Files in robertness/bninfo
Queries and information theoritic operations on Bayesian networks.
.Rbuildignore
.gitignore
CopyOfplots_temp.R
DESCRIPTION
NAMESPACE
R/active_learning.R
R/bninfo.R
R/dimensionality.R
R/information_theory.R
R/performance.R
R/simulation.R
R/tools.R
R/transition_sequence.R
bninfo.Rproj
data-raw/tcell-raw-data-files/1. cd3cd28.xls
data-raw/tcell-raw-data-files/10. cd3cd28icam2+aktinhib.xls
data-raw/tcell-raw-data-files/11. cd3cd28icam2+g0076.xls
data-raw/tcell-raw-data-files/12. cd3cd28icam2+psit.xls
data-raw/tcell-raw-data-files/13. cd3cd28icam2+u0126.xls
data-raw/tcell-raw-data-files/14. cd3cd28icam2+ly.xls
data-raw/tcell-raw-data-files/2. cd3cd28icam2.xls
data-raw/tcell-raw-data-files/3. cd3cd28+aktinhib.xls
data-raw/tcell-raw-data-files/4. cd3cd28+g0076.xls
data-raw/tcell-raw-data-files/5. cd3cd28+psitect.xls
data-raw/tcell-raw-data-files/6. cd3cd28+u0126.xls
data-raw/tcell-raw-data-files/7. cd3cd28+ly.xls
data-raw/tcell-raw-data-files/8. pma.xls
data-raw/tcell-raw-data-files/9. b2camp.xls
data-raw/tcell-raw-data-files/Sachs_Nolan_Perturbation Data Sets_Final.doc
data-raw/tcell-scutari-int.txt
data/alarm_boot.rda
data/averaging_entropies.rda
data/correlation_results.rda
data/discrete_net.rda
data/dream.rda
data/dream_net.rda
data/intervention_experiment.rda
data/isachs.rda
data/results.rda
data/sample_size_sim_results.rda
data/tcell_examples.rda
data/tcells.rda
inst/extdata/copasi_data/no_cycle_no_inh.txt
inst/extdata/copasi_data/no_cycle_with_inh.txt
inst/extdata/copasi_data/normal_model_no_inh.txt
inst/extdata/dream_300dags_uninformative.Rdata
inst/extdata/dream_data/MD-LiverDREAM.csv
inst/extdata/dream_data/PKN-LiverDREAM.sif
inst/extdata/melancon_gaussian.R
inst/extdata/models/IGF_model.cps
inst/extdata/models/IGF_no_cycle.cps
inst/extdata/models/IGF_no_cycle_inh_model.cps
inst/extdata/models/IGF_stochastic.cps
inst/extdata/models/IGF_stochastic2.cps
inst/extdata/models/tcell_models.cps
inst/extdata/ordered_gaussian.R
inst/extdata/sachs.discretised.txt
inst/extdata/scripts/alarm_analysis_1.R
inst/extdata/scripts/alarm_analysis_2.R
inst/extdata/scripts/clear_strength_experiment.R
inst/extdata/scripts/entropy_trajectory_simulation_bayes.R
inst/extdata/scripts/entropy_trajectory_simulation_no_bayes.R
inst/extdata/scripts/entropy_trajectory_visualization2.R
inst/extdata/scripts/entropy_trajectory_visualization_igfr.R
inst/extdata/scripts/equivalence_class_enumeration.R
inst/extdata/scripts/intervention_sim_updated.R
inst/extdata/scripts/iss_parameter_investigation.R
inst/extdata/scripts/no_cycle_processing.R
inst/extdata/sim_results/entropy_trajectory_simulations/IGFR_model/IGFR_averaging_entropies_directed_3-31-16_no_bayes_50iss.Rdata
inst/extdata/sim_results/entropy_trajectory_simulations/averaging_entropies_vanilla_alarm_2-10-16.Rdata
inst/extdata/sim_results/entropy_trajectory_simulations/combined results/averaging_results_with_cs_prior.Rdata
inst/extdata/sim_results/entropy_trajectory_simulations/combined results/entropy_sim_log_3-8-16.txt
inst/extdata/sim_results/entropy_trajectory_simulations/combined results/entropy_trajectory_simulations.Rdata
inst/extdata/sim_results/entropy_trajectory_simulations/combined results/entropy_trajectory_simulations_2-7-16.Rdata
inst/extdata/sim_results/entropy_trajectory_simulations/combined results/entropy_trajectory_simulations_3-8-16_no_bayes_1000iss.Rdata
