FAVITES_ModuleList.json

{
    "ContactNetwork": {
        "NetworkX": {
            "req": []
        },

        "PANGEA": {
            "req": ["Rscript_path", "pangea_yr.start", "pangea_yr.end", "pangea_seed", "pangea_s.INC.recent", "pangea_s.INC.recent.len", "pangea_s.PREV.min", "pangea_s.PREV.max", "pangea_s.PREV.base", "pangea_s.INTERVENTION.start", "pangea_s.INTERVENTION.mul", "pangea_s.ARCHIVAL.n", "pangea_s.MODEL", "pangea_s.PREV.max.n", "pangea_s.INTERVENTION.prop", "pangea_epi.model", "pangea_epi.acute", "pangea_epi.intervention", "pangea_epi.dt", "pangea_epi.import", "pangea_root.edge.fixed", "pangea_v.N0tau", "pangea_v.r", "pangea_v.T50", "pangea_wher.mu", "pangea_wher.sigma", "pangea_bwerm.mu", "pangea_bwerm.sigma", "pangea_er.gamma", "pangea_er.gtr", "pangea_sp.prop.of.sexactive", "pangea_report.prop.recent", "pangea_dbg.GTRparam", "pangea_dbg.rER", "pangea_index.starttime.mode", "pangea_startseq.mode", "pangea_seqtime.mode"],

            "dep": ["ContactNetwork_PANGEA", "ContactNetworkGenerator_PANGEA", "EndCriteria_Instant", "NodeEvolution_PANGEA", "NodeSample_PANGEA", "NumBranchSample_All", "NumTimeSample_PANGEA", "SeedSelection_PANGEA", "SeedSequence_PANGEA", "SequenceEvolution_PANGEA", "SourceSample_PANGEA", "TimeSample_PANGEA", "TransmissionNodeSample_PANGEA", "TransmissionTimeSample_PANGEA", "TreeUnit_Same"]
        }
    },

    "ContactNetworkEdge": {
        "NetworkX": {
            "req": []
        },

        "PANGEA": {
            "req": []
        }
    },

    "ContactNetworkGenerator": {
        "BarabasiAlbert": {
            "req": ["num_cn_nodes", "num_edges_from_new"]
        },

        "BarabasiAlbertExtended": {
            "req": ["num_cn_nodes", "num_edges_from_new", "bae_p", "bae_q"]
        },

        "Barbell": {
            "req": ["barbell_m1", "barbell_m2"]
        },

        "Caveman": {
            "req": ["cave_num_cliques", "cave_clique_size"]
        },

        "CavemanConnected": {
            "req": ["cave_num_cliques", "cave_clique_size"]
        },

        "CavemanRelaxed": {
            "req": ["cave_num_cliques", "cave_clique_size", "cave_prob"]
        },

        "CCMnetPy": {
            "req": []
        },

        "Communities": {
            "req": ["cn_generators", "cn_p_across"]
        },

        "Complete": {
            "req": ["num_cn_nodes"]
        },

        "DegreeDistribution": {
            "req": ["cn_degree_distribution", "cn_tries"]
        },

        "EpiModel": {
            "req": ["Rscript_path", "epimodel_save_session", "epimodel_type", "num_cn_nodes", "epimodel_attributes", "epimodel_nsteps", "num_init_infected", "num_init_recovered", "recovery_rate", "transmission_probability", "act_rate", "average_edge_duration", "epimodel_formation_line", "epimodel_target_stats_line"],

            "dep": ["ContactNetworkGenerator_EpiModel", "EndCriteria_EpiModel", "SeedSelection_EpiModel", "TransmissionNodeSample_EpiModel", "TransmissionTimeSample_EpiModel"]
        },

        "ErdosRenyi": {
            "req": ["num_cn_nodes", "er_prob", "d_or_u"]
        },

        "File": {
            "req": ["contact_network_file"]
        },

        "FileAdjacencyMatrix": {
            "req": ["contact_network_file", "contact_network_delimiter"]
        },

        "NewmanWattsStrogatz": {
            "req": ["num_cn_nodes", "nws_k", "nws_prob"]
        },

        "PANGEA": {
            "req": ["Rscript_path", "pangea_yr.start", "pangea_yr.end", "pangea_seed", "pangea_s.INC.recent", "pangea_s.INC.recent.len", "pangea_s.PREV.min", "pangea_s.PREV.max", "pangea_s.PREV.base", "pangea_s.INTERVENTION.start", "pangea_s.INTERVENTION.mul", "pangea_s.ARCHIVAL.n", "pangea_s.MODEL", "pangea_s.PREV.max.n", "pangea_s.INTERVENTION.prop", "pangea_epi.model", "pangea_epi.acute", "pangea_epi.intervention", "pangea_epi.dt", "pangea_epi.import", "pangea_root.edge.fixed", "pangea_v.N0tau", "pangea_v.r", "pangea_v.T50", "pangea_wher.mu", "pangea_wher.sigma", "pangea_bwerm.mu", "pangea_bwerm.sigma", "pangea_er.gamma", "pangea_er.gtr", "pangea_sp.prop.of.sexactive", "pangea_report.prop.recent", "pangea_dbg.GTRparam", "pangea_dbg.rER", "pangea_index.starttime.mode", "pangea_startseq.mode", "pangea_seqtime.mode"],

            "dep": ["ContactNetwork_PANGEA", "ContactNetworkGenerator_PANGEA", "EndCriteria_Instant", "NodeEvolution_PANGEA", "NodeSample_PANGEA", "NumBranchSample_All", "NumTimeSample_PANGEA", "SeedSelection_PANGEA", "SeedSequence_PANGEA", "SequenceEvolution_PANGEA", "SourceSample_PANGEA", "TimeSample_PANGEA", "TransmissionNodeSample_PANGEA", "TransmissionTimeSample_PANGEA", "TreeUnit_Same"]
        },

        "PangeaSim": {
            "req": ["PangeaSim_Acute"],

            "dep": ["EndCriteria_PangeaSim", "SeedSelection_PangeaSim", "TransmissionNodeSample_PangeaSim", "TransmissionTimeSample_PangeaSim"]
        },

