Files in npetraco/CRFutil

Handy Utility Functions for Use with CRF and gRbase packages

.Rbuildignore

.gitattributes_old

.gitignore

CRFutil.Rproj

DESCRIPTION

Makefile

NAMESPACE

R/UGM_MRF_NLL.R R/UGM_MRF_computeSuffStat.R R/UGM_MRF_makePotentials.R R/conversion_util.R R/crf_util.R R/distribution_util.R R/energy_util.R R/features_util.R R/fit_util.R R/graph_util.R R/likelihood_util.R R/logistic_util.R R/marginal.edge.independence_util.R R/marginal.edge.plot_util.R R/marginal.edge_util.R R/plot_util.R R/potentials_util.R R/prod.potentials_util.R R/simulation_util.R R/sum.product_util.R R/test_util.R R/util.R README.md

TODO

inst/mcmc_ext/logistic_model.bug

inst/mcmc_ext/logistic_model.stan

inst/mcmc_ext/poisson_model.bug

inst/mcmc_ext/poisson_model.stan

man/Eone.Rd man/Etwo.Rd man/KLD.Rd man/UGM_MRF_NLL.Rd man/UGM_MRF_computeSuffStat.Rd man/UGM_MRF_makePotentials.Rd man/adj2formula.Rd man/align.distributions.Rd man/compare_edges.Rd man/compare_edges_SAFEISH.Rd man/complement.at.idx.Rd man/compute.full.distribution.Rd man/compute.model.matrix.Rd man/conditional.config.energy.Rd man/conditional.config.energy.old.Rd man/conditional.config.energy2.Rd man/conditional.energy.gradient.Rd man/config.energy.Rd man/config.potential.Rd man/copy.crf.Rd man/count_row_matches.Rd man/delta.alpha.Rd man/distribution.calc.Rd man/distribution.from.energies.Rd man/distribution.from.potentials.Rd man/dump.crf.Rd man/edge.marginal.Rd man/edges2adj.Rd man/exp_list.Rd man/feature.means.Rd man/fit_bayes_logistic.Rd man/fit_bayes_loglinear.Rd man/fit_bayes_loglinear2.Rd man/fit_bayes_zip.Rd man/fit_empirical.Rd man/fit_logistic.Rd man/fit_loglinear.Rd man/fit_mle.Rd man/fit_mle_params.Rd man/fit_true.Rd man/flatten.marginal.edge.beliefs.Rd man/generate_brunner_lizards.Rd man/generate_gRbase_lizards.Rd man/generate_koller_misconception_model.Rd man/generate_random_model.Rd man/generate_schmidt_small_model.Rd man/generate_star_model.Rd man/generate_tesseract_model.Rd man/generate_triangle_model.Rd man/get.incoming.messages.Rd man/get.node.idxs.Rd man/get.par.idx.Rd man/get.path.Rd man/get.root.paths.Rd man/get_configuration_frequencies.Rd man/glmnet2graph_info.Rd man/grad.negloglik.Rd man/grad.neglogpseudolik.FIXME.Rd man/grad.neglogpseudolik.config.Rd man/init.loopy.message.storage.Rd man/init.message.storage.Rd man/log_list.Rd man/loglin2crf.Rd man/logsumexp.Rd man/logsumexp2.Rd man/make.empty.field.Rd man/make.f2v.msg.Rd man/make.gRbase.beliefs.Rd man/make.gRbase.potentials.Rd man/make.lattice.Rd man/make.par.from.all.potentials.Rd man/make.par.from.potentials.Rd man/make.pots.Rd man/make.v2f.msg.Rd man/marginal.edge.bayes.beleifs.indep.indic.Rd man/marginal.edge.bayes.bels.plot.Rd man/marginal.edge.bayes.loglin.Rd man/marginal.edge.bayes.plot.Rd man/marginal.edge.bayes.potentials.indep.indic.Rd man/marginal.edge.bels.Rd man/marginal.edge.bels.bayes.Rd man/marginal.edge.emp.pr.Rd man/marginal.edge.loglin.Rd man/marginal.edge.mrf.Rd man/message.type.Rd man/mrf.exact.nll.Rd man/mrf.glmnet.logistic.fit.Rd man/mrf.junction.nll.Rd man/mrf.lbp.nll.Rd man/mrf.sample.plot.Rd man/mrf.standard.fit.Rd man/mrf2pwfg.Rd man/negloglik.Rd man/neglogpseudolik.Rd man/neglogpseudolik.config.Rd man/neglogpseudolik2.Rd man/nex.Rd man/node.marginal.Rd man/nodes2params.list.Rd man/nodes2params.list2.Rd man/par2logpots.Rd man/params2nodes.list.Rd man/pass.message.Rd man/phi.component.Rd man/phi.features.Rd man/phi.features.explicit.Rd man/plot_crf.Rd man/process.logistic.fit.JAGS.Rd man/process.logistic.fit.stan.Rd man/pseudolikelihoods.from.energies.Rd man/pseudolikelihoods.from.energies2.Rd man/reorder_configs.Rd man/row.match.Rd man/shift.pots.Rd man/sim.field.random.Rd man/sim.field.random.simplest.Rd man/sim.ising.field.random.Rd man/sim.random.field.Rd man/symbolic.conditional.energy.Rd man/update_CRFutil.Rd

