if (suppressWarnings( requiet("testthat") && requiet("ggeffects") && requiet("glmmTMB") && requiet("pscl") )) { data(Salamanders) m1 <- zeroinfl(count ~ mined | mined, dist = "poisson", data = Salamanders) m2 <- hurdle(count ~ mined | mined, dist = "poisson", zero.dist = "poisson", data = Salamanders) m3 <- hurdle(count ~ mined | mined, dist = "poisson", zero.dist = "binomial", data = Salamanders) m4 <- hurdle(count ~ mined | mined, dist = "poisson", zero.dist = "binomial", link = "log", data = Salamanders) m5 <- suppressWarnings(zeroinfl(count ~ mined | mined, dist = "negbin", link = "log", data = Salamanders)) test_that("ggpredict, pscl", { expect_s3_class(ggpredict(m1, "mined", type = "fe"), "data.frame") expect_s3_class(ggpredict(m1, "mined", type = "fe.zi"), "data.frame") expect_s3_class(ggpredict(m2, "mined", type = "fe"), "data.frame") expect_s3_class(ggpredict(m2, "mined", type = "fe.zi"), "data.frame") expect_s3_class(ggpredict(m3, "mined", type = "fe"), "data.frame") expect_s3_class(ggpredict(m3, "mined", type = "fe.zi"), "data.frame") expect_s3_class(ggpredict(m4, "mined", type = "fe"), "data.frame") expect_s3_class(ggpredict(m4, "mined", type = "fe.zi"), "data.frame") expect_s3_class(ggpredict(m5, "mined", type = "fe"), "data.frame") expect_s3_class(ggpredict(m5, "mined", type = "fe.zi"), "data.frame") }) test_that("ggpredict, pscl", { skip_on_cran() set.seed(123) pr <- ggpredict(m1, "mined", type = "fe.zi") expect_equal(pr$conf.low, c(0.1731, 2.0172), tolerance = 1e-3) model <- zeroinfl(count ~ mined * spp | mined * spp, dist = "poisson", data = Salamanders) set.seed(123) pr <- ggpredict(model, c("mined", "spp"), type = "fe.zi") expect_equal( pr$conf.low, c(0, 0, 0.03704, 1e-05, 1e-05, 0.14815, 0.13418, 1.61886, 0.04808, 1.81329, 0.48571, 3.07055, 3.1093, 1.33136), tolerance = 1e-2 ) }) test_that("ggemmeans, pscl", { expect_s3_class(ggemmeans(m1, "mined", type = "fe"), "data.frame") expect_s3_class(ggemmeans(m1, "mined", type = "fe.zi"), "data.frame") expect_s3_class(ggemmeans(m2, "mined", type = "fe"), "data.frame") expect_s3_class(ggemmeans(m2, "mined", type = "fe.zi"), "data.frame") expect_s3_class(ggemmeans(m3, "mined", type = "fe"), "data.frame") expect_s3_class(ggemmeans(m3, "mined", type = "fe.zi"), "data.frame") expect_s3_class(ggemmeans(m4, "mined", type = "fe"), "data.frame") expect_s3_class(ggemmeans(m4, "mined", type = "fe.zi"), "data.frame") expect_s3_class(ggemmeans(m5, "mined", type = "fe"), "data.frame") expect_s3_class(ggemmeans(m5, "mined", type = "fe.zi"), "data.frame") }) test_that("compare, pscl", { p1 <- ggemmeans(m1, "mined", type = "fe") p2 <- ggpredict(m1, "mined", type = "fe") expect_equal(p1$predicted[1], p2$predicted[1], tolerance = 1e-3) p1 <- ggemmeans(m1, "mined", type = "fe.zi") p2 <- ggpredict(m1, "mined", type = "fe.zi") expect_equal(p1$predicted[1], p2$predicted[1], tolerance = 1e-3) p1 <- ggemmeans(m2, "mined", type = "fe") p2 <- ggpredict(m2, "mined", type = "fe") expect_equal(p1$predicted[1], p2$predicted[1], tolerance = 1e-3) p1 <- ggemmeans(m2, "mined", type = "fe.zi") p2 <- ggpredict(m2, "mined", type = "fe.zi") expect_equal(p1$predicted[1], p2$predicted[1], tolerance = 1e-3) p1 <- ggemmeans(m5, "mined", type = "fe") p2 <- ggpredict(m5, "mined", type = "fe") expect_equal(p1$predicted[1], p2$predicted[1], tolerance = 1e-3) p1 <- ggemmeans(m5, "mined", type = "fe.zi") p2 <- ggpredict(m5, "mined", type = "fe.zi") expect_equal(p1$predicted[1], p2$predicted[1], tolerance = 1e-3) }) #Generate some data set.seed(123) N <- 100 #Samples x <- runif(N, 0, 5) #Predictor 1 z <- runif(N, 0, 5) #Predictor 2 off <- rgamma(N, 3, 2) #Offset variable yhat <- -1 + x * 0.2 + z * -0.2 + z * x * 0.2 + log(off) #Prediction on log scale dat <- data.frame(y = NA, x,z, logOff = log(off)) #Storage dataframe dat$y <- rpois(N, exp(yhat)) #Poisson process dat$y <- ifelse(rbinom(N, 1, 0.3), 0, dat$y) #Zero-inflation process #Fit zeroinfl and glm model #Interaction b/w x and z model <- zeroinfl(y ~ offset(logOff) + x * z | 1, data = dat, dist = 'poisson') test_that("pscl, offset, interaction and CI", { pr <- ggpredict(model, c("x", "z")) expect_equal( pr$conf.low, c(0.10175, 0.10842, 0.07738, 0.15311, 0.17543, 0.14137, 0.2299, 0.28352, 0.25811, 0.34404, 0.45742, 0.47084, 0.51189, 0.73575, 0.85762, 0.75364, 1.17695, 1.55786, 1.08708, 1.86238, 2.81383, 1.51007, 2.8848, 5.01418, 1.9918, 4.32397, 8.65455, 2.51388, 6.28353, 14.25571, 3.09229, 8.96366, 22.76232), tolerance = 1e-3 ) }) }