        "PowerlawClusterGraph": {
            "req": ["num_cn_nodes", "pcg_m", "pcg_p"]
        },

        "RandomPartitionGraph": {
            "req": ["rpg_sizes", "rpg_p_in", "rpg_p_out", "d_or_u"]
        },

        "RegularGraph": {
            "req": ["num_cn_nodes", "cn_degree"]
        },

        "StochasticBlockBA": {
            "req": ["cng_m", "cng_p", "cng_N"]
        },

        "WattsStrogatz": {
            "req": ["num_cn_nodes", "ws_k", "ws_prob"]
        },

        "WattsStrogatzConnected": {
            "req": ["num_cn_nodes", "wsc_k", "wsc_prob", "wsc_tries"]
        }
    },

    "ContactNetworkNode": {
        "NetworkX": {
            "req": []
        },

        "PANGEA": {
            "req": []
        }
    },

    "Driver": {
        "Default": {
            "req": ["out_dir", "random_number_seed"]
        }
    },

    "EndCriteria": {
        "EpiModel": {
            "req": ["Rscript_path", "epimodel_save_session", "epimodel_type", "num_cn_nodes", "epimodel_attributes", "epimodel_nsteps", "num_init_infected", "num_init_recovered", "recovery_rate", "transmission_probability", "act_rate", "average_edge_duration", "epimodel_formation_line", "epimodel_target_stats_line"],

            "dep": ["ContactNetworkGenerator_EpiModel", "EndCriteria_EpiModel", "SeedSelection_EpiModel", "TransmissionNodeSample_EpiModel", "TransmissionTimeSample_EpiModel"]
        },

        "FirstTimeTransmissions": {
            "req": ["end_time", "end_transmissions"]
        },

        "GEMF": {
            "req": ["gemf_path"],

            "dep": ["TransmissionNodeSample_GEMF", "TransmissionTimeSample_GonorrheaHethcoteYorkeGEMF", "TransmissionTimeSample_HIVARTGranichGEMF", "TransmissionTimeSample_HIVPopARTGEMF", "TransmissionTimeSample_SAISGEMF", "TransmissionTimeSample_SAAPPHIIREGEMF", "TransmissionTimeSample_SEIRGEMF", "TransmissionTimeSample_SIGEMF", "TransmissionTimeSample_SIRGEMF", "TransmissionTimeSample_SISGEMF", "TransmissionTimeSample_SVITRGEMF"]
        },

        "Instant": {
            "req": [],

            "dep": ["NodeEvolution_None", "NodeSample_Perfect", "SequenceEvolution_NoMutation", "Sequencing_Perfect", "TransmissionTime_Instant"]
        },

        "PangeaSim": {
            "req": [],

            "dep": ["ContactNetworkGenerator_PangeaSim", "SeedSelection_PangeaSim", "TransmissionNodeSample_PangeaSim", "TransmissionTimeSample_PangeaSim"]
        },

        "Time": {
            "req": ["end_time"]
        },

        "TransmissionFile": {
            "req": ["transmission_network_file"],

            "dep": ["SeedSelection_TransmissionFile", "TransmissionNodeSample_TransmissionFile", "TransmissionTimeSample_TransmissionFile"]
        },

        "Transmissions": {
            "req": ["end_transmissions"]
        }
    },

    "Logging": {
        "File": {
            "req": ["out_dir"]
        },

        "FileSTDOUT": {
            "req": ["out_dir"]
        },

        "FileSTDERR": {
            "req": ["out_dir"]
        },

        "Null": {
            "req": []
        },

        "STDERR": {
            "req": []
        },

        "STDOUT": {
            "req": []
        }
    },

    "NodeAvailability": {
        "Bernoulli": {
            "req": ["node_sample_prob"]
        },

        "None": {
            "req": [],

            "dep": ["NumTimeSample_None", "TimeSample_None"]
        },

        "PANGEA": {
            "req": ["Rscript_path", "pangea_yr.start", "pangea_yr.end", "pangea_seed", "pangea_s.INC.recent", "pangea_s.INC.recent.len", "pangea_s.PREV.min", "pangea_s.PREV.max", "pangea_s.PREV.base", "pangea_s.INTERVENTION.start", "pangea_s.INTERVENTION.mul", "pangea_s.ARCHIVAL.n", "pangea_s.MODEL", "pangea_s.PREV.max.n", "pangea_s.INTERVENTION.prop", "pangea_epi.model", "pangea_epi.acute", "pangea_epi.intervention", "pangea_epi.dt", "pangea_epi.import", "pangea_root.edge.fixed", "pangea_v.N0tau", "pangea_v.r", "pangea_v.T50", "pangea_wher.mu", "pangea_wher.sigma", "pangea_bwerm.mu", "pangea_bwerm.sigma", "pangea_er.gamma", "pangea_er.gtr", "pangea_sp.prop.of.sexactive", "pangea_report.prop.recent", "pangea_dbg.GTRparam", "pangea_dbg.rER", "pangea_index.starttime.mode", "pangea_startseq.mode", "pangea_seqtime.mode"],

            "dep": ["ContactNetwork_PANGEA", "ContactNetworkGenerator_PANGEA", "EndCriteria_Instant", "NodeEvolution_PANGEA", "NodeSample_PANGEA", "NumBranchSample_All", "NumTimeSample_PANGEA", "SeedSelection_PANGEA", "SeedSequence_PANGEA", "SequenceEvolution_PANGEA", "SourceSample_PANGEA", "TimeSample_PANGEA", "TransmissionNodeSample_PANGEA", "TransmissionTimeSample_PANGEA", "TreeUnit_Same"]
        },

        "Perfect": {
            "req": []
        },

        "TransmissionWeighted": {
            "req": ["node_sample_fraction"]
        }
    },

    "NodeEvolution": {
        "BirthDeath": {
            "req": ["bd_birth", "bd_birth_sd", "bd_death", "bd_death_sd"]
        },

        "DualBirth": {
            "req": ["dualbirth_path", "rate_A", "rate_B"]
        },