tests/.DS_Store

tests/Koller-Friedman_Misconception.R tests/LLvsPLL_wierd_triange_test.R tests/LLvsPLL_wierd_triange_test2.R tests/LLvsPLL_wierd_triange_test3.R tests/LLvsPLL_wierd_triange_test4.R tests/LLvsPLL_wierd_triange_test4a.R tests/Schmidt_Small.R tests/Slayer_conditional-energies_fearure-vs-featurefunc-formulation.R tests/Slayer_example.R

tests/Z_explore-symbolic_energy.nb

tests/Z_explore-symbolic_energy2.nb

tests/Z_explore-symbolic_energy2a.nb

tests/betancourt_diagnostics.R tests/bigger_model_tests/config_probs_test1.R tests/bigger_model_tests/config_probs_test2.R tests/bigger_model_tests/config_probs_test3.R tests/bigger_model_tests/config_probs_test4.R tests/bigger_model_tests/config_probs_test5.R tests/bigger_model_tests/config_probs_test6.R tests/bigger_model_tests/config_probs_test6a.R tests/bigger_model_tests/config_probs_test7.R tests/bigger_model_tests/config_probs_test8.R tests/bigger_model_tests/distribution.calc_test.R tests/cond.phi.mat.test.R tests/conversions_test1.R tests/copy_test.R tests/dust_proto1.R tests/full_gradient_test1.R tests/full_gradient_test2.R tests/full_gradient_test3.R tests/full_gradient_test3a_com.R tests/full_gradient_test3a_com_OUTPUT.R tests/full_gradient_test3b_fit.R tests/full_gradient_test3b_fit_OUTPUT.R tests/full_gradient_test3c_fit.R tests/full_gradient_test4.R tests/get.param.idx.tests.R tests/get.param.idx.tests2.R tests/ising_proto1.R tests/known_gradient_test.R tests/lattace_test1.R tests/lattace_test2.R tests/lik-pseudolik_compare-to-mathematica1.R tests/load.dust.data.R tests/marginal_edge_bels_test1.R tests/marginal_edge_explore1.R tests/marginal_edge_explore2.R tests/marginal_edge_explore3.R tests/marginal_edge_explore4.R tests/marginal_edge_explore5.R tests/marginal_edge_explore6.R tests/marginal_edge_explore6a.R tests/marginal_edge_explore6b.R tests/marginal_edge_explore6c.R tests/marginal_edge_flatten-beliefs_test.R tests/marginal_edge_plot_test1.R tests/marginal_edge_plot_test2.R tests/marginal_edge_plot_test2a.R tests/marginal_edge_plot_test2a_bayescheck.R tests/marginal_edge_plot_test2a_bayescheck2.R tests/marginal_edge_plot_test2a_bayescheck3.R tests/marginal_edge_plot_test2a_bayescheck4.R tests/marginal_edge_plot_test2a_mlecheck.R tests/marginal_edge_plot_test2a_mlecheck2.R tests/mean_thetahat.phi_longway.R tests/mean_thetahat.phi_marginals-way_NOT-GENERAL-ENOUGH.R tests/mean_thetahat.phi_marginals-way_test1.R tests/message-passing_tests/factor_graph_test1.R tests/message-passing_tests/factor_graph_test2.R tests/message-passing_tests/factor_graph_test3.R tests/message-passing_tests/message_schedules_test1.R tests/message-passing_tests/message_schedules_test2.R tests/message-passing_tests/message_schedules_test3.R tests/message-passing_tests/message_schedules_test3a.R tests/message-passing_tests/message_schedules_test3b.R tests/message-passing_tests/message_schedules_test3c.R tests/message-passing_tests/message_schedules_test3d.R tests/message-passing_tests/message_schedules_test4.R tests/message-passing_tests/mrf_message_pass_simple.R tests/message-passing_tests/new_gRbase_function_tests-2021.R tests/message-passing_tests/passing_loopy_test1.R tests/message-passing_tests/passing_loopy_test1a.R tests/message-passing_tests/passing_loopy_test2.R tests/message-passing_tests/passing_test1.R tests/message-passing_tests/passing_test1a.R tests/message-passing_tests/passing_test1b.R tests/message-passing_tests/passing_test2.R tests/message-passing_tests/passing_test3.R tests/message-passing_tests/passing_test3a.R tests/message-passing_tests/prototypes_tests1.R tests/message-passing_tests/rootpaths_test1.R tests/message-passing_tests/rootpaths_test2.R tests/message-passing_tests/schedules_and_rules_test1.R

