Files in thednainus/HIVepisimAnalysis

Functions to analyse results from network analysis

Analyses/MSMpopulation_simulations/OSG/resample_trajectory_OSG.R Analyses/MSMpopulation_simulations/create_pbs_HIVepidemics.R Analyses/MSMpopulation_simulations/create_pbs_file_LOGweights_summary.R Analyses/MSMpopulation_simulations/get_quantiles_best_fit_trajectory_forReplicates.R Analyses/MSMpopulation_simulations/plot_best_fit_trajectory_forReplicates.R Analyses/MSMpopulation_simulations/resample_trajectory.R Analyses/consensus_sequences/1.Processing_networks_cluster_v10.R Analyses/consensus_sequences/2.Simulate_sequence_alignments_v2.R Analyses/consensus_sequences/3.Estimate_trees_sampler2_v5.R Analyses/consensus_sequences/3.Estimate_trees_v5.R Analyses/consensus_sequences/4.Date_tree_and_infectorProbability_sampler2_v1.R Analyses/consensus_sequences/Results_PRC/PRC_all.R Analyses/consensus_sequences/Results_PRC/plot_prc.R Analyses/consensus_sequences/Results_PRC/plot_prc_mainFigures.R Analyses/consensus_sequences/Results_PRC/plots/PRC_params1_sampler1_250mig.pdf Analyses/consensus_sequences/Results_PRC/plots/PRC_params1_sampler1_500mig.pdf Analyses/consensus_sequences/Results_PRC/plots/PRC_params1_sampler1_750mig.pdf Analyses/consensus_sequences/Results_PRC/plots/PRC_params1_sampler2_250mig.pdf Analyses/consensus_sequences/Results_PRC/plots/PRC_params1_sampler2_500mig.pdf Analyses/consensus_sequences/Results_PRC/plots/PRC_params1_sampler2_750mig.pdf Analyses/consensus_sequences/Results_PRC/plots/PRC_params2_sampler1_250mig.pdf Analyses/consensus_sequences/Results_PRC/plots/PRC_params2_sampler1_500mig.pdf Analyses/consensus_sequences/Results_PRC/plots/PRC_params2_sampler1_750mig.pdf Analyses/consensus_sequences/Results_PRC/plots/PRC_params2_sampler2_250mig.pdf Analyses/consensus_sequences/Results_PRC/plots/PRC_params2_sampler2_500mig.pdf Analyses/consensus_sequences/Results_PRC/plots/PRC_params2_sampler2_750mig.pdf Analyses/consensus_sequences/Results_PRC/plots/main_Figures/PRC_params1_sampler1_250mig.pdf Analyses/consensus_sequences/Results_PRC/plots/main_Figures/PRC_params1_sampler1_500mig.pdf Analyses/consensus_sequences/Results_PRC/plots/main_Figures/PRC_params1_sampler1_750mig.pdf Analyses/consensus_sequences/Results_PRC/plots/main_Figures/PRC_params2_sampler1_250mig.pdf Analyses/consensus_sequences/Results_PRC/plots/main_Figures/PRC_params2_sampler1_500mig.pdf Analyses/consensus_sequences/Results_PRC/plots/main_Figures/PRC_params2_sampler1_750mig.pdf Analyses/consensus_sequences/Results_PRC/results_Precision_Recall_consensus_sequences_mergedData.R Analyses/consensus_sequences/TP_TN_FP_FN_estimation.R Analyses/consensus_sequences/TP_TN_FP_FN_estimation_threshold90.R Analyses/consensus_sequences/analyse_total_tips.R Analyses/consensus_sequences/create_input_files_iqtree.R Analyses/consensus_sequences/create_tables_paper.R Analyses/consensus_sequences/get_missing_jobs.R Analyses/consensus_sequences/get_total_tips.R Analyses/consensus_sequences/get_total_tips_10000bp.R Analyses/consensus_sequences/results_totalPairs_consensus_sequences_mergedData.R Analyses/consensus_sequences/summarize_data_curves_replicates_10000bp.R Analyses/consensus_sequences/summarize_data_curves_replicates_1000bp.R Analyses/consensus_sequences/summarize_data_curves_replicates_trueTrees.R Analyses/deep_sequencing/1.Processing_networks_deep_sequencing_cluster_v7.R Analyses/deep_sequencing/2.Estimate_W_threshold.R