        "File": {
            "req": ["tree_file"]
        },

        "None": {
            "req": []
        },

        "PANGEA": {
            "req": ["Rscript_path", "pangea_yr.start", "pangea_yr.end", "pangea_seed", "pangea_s.INC.recent", "pangea_s.INC.recent.len", "pangea_s.PREV.min", "pangea_s.PREV.max", "pangea_s.PREV.base", "pangea_s.INTERVENTION.start", "pangea_s.INTERVENTION.mul", "pangea_s.ARCHIVAL.n", "pangea_s.MODEL", "pangea_s.PREV.max.n", "pangea_s.INTERVENTION.prop", "pangea_epi.model", "pangea_epi.acute", "pangea_epi.intervention", "pangea_epi.dt", "pangea_epi.import", "pangea_root.edge.fixed", "pangea_v.N0tau", "pangea_v.r", "pangea_v.T50", "pangea_wher.mu", "pangea_wher.sigma", "pangea_bwerm.mu", "pangea_bwerm.sigma", "pangea_er.gamma", "pangea_er.gtr", "pangea_sp.prop.of.sexactive", "pangea_report.prop.recent", "pangea_dbg.GTRparam", "pangea_dbg.rER", "pangea_index.starttime.mode", "pangea_startseq.mode", "pangea_seqtime.mode"],

            "dep": ["ContactNetwork_PANGEA", "ContactNetworkGenerator_PANGEA", "EndCriteria_Instant", "NodeEvolution_PANGEA", "NodeSample_PANGEA", "NumBranchSample_All", "NumTimeSample_PANGEA", "SeedSelection_PANGEA", "SeedSequence_PANGEA", "SequenceEvolution_PANGEA", "SourceSample_PANGEA", "TimeSample_PANGEA", "TransmissionNodeSample_PANGEA", "TransmissionTimeSample_PANGEA", "TreeUnit_Same"]
        },

        "TransmissionTree": {
            "req": []
        },

        "VirusTreeSimulator": {
            "req": ["java_path", "vts_model", "vts_n0", "vts_growthRate", "vts_t50", "vts_max_attempts"]
        },

        "Yule": {
            "req": ["dualbirth_path", "yule_rate"]
        }
    },

    "NumBranchSample": {
        "All": {
            "req": []
        },

        "Fixed": {
            "req": ["num_viruses_per_cn_sample"]
        },

        "Single": {
            "req": []
        }
    },

    "NumTimeSample": {
        "File": {
            "req": ["sample_time_file"],

            "dep": ["TimeSample_File"]
        },

        "Fixed": {
            "req": ["num_sample_times_per_individual"]
        },

        "None": {
            "req": [],

            "dep": ["NodeAvailability_None", "TimeSample_None"]
        },

        "Once": {
            "req": []
        },

        "PANGEA": {
            "req": ["Rscript_path", "pangea_yr.start", "pangea_yr.end", "pangea_seed", "pangea_s.INC.recent", "pangea_s.INC.recent.len", "pangea_s.PREV.min", "pangea_s.PREV.max", "pangea_s.PREV.base", "pangea_s.INTERVENTION.start", "pangea_s.INTERVENTION.mul", "pangea_s.ARCHIVAL.n", "pangea_s.MODEL", "pangea_s.PREV.max.n", "pangea_s.INTERVENTION.prop", "pangea_epi.model", "pangea_epi.acute", "pangea_epi.intervention", "pangea_epi.dt", "pangea_epi.import", "pangea_root.edge.fixed", "pangea_v.N0tau", "pangea_v.r", "pangea_v.T50", "pangea_wher.mu", "pangea_wher.sigma", "pangea_bwerm.mu", "pangea_bwerm.sigma", "pangea_er.gamma", "pangea_er.gtr", "pangea_sp.prop.of.sexactive", "pangea_report.prop.recent", "pangea_dbg.GTRparam", "pangea_dbg.rER", "pangea_index.starttime.mode", "pangea_startseq.mode", "pangea_seqtime.mode"],

            "dep": ["ContactNetwork_PANGEA", "ContactNetworkGenerator_PANGEA", "EndCriteria_Instant", "NodeEvolution_PANGEA", "NodeSample_PANGEA", "NumBranchSample_All", "NumTimeSample_PANGEA", "SeedSelection_PANGEA", "SeedSequence_PANGEA", "SequenceEvolution_PANGEA", "SourceSample_PANGEA", "TimeSample_PANGEA", "TransmissionNodeSample_PANGEA", "TransmissionTimeSample_PANGEA", "TreeUnit_Same"]
        },

        "Poisson": {
            "req": ["num_time_sample_lambda"]
        }
    },

    "SeedSelection": {
        "ClustersBernoulli": {
            "req": ["seed_k", "seed_m", "seed_p"]
        },

        "CommunityRandom": {
            "req": ["num_seeds_each_community"]
        },

        "CommunityRandomConstant": {
            "req": ["num_seeds_per_community"]
        },

        "EdgeWeighted": {
            "req": ["num_seeds"]
        },
		
		"EpiModel": {
            "req": ["Rscript_path", "epimodel_save_session", "epimodel_type", "num_cn_nodes", "epimodel_attributes", "epimodel_nsteps", "num_init_infected", "num_init_recovered", "recovery_rate", "transmission_probability", "act_rate", "average_edge_duration", "epimodel_formation_line", "epimodel_target_stats_line"],

            "dep": ["ContactNetworkGenerator_EpiModel", "EndCriteria_EpiModel", "SeedSelection_EpiModel", "TransmissionNodeSample_EpiModel", "TransmissionTimeSample_EpiModel"]
        },