inst/extdata/sim_results/entropy_trajectory_simulations/combined results/entropy_trajectory_simulations_feb_3.Rdata
inst/extdata/sim_results/entropy_trajectory_simulations/combined results/entropy_trajectory_simulations_unsure_feb_3.Rdata
inst/extdata/sim_results/entropy_trajectory_simulations/no_prior_edges/averaging_entropies_vanilla_2-7-16.Rdata
inst/extdata/sim_results/entropy_trajectory_simulations/no_prior_edges/averaging_entropies_vanilla_2-8-16.Rdata
inst/extdata/sim_results/entropy_trajectory_simulations/no_prior_edges/averaging_entropies_vanilla_3-12-16_no_bayes_1500iss.Rdata
inst/extdata/sim_results/entropy_trajectory_simulations/no_prior_edges/averaging_entropies_vanilla_3-12-16_no_bayes_2000iss.Rdata
inst/extdata/sim_results/entropy_trajectory_simulations/no_prior_edges/averaging_entropies_vanilla_3-12-16_no_bayes_2500iss.Rdata
inst/extdata/sim_results/entropy_trajectory_simulations/no_prior_edges/averaging_entropies_vanilla_3-28-16_no_bayes_1000iss.Rdata
inst/extdata/sim_results/entropy_trajectory_simulations/no_prior_edges/averaging_entropies_vanilla_3-6-16.Rdata
inst/extdata/sim_results/entropy_trajectory_simulations/no_prior_edges/averaging_entropies_vanilla_3-6-16_no_bayes.Rdata
inst/extdata/sim_results/entropy_trajectory_simulations/no_prior_edges/averaging_entropies_vanilla_3-6-16_no_bayes_500iss.Rdata
inst/extdata/sim_results/entropy_trajectory_simulations/no_prior_edges/averaging_entropies_vanilla_3-8-16_no_bayes_1000iss.Rdata
inst/extdata/sim_results/entropy_trajectory_simulations/no_prior_edges/averaging_entropies_vanilla_alarm_2-10-16.Rdata
inst/extdata/sim_results/entropy_trajectory_simulations/with_prior_edges/averaging_entropies_directed_2-7-16.Rdata
inst/extdata/sim_results/entropy_trajectory_simulations/with_prior_edges/averaging_entropies_directed_2-8-16.Rdata
inst/extdata/sim_results/entropy_trajectory_simulations/with_prior_edges/averaging_entropies_directed_3-12-16_no_bayes_1500iss.Rdata
inst/extdata/sim_results/entropy_trajectory_simulations/with_prior_edges/averaging_entropies_directed_3-12-16_no_bayes_2000iss.Rdata
inst/extdata/sim_results/entropy_trajectory_simulations/with_prior_edges/averaging_entropies_directed_3-12-16_no_bayes_2500iss.Rdata
inst/extdata/sim_results/entropy_trajectory_simulations/with_prior_edges/averaging_entropies_directed_3-21-16_no_bayes_1500iss.Rdata
inst/extdata/sim_results/entropy_trajectory_simulations/with_prior_edges/averaging_entropies_directed_3-28-16_no_bayes_1000iss.Rdata
inst/extdata/sim_results/entropy_trajectory_simulations/with_prior_edges/averaging_entropies_directed_3-6-16_no_bayes.Rdata
inst/extdata/sim_results/entropy_trajectory_simulations/with_prior_edges/averaging_entropies_directed_3-6-16_no_bayes_500iss.Rdata
inst/extdata/sim_results/entropy_trajectory_simulations/with_prior_edges/averaging_entropies_directed_3-8-16_no_bayes_1000iss.Rdata
inst/extdata/sim_results/entropy_trajectory_simulations/with_prior_edges/averaging_entropies_undirected_2-7-16.Rdata
inst/extdata/sim_results/entropy_trajectory_simulations/with_prior_edges/averaging_entropies_undirected_2-8-16.Rdata
inst/extdata/sim_results/entropy_trajectory_simulations/with_prior_edges/averaging_entropies_undirected_3-6-16_no_bayes_500iss.Rdata
inst/extdata/sim_results/entropy_trajectory_simulations/with_prior_edges/averaging_entropies_undirected_3-8-16_no_bayes_1000iss.Rdata
