# suppressPackageStartupMessages({ # library(bgms) # }) # data <- na.omit(Wenchuan) # # ##-------------------------------- # ## Fitting with bgms # ##-------------------------------- # set.seed(123) # res_bgms <- easybgm(data[1:100, 1:5], type = "ordinal", # package = "bgms", save = T, centrality = T, iter = 1000) # test_that("easybgm works for bgms", { # testthat::expect_snapshot(summary(res_bgms)) # }) # # ##-------------------------------- # ## Plotting with bgms # ##-------------------------------- # # # 1. Network plot # network_bgms <- plot_network(res_bgms) # vdiffr::expect_doppelganger("network plot bgms", network_bgms) # # # 2. Evidence plot # evidence_bgms <- plot_network(res_bgms) # vdiffr::expect_doppelganger("evidence plot bgms", evidence_bgms) # # # 3. Posterior structure plot # poststruc_bgms <- plot_structure_probabilities(res_bgms) # vdiffr::expect_doppelganger("posterior structure plot bgms", poststruc_bgms) # # # 4. Posterior complexity plot # postcompl_bgms <- plot_complexity_probabilities(res_bgms) # vdiffr::expect_doppelganger("posterior complexity plot bgms", postcompl_bgms) # # # 5. structure plot # struc_bgms <- plot_structure(res_bgms) # vdiffr::expect_doppelganger("structure plot bgms", struc_bgms) # # # 6. HDI plot # HDI_bgms <-plot_parameterHDI(res_bgms) # vdiffr::expect_doppelganger("HDI plot bgms", HDI_bgms) # # # 7. centrality plot # centrality_bgms <-plot_centrality(res_bgms) # vdiffr::expect_doppelganger("centrality plot bgms", centrality_bgms) # # ##-------------------------------- # ## Fitting with BDgraph # ##-------------------------------- # set.seed(123) # res_bdgraph <- suppressWarnings(easybgm(data[1:100, 1:5], type = "continuous", # package = "BDgraph", save = T, centrality = T, iter = 1000)) # test_that("easybgm works for bdgraph", { # testthat::expect_snapshot(summary(res_bdgraph)) # }) # # ##-------------------------------- # ## Plotting with BDgraph # ##-------------------------------- # # #1. Network plot # network_bdgraph <- plot_network(res_bdgraph) # vdiffr::expect_doppelganger("network plot Bdgraph", network_bdgraph) # # # 2. Evidence plot # evidence_bdgraph <- plot_network(res_bdgraph) # vdiffr::expect_doppelganger("evidence plot Bdgraph", evidence_bdgraph) # # # 3. Posterior structure plot # poststruc_bdgraph <- plot_structure_probabilities(res_bdgraph) # vdiffr::expect_doppelganger("posterior structure plot Bdgraph", poststruc_bdgraph) # # # 4. Posterior complexity plot # postcompl_bdgraph <- plot_complexity_probabilities(res_bdgraph) # vdiffr::expect_doppelganger("posterior complexity plot Bdgraph", postcompl_bdgraph) # # # 5. structure plot # struc_bdgraph <- plot_structure(res_bdgraph) # vdiffr::expect_doppelganger("structure plot Bdgraph", struc_bdgraph) # # # 6. HDI plot # HDI_bdgraph <- suppressWarnings(plot_parameterHDI(res_bdgraph)) # vdiffr::expect_doppelganger("HDI plot Bdgraph", HDI_bdgraph) # # # 7. centrality plot # centrality_bdgraph <-plot_centrality(res_bdgraph) # vdiffr::expect_doppelganger("centrality plot Bdgraph", centrality_bdgraph) # # ##-------------------------------- # ## Fitting with BGGM # ##-------------------------------- # # DOES NOT WORK, output keeps changing slightly despite set.seed # # set.seed(123) # # res_bggm <- easybgm(data[1:300, 1:5], type = "continuous", # # package = "BGGM") # # test_that("easybgm works for bggm", { # # vdiffr::expect_snapshot(summary(res_bggm)) # # }) # # # ##-------------------------------- # ## Fitting with bgms # ##-------------------------------- # # # set.seed(123) # data <- na.omit(Wenchuan) # fit_bgms <- bgm(data[1:100, 1:5], iter = 1000) # network_bgmfit <- plot_network(fit_bgms) # vdiffr::expect_doppelganger("network plot using bgm to fit", network_bgmfit) #