        "PANGEA": {
            "req": ["Rscript_path", "pangea_yr.start", "pangea_yr.end", "pangea_seed", "pangea_s.INC.recent", "pangea_s.INC.recent.len", "pangea_s.PREV.min", "pangea_s.PREV.max", "pangea_s.PREV.base", "pangea_s.INTERVENTION.start", "pangea_s.INTERVENTION.mul", "pangea_s.ARCHIVAL.n", "pangea_s.MODEL", "pangea_s.PREV.max.n", "pangea_s.INTERVENTION.prop", "pangea_epi.model", "pangea_epi.acute", "pangea_epi.intervention", "pangea_epi.dt", "pangea_epi.import", "pangea_root.edge.fixed", "pangea_v.N0tau", "pangea_v.r", "pangea_v.T50", "pangea_wher.mu", "pangea_wher.sigma", "pangea_bwerm.mu", "pangea_bwerm.sigma", "pangea_er.gamma", "pangea_er.gtr", "pangea_sp.prop.of.sexactive", "pangea_report.prop.recent", "pangea_dbg.GTRparam", "pangea_dbg.rER", "pangea_index.starttime.mode", "pangea_startseq.mode", "pangea_seqtime.mode"],

            "dep": ["ContactNetwork_PANGEA", "ContactNetworkGenerator_PANGEA", "EndCriteria_Instant", "NodeEvolution_PANGEA", "NodeSample_PANGEA", "NumBranchSample_All", "NumTimeSample_PANGEA", "SeedSelection_PANGEA", "SeedSequence_PANGEA", "SequenceEvolution_PANGEA", "SourceSample_PANGEA", "TimeSample_PANGEA", "TransmissionNodeSample_PANGEA", "TransmissionTimeSample_PANGEA", "TreeUnit_Same"]
        },

        "PangeaSim": {
            "req": [],

            "dep": ["ContactNetworkGenerator_PangeaSim", "EndCriteria_PangeaSim", "TransmissionNodeSample_PangeaSim", "TransmissionTimeSample_PangeaSim"]
        },

        "Random": {
            "req": ["num_seeds"]
        },

        "TransmissionFile": {
            "req": ["transmission_network_file"],

            "dep": ["EndCriteria_TransmissionFile", "TransmissionNodeSample_TransmissionFile", "TransmissionTimeSample_TransmissionFile"]
        }
    },

    "SeedSequence": {
        "CommunityVirusMigrationCoalescentGTRGamma": {
            "req": ["hmmemit_path", "msms_path", "seqgen_path", "viral_sequence_type", "community_seed_populations", "community_seed_migration_rates", "community_seed_scaled_mutation_rate", "seqgen_a_to_c", "seqgen_a_to_g", "seqgen_a_to_t", "seqgen_c_to_g", "seqgen_c_to_t", "seqgen_g_to_t", "seqgen_freq_a", "seqgen_freq_c", "seqgen_freq_g", "seqgen_freq_t", "seqgen_gamma_shape", "seqgen_num_gamma_rate_categories"]
        },

        "CommunityVirusPureCoalescentGTRGamma": {
            "req": ["hmmemit_path", "seqgen_path", "viral_sequence_type", "community_root_population", "community_seed_populations", "seqgen_a_to_c", "seqgen_a_to_g", "seqgen_a_to_t", "seqgen_c_to_g", "seqgen_c_to_t", "seqgen_g_to_t", "seqgen_freq_a", "seqgen_freq_c", "seqgen_freq_g", "seqgen_freq_t", "seqgen_gamma_shape", "seqgen_num_gamma_rate_categories"]
        },

        "HMMBuildEmit": {
            "req": ["hmmbuild_path", "hmmbuild_options", "hmmbuild_msafile", "hmmemit_path", "hmmemit_options"]
        },

        "HMMEmit": {
            "req": ["hmmemit_path", "hmmemit_hmmfile", "hmmemit_options"]
        },

        "NoSeqs": {
            "req": []
        },

        "PANGEA": {
            "req": ["Rscript_path", "pangea_yr.start", "pangea_yr.end", "pangea_seed", "pangea_s.INC.recent", "pangea_s.INC.recent.len", "pangea_s.PREV.min", "pangea_s.PREV.max", "pangea_s.PREV.base", "pangea_s.INTERVENTION.start", "pangea_s.INTERVENTION.mul", "pangea_s.ARCHIVAL.n", "pangea_s.MODEL", "pangea_s.PREV.max.n", "pangea_s.INTERVENTION.prop", "pangea_epi.model", "pangea_epi.acute", "pangea_epi.intervention", "pangea_epi.dt", "pangea_epi.import", "pangea_root.edge.fixed", "pangea_v.N0tau", "pangea_v.r", "pangea_v.T50", "pangea_wher.mu", "pangea_wher.sigma", "pangea_bwerm.mu", "pangea_bwerm.sigma", "pangea_er.gamma", "pangea_er.gtr", "pangea_sp.prop.of.sexactive", "pangea_report.prop.recent", "pangea_dbg.GTRparam", "pangea_dbg.rER", "pangea_index.starttime.mode", "pangea_startseq.mode", "pangea_seqtime.mode"],

            "dep": ["ContactNetwork_PANGEA", "ContactNetworkGenerator_PANGEA", "EndCriteria_Instant", "NodeEvolution_PANGEA", "NodeSample_PANGEA", "NumBranchSample_All", "NumTimeSample_PANGEA", "SeedSelection_PANGEA", "SeedSequence_PANGEA", "SequenceEvolution_PANGEA", "SourceSample_PANGEA", "TimeSample_PANGEA", "TransmissionNodeSample_PANGEA", "TransmissionTimeSample_PANGEA", "TreeUnit_Same"]
        },

        "Random": {
            "req": ["seed_sequence_length"]
        },

        "RandomCodon": {
            "req": ["seed_sequence_codon_length"]
        },

        "RandomWeighted": {
            "req": ["seed_sequence_length", "seed_prob_A", "seed_prob_C", "seed_prob_G"]
        },

        "User": {
            "req": ["num_seeds", "seed_seqs"]
        },

        "Virus": {
            "req": ["hmmemit_path", "viral_sequence_type"]
        },

        "VirusBirthDeathGTRCodon": {
            "req": ["hmmemit_path", "seqgen_path", "viral_sequence_type", "seed_birth_rate", "seed_death_rate", "seqgen_a_to_c", "seqgen_a_to_g", "seqgen_a_to_t", "seqgen_c_to_g", "seqgen_c_to_t", "seqgen_g_to_t", "seqgen_freq_a", "seqgen_freq_c", "seqgen_freq_g", "seqgen_freq_t", "seqgen_codon_site1_rate", "seqgen_codon_site2_rate", "seqgen_codon_site3_rate"]
        },