tests/nodes2params.nb

tests/nxm-grid_gen_data_and_MLE_fit_STRESS-tests.R tests/pll_troubleshooing1.R tests/pll_troubleshooing2.R tests/pll_troubleshooing3_HUHQQQQ.R tests/pll_troubleshooing3_HUHQQQQ_Two_nodes_only.R tests/pll_troubleshooing3a.R tests/pll_troubleshooing3b.R tests/pseudo-lik_surf_redo-A-B_2-node-2-param_test1.R tests/pseudo-lik_surf_redo-A-B_2-node-2-param_test2.R

tests/pseudo-lik_surf_test.nb

tests/pseudo-lik_surf_test1.R tests/pseudo-lik_surf_test2.R tests/pseudo-lik_surf_test2a.R tests/pseudo-lik_surf_test2b.R tests/pseudo-lik_surf_test2c.R tests/pseudo-lik_surf_test2d.R tests/pseudo-lik_surf_test3.R tests/pseudo-lik_surf_test4.R tests/pseudo-lik_surf_test4a.R tests/pseudo-lik_surf_test4b.R tests/pseudo-lik_surf_test5a.R tests/pseudo-lik_surf_test5b.R

tests/pseudo-lik_surf_test_A-B_EXACT.nb

tests/pseudo-lik_surf_test_A-B_SAMPLE.nb

tests/pseudo-lik_surf_test_A-B_SAMPLE_COMPARE-TO-R.nb

tests/pseudo-lik_vs_lik_test1.R tests/pseudo_grad_tests1.R tests/pseudo_grad_tests10.R tests/pseudo_grad_tests2.R tests/pseudo_grad_tests3.R tests/pseudo_grad_tests4.R tests/pseudo_grad_tests5.R tests/pseudo_grad_tests6.R tests/pseudo_grad_tests7.R tests/pseudo_grad_tests8.R tests/pseudo_grad_tests8a.R tests/pseudo_grad_tests8b.R tests/pseudo_grad_tests8c.R tests/pseudo_grad_tests8d.R tests/pseudo_grad_tests9.R tests/psl_grad_take2_test1.R tests/psl_grad_take2_test2.R tests/psl_v_lik_fit_test1.R tests/psl_v_lik_fit_test2_KNM.R