inst/extdata/sim_results/entropy_trajectory_simulations/with_prior_edges/averaging_entropies_undirected_bl_2-7-16.Rdata
inst/extdata/sim_results/entropy_trajectory_simulations/with_prior_edges/averaging_entropies_with_bl_2-7-16.Rdata
inst/extdata/tcell.R
man/active_learning.Rd
man/add_singletons.Rd
man/arcs2names.Rd
man/ba_whitelist.Rd
man/bayes_correction.Rd
man/bninfo-package.Rd
man/boot_dags.Rd
man/break_cycles.Rd
man/build_triplet_network.Rd
man/conditional_entropy_query.Rd
man/construct_bn.Rd
man/count_positives.Rd
man/cpd_entropy_query.Rd
man/ctsdag.Rd
man/dream_net.Rd
man/edge_entropy.Rd
man/entropy.Rd
man/fit2net.Rd
man/fix_node.Rd
man/get_performance.Rd
man/get_upstream_edges.Rd
man/infer_from_start_net.Rd
man/info_gain.Rd
man/l1_error.Rd
man/melancon_boot.Rd
man/name_edge_df.Rd
man/name_edges.Rd
man/ordered_boot.Rd
man/passive_learning.Rd
man/performance_arc_list.Rd
man/performance_outcomes.Rd
man/performance_plot.Rd
man/progress_plot.Rd
man/propagate_orientation.Rd
man/random_graph.Rd
man/rebuild_strength.Rd
man/reduce_averaging.Rd
man/sample_size_sim.Rd
man/scramble.Rd
man/select_next_intervention.Rd
man/select_random_intervention.Rd
man/sim_cond_ind_cor.Rd
man/sim_gbn.Rd
man/sim_median_cor.Rd
man/skewed_beta.Rd
man/strength_plot.Rd
man/tcell_examples.Rd
man/test_dag.Rd
man/test_markov_dependence_learning.Rd
man/triplet_network.Rd
man/v_array.Rd
man/zero_gain_prob.Rd
plots_temp.R
simulation_log.txt
tests/M_base.rda
tests/model_averaging.rda
tests/ssachs.rda
tests/test_data.R
tests/testthat.R
tests/testthat/tcell_averaging.rda
tests/testthat/test-active_learning.R
tests/testthat/test-parallel.R
tests/testthat/test-performance.R
tests/testthat/test-simulation.R
tests/testthat/test-tools.R
tests/testthat/test-transition_sequence.R
vignettes/L1_edge_error.Rmd
vignettes/active_learning_dream.Rmd
vignettes/active_learning_dream2.Rmd
vignettes/active_learning_tcell.Rmd
vignettes/active_learning_tcell2.Rmd
vignettes/averaging_entropy.Rmd
vignettes/bibliography.bib
vignettes/causal_priors.Rmd
vignettes/counterfactual_model_building.Rmd
vignettes/counterfactual_model_building.nb.html
vignettes/dimensionality.Rmd
vignettes/dream_data.Rmd
vignettes/evaluating_interventions.Rmd
vignettes/information_theory.Rmd
vignettes/intervention_bootstrap.Rmd
vignettes/objects/dream/L1_informative.Rdata
vignettes/objects/dream/L1_uninformative.Rdata
vignettes/objects/dream/al_results_informative.Rdata
vignettes/objects/dream/al_results_uninformative.Rdata
vignettes/objects/dream/dags_informative.Rdata
vignettes/objects/dream/dags_uninformative.Rdata
vignettes/objects/dream/random_IG_P0.Rdata
vignettes/objects/dream/random_l1.Rdata
vignettes/objects/dream/random_tpr.Rdata
vignettes/objects/dream/tpr_informative.Rdata
vignettes/objects/dream/tpr_uninformative.Rdata
vignettes/objects/tcells/L1_informative.Rdata
vignettes/objects/tcells/L1_uninformative.Rdata
vignettes/objects/tcells/al_results_uninformative.Rdata
vignettes/objects/tcells/dags_informative.Rdata
vignettes/objects/tcells/dags_uninformative.Rdata
vignettes/objects/tcells/random_IG_P0.Rdata
vignettes/objects/tcells/random_l1.Rdata
vignettes/objects/tcells/random_tpr.Rdata
vignettes/objects/tcells/tpr_informative.Rdata
vignettes/objects/tcells/tpr_uninformative.Rdata
vignettes/performance.Rmd
vignettes/posterior_predictive.Rmd
vignettes/prior_edge_performance_improvement.Rmd
vignettes/raf_mek.Rmd
vignettes/stan_model_for_counterfactual_prediction.R