        "VirusBirthDeathGTRGamma": {
            "req": ["hmmemit_path", "seqgen_path", "viral_sequence_type", "seed_birth_rate", "seed_death_rate", "seqgen_a_to_c", "seqgen_a_to_g", "seqgen_a_to_t", "seqgen_c_to_g", "seqgen_c_to_t", "seqgen_g_to_t", "seqgen_freq_a", "seqgen_freq_c", "seqgen_freq_g", "seqgen_freq_t", "seqgen_gamma_shape", "seqgen_num_gamma_rate_categories"]
        },

        "VirusMeanCoalescentGTRCodon": {
            "req": ["hmmemit_path", "seqgen_path", "viral_sequence_type", "seed_population", "seqgen_a_to_c", "seqgen_a_to_g", "seqgen_a_to_t", "seqgen_c_to_g", "seqgen_c_to_t", "seqgen_g_to_t", "seqgen_freq_a", "seqgen_freq_c", "seqgen_freq_g", "seqgen_freq_t", "seqgen_codon_site1_rate", "seqgen_codon_site2_rate", "seqgen_codon_site3_rate"]
        },

        "VirusMeanCoalescentGTRGamma": {
            "req": ["hmmemit_path", "seqgen_path", "viral_sequence_type", "seed_population", "seqgen_a_to_c", "seqgen_a_to_g", "seqgen_a_to_t", "seqgen_c_to_g", "seqgen_c_to_t", "seqgen_g_to_t", "seqgen_freq_a", "seqgen_freq_c", "seqgen_freq_g", "seqgen_freq_t", "seqgen_gamma_shape", "seqgen_num_gamma_rate_categories"]
        },

        "VirusNonHomYuleHeightGTRGamma": {
            "req": ["hmmemit_path", "seqgen_path", "viral_sequence_type", "seed_speciation_rate_func", "seed_height", "seqgen_a_to_c", "seqgen_a_to_g", "seqgen_a_to_t", "seqgen_c_to_g", "seqgen_c_to_t", "seqgen_g_to_t", "seqgen_freq_a", "seqgen_freq_c", "seqgen_freq_g", "seqgen_freq_t", "seqgen_gamma_shape", "seqgen_num_gamma_rate_categories"]
        },

        "VirusPureCoalescentGTRCodon": {
            "req": ["hmmemit_path", "seqgen_path", "viral_sequence_type", "seed_population", "seqgen_a_to_c", "seqgen_a_to_g", "seqgen_a_to_t", "seqgen_c_to_g", "seqgen_c_to_t", "seqgen_g_to_t", "seqgen_freq_a", "seqgen_freq_c", "seqgen_freq_g", "seqgen_freq_t", "seqgen_codon_site1_rate", "seqgen_codon_site2_rate", "seqgen_codon_site3_rate"]
        },

        "VirusPureCoalescentGTRGamma": {
            "req": ["hmmemit_path", "seqgen_path", "viral_sequence_type", "seed_population", "seqgen_a_to_c", "seqgen_a_to_g", "seqgen_a_to_t", "seqgen_c_to_g", "seqgen_c_to_t", "seqgen_g_to_t", "seqgen_freq_a", "seqgen_freq_c", "seqgen_freq_g", "seqgen_freq_t", "seqgen_gamma_shape", "seqgen_num_gamma_rate_categories"]
        },

        "VirusYuleHeightGTRGamma": {
            "req": ["hmmemit_path", "seqgen_path", "viral_sequence_type", "seed_height", "seqgen_a_to_c", "seqgen_a_to_g", "seqgen_a_to_t", "seqgen_c_to_g", "seqgen_c_to_t", "seqgen_g_to_t", "seqgen_freq_a", "seqgen_freq_c", "seqgen_freq_g", "seqgen_freq_t", "seqgen_gamma_shape", "seqgen_num_gamma_rate_categories"]
        }
    },

    "SequenceEvolution": {
        "EmpiricalCodonModelPyvolve": {
            "req": ["ecm_type", "ecm_alpha", "ecm_beta", "ecm_omega", "ecm_codon_frequencies_dictionary"]
        },

        "File": {
            "req": ["errorfree_sequence_file"]
        },

        "GTRCodonSeqGen": {
            "req": ["seqgen_path", "seqgen_a_to_c", "seqgen_a_to_g", "seqgen_a_to_t", "seqgen_c_to_g", "seqgen_c_to_t", "seqgen_g_to_t", "seqgen_freq_a", "seqgen_freq_c", "seqgen_freq_g", "seqgen_freq_t", "seqgen_codon_site1_rate", "seqgen_codon_site2_rate", "seqgen_codon_site3_rate"]
        },

        "GTRGammaSeqGen": {
            "req": ["seqgen_path", "seqgen_a_to_c", "seqgen_a_to_g", "seqgen_a_to_t", "seqgen_c_to_g", "seqgen_c_to_t", "seqgen_g_to_t", "seqgen_freq_a", "seqgen_freq_c", "seqgen_freq_g", "seqgen_freq_t", "seqgen_gamma_shape", "seqgen_num_gamma_rate_categories"]
        },

        "MechanisticCodonModelPyvolve": {
            "req": ["mcm_style", "mcm_alpha", "mcm_beta", "mcm_omega", "mcm_kappa", "mcm_codon_frequencies_dictionary", "mcm_mutation_rates_dictionary"]
        },

        "NoMutation": {
            "req": []
        },

        "NoSeqs": {
            "req": []
        },

        "NucleotideModelPyvolve": {
            "req": ["nuc_kappa", "nuc_frequencies_dictionary", "nuc_mutation_rates_dictionary"]
        },