tests/psl_v_lik_fit_test2_KNM.csv

tests/psl_v_lik_fit_test2_LIK.R tests/psl_v_lik_fit_test2_PSL.R tests/regression_tests/10.tangle.R tests/regression_tests/1_rv.R tests/regression_tests/1_rv_a.R tests/regression_tests/2_rv.R tests/regression_tests/glmnet_tests/glmnet_logistic_fit_test1.R tests/regression_tests/hojsgaard_model_tests/cube_model/cube_control.poi-and-zero-poi.R tests/regression_tests/hojsgaard_model_tests/loglin_glm-vs-loglm_hoj-liz.R tests/regression_tests/hojsgaard_model_tests/loglin_vs_CRF.R tests/regression_tests/hojsgaard_model_tests/loglin_vs_CRF_corrected.R tests/regression_tests/hojsgaard_model_tests/random.graph.R tests/regression_tests/hojsgaard_model_tests/randomg_glmnet.R

tests/regression_tests/hojsgaard_model_tests/randomg_zip.RData

tests/regression_tests/hojsgaard_model_tests/slayer_model/slayer.r tests/regression_tests/hojsgaard_model_tests/soren1.R tests/regression_tests/hojsgaard_model_tests/stan_loglin_test1.R

tests/regression_tests/hojsgaard_model_tests/stan_loglin_test1.stan

tests/regression_tests/hojsgaard_model_tests/tesseract_model/M.RData

tests/regression_tests/hojsgaard_model_tests/tesseract_model/bfit.RData

tests/regression_tests/hojsgaard_model_tests/tesseract_model/samps.RData

tests/regression_tests/hojsgaard_model_tests/tesseract_model/tesseract_Stan-loglin-analysis.R

tests/regression_tests/hojsgaard_model_tests/tesseract_model/tesseract_bayes_loglin_model.dist.RData

tests/regression_tests/hojsgaard_model_tests/tesseract_model/tesseract_dist-fit-compare.R tests/regression_tests/hojsgaard_model_tests/tesseract_model/tesseract_exact_true_model.R tests/regression_tests/hojsgaard_model_tests/tesseract_model/tesseract_mle-analysis.R

tests/regression_tests/hojsgaard_model_tests/tesseract_model/tesseract_mle_model.dist.RData

tests/regression_tests/hojsgaard_model_tests/tesseract_model/tesseract_model_matrix_and_JAGS-loglin_fit.R tests/regression_tests/hojsgaard_model_tests/tesseract_model/tesseract_model_matrix_and_Stan-loglin_fit.R

tests/regression_tests/hojsgaard_model_tests/tesseract_model/tesseract_true_model.dist.RData

tests/regression_tests/hojsgaard_model_tests/triangle_model/triangle-model_bayes-loglin1.R tests/regression_tests/hojsgaard_model_tests/triangle_model/triangle-model_bayes-loglin2.R tests/regression_tests/hojsgaard_model_tests/triangle_model/triangle-model_bayes-loglin_Notes-example.R tests/regression_tests/hojsgaard_model_tests/triangle_model/triangle-model_bayes-loglin_Notes-example_JAGS.R tests/regression_tests/hojsgaard_model_tests/triangle_model/triangle-model_bayes-lr.R tests/regression_tests/hojsgaard_model_tests/triangle_model/triangle-model_loglin-gRim.R tests/regression_tests/hojsgaard_model_tests/triangle_model/triangle-model_loglin-modelmatrix.R tests/regression_tests/hojsgaard_model_tests/triangle_model/triangle-model_loglin_vs_emp_vs_bayeslr_vs_mlelr_vs_true.R tests/regression_tests/hojsgaard_model_tests/triangle_model/triangle-model_loglin_vs_emp_vs_bayeslr_vs_mlelr_vs_true2.R tests/regression_tests/hojsgaard_model_tests/triangle_model/triangle-model_mle-lr.R tests/regression_tests/hojsgaard_model_tests/triangle_model/triangle-model_mrf.R tests/regression_tests/hojsgaard_model_tests/triangle_model/triangle-model_psl.R tests/regression_tests/hojsgaard_model_tests/triangle_model/triangle-model_sample_generation.R tests/regression_tests/hojsgaard_model_tests/triangle_model/triangle_comparison_template1.R tests/regression_tests/hojsgaard_model_tests/triangle_model/triangle_comparison_template2.R

tests/regression_tests/hojsgaard_model_tests/triangle_model/triangle_data/triangle_bayes-lr_dist.RData

tests/regression_tests/hojsgaard_model_tests/triangle_model/triangle_data/triangle_empirical_dist.RData

