = 11.5294629371935, BMDL = 3.54819293851276, BMDU = 21.0396223458889) )
})

test_that("Weibull", {
     set.seed(5981)
     mData <- build_single_dichotomous_dataset()
     c = single_dichotomous_fit(mData[,1],mData[,2],mData[,3],model_type = "weibull", fit_type = "mcmc")
     validate_model(c,  "Model: Weibull" ,  c(-2.86014800998383, 0.661116573139896, 0.438604630748536) ,  c(BMD = 5.1170096470376, BMDL = 1.46662721211377, BMDU = 11.8009898041251) )
})

test_that("Plots", {
        set.seed(5981)
        mData <- build_single_dichotomous_dataset()
        c = single_dichotomous_fit(mData[,1],mData[,2],mData[,3],model_type = "weibull", fit_type = "mcmc")
        mcmc_plot <- plot(c)
        expect_identical(mcmc_plot$labels$x, "Dose")
        expect_identical(mcmc_plot$labels$y, "Proportion")
        #TODO should the title have the distribution name?
        expect_identical(mcmc_plot$labels$title, "Model: Weibull")
        c = single_dichotomous_fit(mData[,1],mData[,2],mData[,3],model_type = "hill", fit_type = "mcmc")
        mcmc_plot <- plot(c)
        expect_identical(mcmc_plot$labels$x, "Dose")
        expect_identical(mcmc_plot$labels$y, "Proportion")
        #TODO should the title have the distribution name?
        expect_identical(mcmc_plot$labels$title, "Model:  Hill")
})