        "PANGEA": {
            "req": ["Rscript_path", "pangea_yr.start", "pangea_yr.end", "pangea_seed", "pangea_s.INC.recent", "pangea_s.INC.recent.len", "pangea_s.PREV.min", "pangea_s.PREV.max", "pangea_s.PREV.base", "pangea_s.INTERVENTION.start", "pangea_s.INTERVENTION.mul", "pangea_s.ARCHIVAL.n", "pangea_s.MODEL", "pangea_s.PREV.max.n", "pangea_s.INTERVENTION.prop", "pangea_epi.model", "pangea_epi.acute", "pangea_epi.intervention", "pangea_epi.dt", "pangea_epi.import", "pangea_root.edge.fixed", "pangea_v.N0tau", "pangea_v.r", "pangea_v.T50", "pangea_wher.mu", "pangea_wher.sigma", "pangea_bwerm.mu", "pangea_bwerm.sigma", "pangea_er.gamma", "pangea_er.gtr", "pangea_sp.prop.of.sexactive", "pangea_report.prop.recent", "pangea_dbg.GTRparam", "pangea_dbg.rER", "pangea_index.starttime.mode", "pangea_startseq.mode", "pangea_seqtime.mode"],

            "dep": ["ContactNetwork_PANGEA", "ContactNetworkGenerator_PANGEA", "EndCriteria_Instant", "NodeEvolution_PANGEA", "NodeSample_PANGEA", "NumBranchSample_All", "NumTimeSample_PANGEA", "SeedSelection_PANGEA", "SeedSequence_PANGEA", "SequenceEvolution_PANGEA", "SourceSample_PANGEA", "TimeSample_PANGEA", "TransmissionNodeSample_PANGEA", "TransmissionTimeSample_PANGEA", "TreeUnit_Same"]
        },

        "Pyvolve": {
            "req": ["pyvolve_model_type", "pyvolve_custom_model_parameters_dictionary", "pyvolve_state_frequencies_class", "pyvolve_state_frequencies_parameters_dictionary"]
        },

        "SeqGen": {
            "req": ["seqgen_path", "seqgen_args"]
        }
    },

    "Sequencing": {
        "ART454Amplicon": {
            "req": ["art_454_path", "art_454_options", "art_454_amplicon_mode", "art_454_reads_pairs_per_amplicon", "out_dir"]
        },
        "ART454PairedEnd": {
            "req": ["art_454_path", "art_454_options", "art_454_fold_coverage", "art_454_mean_frag_len", "art_454_std_dev", "out_dir"]
        },
        "ART454SingleEnd": {
            "req": ["art_454_path", "art_454_options", "art_454_fold_coverage", "out_dir"]
        },
        "ARTillumina": {
            "req": ["art_illumina_path", "art_illumina_options", "out_dir"]
        },
        "ARTSOLiDAmpliconMatePair": {
            "req": ["art_SOLiD_path", "art_SOLiD_options", "art_SOLiD_len_read", "art_SOLiD_read_pairs_per_amplicon", "out_dir"]
        },
        "ARTSOLiDAmpliconPairedEnd": {
            "req": ["art_SOLiD_path", "art_SOLiD_options", "art_SOLiD_len_read_F3", "art_SOLiD_len_read_F5", "art_SOLiD_read_pairs_per_amplicon", "out_dir"]
        },
        "ARTSOLiDAmpliconSingleEnd": {
            "req": ["art_SOLiD_path", "art_SOLiD_options", "art_SOLiD_len_read", "art_SOLiD_reads_per_amplicon", "out_dir"]
        },
        "ARTSOLiDMatePair": {
            "req": ["art_SOLiD_path", "art_SOLiD_options", "art_SOLiD_len_read", "art_SOLiD_fold_coverage", "art_SOLiD_mean_frag_len", "art_SOLiD_std_dev", "out_dir"]
        },
        "ARTSOLiDPairedEnd": {
            "req": ["art_SOLiD_path", "art_SOLiD_options", "art_SOLiD_len_read_F3", "art_SOLiD_len_read_F5", "art_SOLiD_fold_coverage", "art_SOLiD_mean_frag_len", "art_SOLiD_std_dev", "out_dir"]
        },
        "ARTSOLiDSingleEnd": {
            "req": ["art_SOLiD_path", "art_SOLiD_options", "art_SOLiD_len_read", "art_SOLiD_fold_coverage", "out_dir"]
        },

        "DWGSIM": {
            "req": ["dwgsim_path", "dwgsim_options", "out_dir"]
        },

        "GrinderSanger": {
            "req": ["grinder_path", "out_dir"]
        },

        "NoSeqs": {
            "req": []
        },

        "Perfect": {
            "req": ["out_dir"]
        }
    },

    "SourceSample": {
        "PANGEA": {
            "req": ["Rscript_path", "pangea_yr.start", "pangea_yr.end", "pangea_seed", "pangea_s.INC.recent", "pangea_s.INC.recent.len", "pangea_s.PREV.min", "pangea_s.PREV.max", "pangea_s.PREV.base", "pangea_s.INTERVENTION.start", "pangea_s.INTERVENTION.mul", "pangea_s.ARCHIVAL.n", "pangea_s.MODEL", "pangea_s.PREV.max.n", "pangea_s.INTERVENTION.prop", "pangea_epi.model", "pangea_epi.acute", "pangea_epi.intervention", "pangea_epi.dt", "pangea_epi.import", "pangea_root.edge.fixed", "pangea_v.N0tau", "pangea_v.r", "pangea_v.T50", "pangea_wher.mu", "pangea_wher.sigma", "pangea_bwerm.mu", "pangea_bwerm.sigma", "pangea_er.gamma", "pangea_er.gtr", "pangea_sp.prop.of.sexactive", "pangea_report.prop.recent", "pangea_dbg.GTRparam", "pangea_dbg.rER", "pangea_index.starttime.mode", "pangea_startseq.mode", "pangea_seqtime.mode"],

            "dep": ["ContactNetwork_PANGEA", "ContactNetworkGenerator_PANGEA", "EndCriteria_Instant", "NodeEvolution_PANGEA", "NodeSample_PANGEA", "NumBranchSample_All", "NumTimeSample_PANGEA", "SeedSelection_PANGEA", "SeedSequence_PANGEA", "SequenceEvolution_PANGEA", "SourceSample_PANGEA", "TimeSample_PANGEA", "TransmissionNodeSample_PANGEA", "TransmissionTimeSample_PANGEA", "TreeUnit_Same"]
        },