Analyses/deep_sequencing/2.Simulate_sequence_alignments_deep_sequencing_v4.R Analyses/deep_sequencing/2.Simulate_sequence_alignments_deep_sequencing_v4_mod.R Analyses/deep_sequencing/3.Simulate_Illumina_reads_v4.R Analyses/deep_sequencing/4.Map_reads_shiver_v4.R Analyses/deep_sequencing/5.Prepare_for_phyloscanner_v4.R Analyses/deep_sequencing/6.CreateWindows_Run_phyloscanner_read_align.R Analyses/deep_sequencing/6.Run_phyloscanner_read_alignments_v7_340window.R Analyses/deep_sequencing/7.Estimate_trees_reads_IQTREE_v2.R Analyses/deep_sequencing/8.Run_phyloscanner_part2_v4.R Analyses/deep_sequencing/Result_analyses/False_positives.R Analyses/deep_sequencing/Result_analyses/False_positives_difference_timeTrans.R Analyses/deep_sequencing/Result_analyses/Plots/PRC_deepseq_mig250_750_w0.01.pdf Analyses/deep_sequencing/Result_analyses/Plots/PRC_deepseq_mig500_w0.01.pdf Analyses/deep_sequencing/Result_analyses/True_Negatives.R Analyses/deep_sequencing/Result_analyses/True_negatives_difference_timeTrans.R Analyses/deep_sequencing/Result_analyses/True_positives_difference_timeTrans.R Analyses/deep_sequencing/Result_analyses/plot_time_sampling.R Analyses/deep_sequencing/Result_analyses/separate_TP_FP_TN_FN.R Analyses/deep_sequencing/Result_analyses/summarize_phyloscanner_results_directness.R Analyses/deep_sequencing/Result_analyses/summarize_phyloscanner_results_thresholds.R Analyses/deep_sequencing/Result_analyses/summarize_phyloscanner_results_v5.R Analyses/deep_sequencing/Result_analyses/teste_find_chain.R Analyses/deep_sequencing/Result_analyses/who_infected_whom.R Analyses/deep_sequencing/create_pbs_ARTIllumina_v2.R Analyses/deep_sequencing/create_pbs_phyloscanner_part1.R Analyses/deep_sequencing/create_pbs_phyloscanner_part2_v2.R Analyses/deep_sequencing/create_pbs_phyloscanner_part2_v3.R Analyses/deep_sequencing/create_pbs_shiver.R Analyses/deep_sequencing/plot_prc_mainFigures.R Analyses/simulation_parameters.R Manuscript/Supplementary_tables.pdf R/W_utils.R R/cluster_utils.R R/phylo_utils.R R/sampling_utils.R R/summary_utils.R R/utils.R README.md inst/data/incidence_HIVdiagnosis.R man/add_observed_values.Rd man/add_observed_values_direction.Rd man/add_observed_values_directness.Rd man/add_root_edge.Rd man/add_root_edge2.Rd man/add_sampled_times.Rd man/check_linked_transmissions.Rd man/check_true_pair.Rd man/check_true_pair_directness.Rd man/check_true_transmissions.Rd man/compute_log_importance_weight_incidence.Rd man/compute_log_importance_weight_newDx.Rd man/convert_branches.Rd man/create_inf_csv.Rd man/create_inf_csv2.Rd man/create_sample_csv.Rd man/create_sample_csv2.Rd man/create_times_tsv.Rd man/create_transmissions_tsv.Rd man/days2years.Rd man/est_sampleSize.Rd man/get.transmat.phylo.Rd man/get_cd4s.Rd man/get_cd4s_sampling.Rd man/get_chain.Rd man/get_difference.Rd man/get_epi_data.Rd man/get_id_by_location.Rd man/get_n_by_origin.Rd man/get_newTip_names.Rd man/get_newids.Rd man/get_origin_at_samplingTime.Rd man/get_precision_recall.Rd man/get_rates.Rd man/get_rates2.Rd man/get_subset_tips.Rd man/get_tipNames.Rd man/get_tip_cherry.Rd man/keep_row.Rd man/merge_trees.Rd man/name_of_tips.Rd man/order_IDs_byDate.Rd man/recency_test.Rd man/reorder_tip_names.Rd man/replace_dups.Rd man/sampleIDs.Rd man/sampleIDs2.Rd man/selectIDs.Rd man/set_sampledIDs.Rd man/split_dirs.Rd man/summarize_all_data.Rd man/summarize_data.Rd man/summarize_trans.Rd man/summarize_trans_compl.Rd man/summaryW.Rd man/summaryW2.Rd man/time_atSeroconversion.Rd man/validadeW.Rd man/wiw.Rd