tests/regression_tests/hojsgaard_model_tests/triangle_model/triangle_data/triangle_exact_dist.RData

tests/regression_tests/hojsgaard_model_tests/triangle_model/triangle_data/triangle_loglin_MM_dist.RData

tests/regression_tests/hojsgaard_model_tests/triangle_model/triangle_data/triangle_loglin_dist.RData

tests/regression_tests/hojsgaard_model_tests/triangle_model/triangle_data/triangle_mle-lr_dist.RData

tests/regression_tests/hojsgaard_model_tests/triangle_model/triangle_data/triangle_mrf_dist.RData

tests/regression_tests/hojsgaard_model_tests/triangle_model/triangle_data/triangle_psl_dist.RData

tests/regression_tests/hojsgaard_model_tests/triangle_model/triangle_data/triangle_samp.RData

tests/regression_tests/hojsgaard_model_tests/triangle_model/vanalla.poisson.regression.stan

tests/regression_tests/hojsgaard_model_tests/triangle_model/vanalla.poisson.regression2.stan

tests/regression_tests/hojsgaard_model_tests/triangle_model/vanalla.poisson.regression2a

tests/regression_tests/hojsgaard_model_tests/triangle_model/vanalla.poisson.regression2a.stan

tests/regression_tests/hojsgaard_model_tests/triangle_model/vanalla.poisson.regression2b.stan

tests/regression_tests/hojsgaard_model_tests/zero_inflated_fish/fish.R tests/regression_tests/hojsgaard_model_tests/zero_inflated_fish/fish_control_optimized.R

tests/regression_tests/hojsgaard_model_tests/zero_inflated_fish/zero_inflated_poisson.stan

tests/regression_tests/hojsgaard_model_tests/zero_inflated_fish/zero_inflated_poisson_optimized_DOESNT_WORK_RIGHT.stan

tests/regression_tests/hojsgaard_model_tests/zero_inflated_fish/zero_inflated_poisson_take2.stan

tests/regression_tests/hojsgaard_model_tests/zero_inflated_fish/zero_inflated_poisson_take3.stan

tests/regression_tests/hojsgaard_model_tests/zero_inflated_fish/zero_inflated_random_graph.R

tests/regression_tests/logistic_model1.stan

tests/regression_tests/logistic_simplifications.nb

tests/regression_tests/logistic_test_jags.R tests/regression_tests/regress_test1.R tests/regression_tests/regress_test2.R tests/regression_tests/regress_test3.R tests/regression_tests/regress_test3a.R tests/regression_tests/regress_test3b.R tests/regression_tests/regress_test4.R tests/regression_tests/regress_test_generic.R tests/regression_tests/triangle_logistic-regress_bayes.R tests/regression_tests/triangle_logistic-regress_bayes_JAGS.R tests/regression_tests/triangle_logistic-regress_bayes_JAGS2.R tests/regression_tests/triangle_logistic-regress_bayes_JAGS3.R

tests/rnd_thetas.csv

tests/rnd_thetas_vic_output.csv

tests/sample_data_sets_test1.R

tests/samps.csv

tests/samps_OLD.RData

tests/simulation_node_ordering_check.R tests/symb.cond.ener.test1.R tests/symb.cond.ener.test2.R

tests/symb_reg1.nb

tests/test1.R tests/test1a.R tests/test1b.R tests/test1c.R tests/test2.R tests/test2a.R tests/test2b.R tests/test2c.R tests/test2d.R tests/test2d1.R tests/test2e.R tests/test3_log-lik.R

tests/test3_log-lik.nb

tests/test3_pseudo-lik.R tests/test4_cond_E.R tests/test4_cond_E_2.R tests/test4_cond_E_3.R

tests/test4_psl-test.nb

tests/test4_psl-test2.nb

tests/test4_psl-test2a.nb

tests/test4_psl-test3.nb

tests/test_model_matrix.R tests/test_model_matrix2.R tests/test_model_matrix_Slayer-PROBLEM.R tests/test_model_matrix_Slayer.R tests/test_nodes2params.R tests/triangle_logits_for_symb.R

npetraco/CRFutil documentation built on Nov. 23, 2023, 11:30 a.m.