        "Random": {
            "req": []
        }
    },

    "TimeSample": {
        "End": {
            "req": [],

            "dep": ["NumTimeSample_Once"]
        },

        "File": {
            "req": ["sample_time_file"],

            "dep": ["NumTimeSample_File"]
        },

        "Gamma": {
            "req": ["ts_gamma_shape", "ts_gamma_scale"]
        },

        "GranichFirstART": {
            "req": [],

            "dep": ["NumTimeSample_Once", "TransmissionTimeSample_HIVARTGranichGEMF"]
        },

        "Infection": {
            "req": [],

            "dep": ["NumTimeSample_Once"]
        },

        "None": {
            "req": [],

            "dep": ["NodeAvailability_None", "NumTimeSample_None"]
        },

        "PANGEA": {
            "req": ["Rscript_path", "pangea_yr.start", "pangea_yr.end", "pangea_seed", "pangea_s.INC.recent", "pangea_s.INC.recent.len", "pangea_s.PREV.min", "pangea_s.PREV.max", "pangea_s.PREV.base", "pangea_s.INTERVENTION.start", "pangea_s.INTERVENTION.mul", "pangea_s.ARCHIVAL.n", "pangea_s.MODEL", "pangea_s.PREV.max.n", "pangea_s.INTERVENTION.prop", "pangea_epi.model", "pangea_epi.acute", "pangea_epi.intervention", "pangea_epi.dt", "pangea_epi.import", "pangea_root.edge.fixed", "pangea_v.N0tau", "pangea_v.r", "pangea_v.T50", "pangea_wher.mu", "pangea_wher.sigma", "pangea_bwerm.mu", "pangea_bwerm.sigma", "pangea_er.gamma", "pangea_er.gtr", "pangea_sp.prop.of.sexactive", "pangea_report.prop.recent", "pangea_dbg.GTRparam", "pangea_dbg.rER", "pangea_index.starttime.mode", "pangea_startseq.mode", "pangea_seqtime.mode"],

            "dep": ["ContactNetwork_PANGEA", "ContactNetworkGenerator_PANGEA", "EndCriteria_Instant", "NodeEvolution_PANGEA", "NodeSample_PANGEA", "NumBranchSample_All", "NumTimeSample_PANGEA", "SeedSelection_PANGEA", "SeedSequence_PANGEA", "SequenceEvolution_PANGEA", "SourceSample_PANGEA", "TimeSample_PANGEA", "TransmissionNodeSample_PANGEA", "TransmissionTimeSample_PANGEA", "TreeUnit_Same"]
        },

        "SAAPPHIIREFirstAscertain": {
            "req": [],

            "dep": ["NumTimeSample_Once", "TransmissionTimeSample_SAAPPHIIREGEMF", "TransmissionTimeSample_SAPHIREGEMF"]
        },

        "TruncatedNormal": {
            "req": ["ts_truncnorm_loc", "ts_truncnorm_scale"]
        },

        "TruncatedExponential": {
            "req": []
        },

        "Uniform": {
            "req": []
        }
    },

    "TransmissionNodeSample": {
        "EpiModel": {
            "req": ["Rscript_path", "epimodel_save_session", "epimodel_type", "num_cn_nodes", "epimodel_attributes", "epimodel_nsteps", "num_init_infected", "num_init_recovered", "recovery_rate", "transmission_probability", "act_rate", "average_edge_duration", "epimodel_formation_line", "epimodel_target_stats_line"],

            "dep": ["ContactNetworkGenerator_EpiModel", "EndCriteria_EpiModel", "SeedSelection_EpiModel", "TransmissionNodeSample_EpiModel", "TransmissionTimeSample_EpiModel"]
        },

        "GEMF": {
            "req": ["gemf_path"],

            "dep": ["EndCriteria_GEMF", "TransmissionTimeSample_GonorrheaHethcoteYorkeGEMF", "TransmissionTimeSample_HIVARTGranichGEMF", "TransmissionTimeSample_HIVPopARTGEMF", "TransmissionTimeSample_SAISGEMF", "TransmissionTimeSample_SAAPPHIIREGEMF", "TransmissionTimeSample_SEIRGEMF", "TransmissionTimeSample_SIGEMF", "TransmissionTimeSample_SIRGEMF", "TransmissionTimeSample_SISGEMF", "TransmissionTimeSample_SVITRGEMF"]
        },

        "RandomMultiInfection": {
            "req": []
        },

        "RandomSingleInfection": {
            "req": []
        },

        "PANGEA": {
            "req": ["Rscript_path", "pangea_yr.start", "pangea_yr.end", "pangea_seed", "pangea_s.INC.recent", "pangea_s.INC.recent.len", "pangea_s.PREV.min", "pangea_s.PREV.max", "pangea_s.PREV.base", "pangea_s.INTERVENTION.start", "pangea_s.INTERVENTION.mul", "pangea_s.ARCHIVAL.n", "pangea_s.MODEL", "pangea_s.PREV.max.n", "pangea_s.INTERVENTION.prop", "pangea_epi.model", "pangea_epi.acute", "pangea_epi.intervention", "pangea_epi.dt", "pangea_epi.import", "pangea_root.edge.fixed", "pangea_v.N0tau", "pangea_v.r", "pangea_v.T50", "pangea_wher.mu", "pangea_wher.sigma", "pangea_bwerm.mu", "pangea_bwerm.sigma", "pangea_er.gamma", "pangea_er.gtr", "pangea_sp.prop.of.sexactive", "pangea_report.prop.recent", "pangea_dbg.GTRparam", "pangea_dbg.rER", "pangea_index.starttime.mode", "pangea_startseq.mode", "pangea_seqtime.mode"],

            "dep": ["ContactNetwork_PANGEA", "ContactNetworkGenerator_PANGEA", "EndCriteria_Instant", "NodeEvolution_PANGEA", "NodeSample_PANGEA", "NumBranchSample_All", "NumTimeSample_PANGEA", "SeedSelection_PANGEA", "SeedSequence_PANGEA", "SequenceEvolution_PANGEA", "SourceSample_PANGEA", "TimeSample_PANGEA", "TransmissionNodeSample_PANGEA", "TransmissionTimeSample_PANGEA", "TreeUnit_Same"]
        },

        "PangeaSim": {
            "req": [],

            "dep": ["ContactNetworkGenerator_PangeaSim", "EndCriteria_PangeaSim", "SeedSelection_PangeaSim", "TransmissionTimeSample_PangeaSim"]
        },

        "SI": {
            "req": ["infection_rate"],

            "dep": ["TransmissionTimeSample_SI"]
        },

        "TransmissionFile": {
            "req": ["transmission_network_file"],

            "dep": ["EndCriteria_TransmissionFile", "SeedSelection_TransmissionFile", "TransmissionTimeSample_TransmissionFile"]
        }
    },

    "TransmissionTimeSample": {
        "EpiModel": {
            "req": ["Rscript_path", "epimodel_save_session", "epimodel_type", "num_cn_nodes", "epimodel_attributes", "epimodel_nsteps", "num_init_infected", "num_init_recovered", "recovery_rate", "transmission_probability", "act_rate", "average_edge_duration", "epimodel_formation_line", "epimodel_target_stats_line"],

            "dep": ["ContactNetworkGenerator_EpiModel", "EndCriteria_EpiModel", "SeedSelection_EpiModel", "TransmissionNodeSample_EpiModel", "TransmissionTimeSample_EpiModel"]
        },

        "Exponential": {
            "req": ["time_sample_rate"]
        },

        "Fixed": {
            "req": ["fixed_transmission_time_delta"]
        },

        "GonorrheaHethcoteYorkeGEMF": {
            "req": ["gemf_path", "end_time", "gon_ma_to_ms", "gon_ms_to_ma", "gon_ms_to_mis_seed", "gon_ms_to_mis_by_mis", "gon_ms_to_mis_by_mia", "gon_ms_to_mis_by_fis", "gon_ms_to_mis_by_fia", "gon_ms_to_mia_seed", "gon_ms_to_mia_by_mis", "gon_ms_to_mia_by_mia", "gon_ms_to_mia_by_fis", "gon_ms_to_mia_by_fia", "gon_mis_to_ma", "gon_mis_to_ms", "gon_mia_to_ma", "gon_mia_to_ms", "gon_fa_to_fs", "gon_fs_to_fa", "gon_fs_to_fis_seed", "gon_fs_to_fis_by_mis", "gon_fs_to_fis_by_mia", "gon_fs_to_fis_by_fis", "gon_fs_to_fis_by_fia", "gon_fs_to_fia_seed", "gon_fs_to_fia_by_mis", "gon_fs_to_fia_by_mia", "gon_fs_to_fia_by_fis", "gon_fs_to_fia_by_fia", "gon_fis_to_fa", "gon_fis_to_fs", "gon_fia_to_fa", "gon_fia_to_fs"],

            "dep": ["EndCriteria_GEMF", "TransmissionNodeSample_GEMF"]
        },

        "HIVARTGranichGEMF": {
            "req": ["gemf_path", "end_time", "hiv_freq_ns", "hiv_freq_s", "hiv_freq_i1", "hiv_freq_i2", "hiv_freq_i3", "hiv_freq_i4", "hiv_freq_a1", "hiv_freq_a2", "hiv_freq_a3", "hiv_freq_a4", "hiv_freq_d", "hiv_ns_to_s", "hiv_ns_to_d", "hiv_s_to_i1_seed", "hiv_s_to_i1_by_i1", "hiv_s_to_i1_by_i2", "hiv_s_to_i1_by_i3", "hiv_s_to_i1_by_i4", "hiv_s_to_i1_by_a1", "hiv_s_to_i1_by_a2", "hiv_s_to_i1_by_a3", "hiv_s_to_i1_by_a4","hiv_s_to_d", "hiv_i1_to_i2", "hiv_i1_to_a1", "hiv_i1_to_d", "hiv_i2_to_i3", "hiv_i2_to_a2", "hiv_i2_to_d", "hiv_i3_to_i4", "hiv_i3_to_a3", "hiv_i3_to_d", "hiv_i4_to_a4", "hiv_i4_to_d", "hiv_a1_to_i1", "hiv_a1_to_a2", "hiv_a1_to_d", "hiv_a2_to_i2", "hiv_a2_to_a3", "hiv_a2_to_d", "hiv_a3_to_i3", "hiv_a3_to_a4", "hiv_a3_to_d", "hiv_a4_to_i4", "hiv_a4_to_d"],

            "dep": ["EndCriteria_GEMF", "TransmissionNodeSample_GEMF"]
        },

        "HIVPopARTGEMF": {
            "req": ["gemf_path", "end_time", "hiv_msu_to_mspc", "hiv_msu_to_mia_by_miah", "hiv_msu_to_mia_by_mia", "hiv_msu_to_mia_by_mi1", "hiv_msu_to_mia_by_mi2", "hiv_msu_to_mia_by_mi3", "hiv_msu_to_mia_by_mi4", "hiv_msu_to_mia_by_mj1", "hiv_msu_to_mia_by_mj2", "hiv_msu_to_mia_by_mj3", "hiv_msu_to_mia_by_mj4", "hiv_msu_to_mia_by_mt1", "hiv_msu_to_mia_by_mt2", "hiv_msu_to_mia_by_mt3", "hiv_msu_to_mia_by_mt4", "hiv_msu_to_mia_by_ma1", "hiv_msu_to_mia_by_ma2", "hiv_msu_to_mia_by_ma3", "hiv_msu_to_mia_by_ma4", "hiv_msu_to_mia_by_fia", "hiv_msu_to_mia_by_fi1", "hiv_msu_to_mia_by_fi2", "hiv_msu_to_mia_by_fi3", "hiv_msu_to_mia_by_fi4", "hiv_msu_to_mia_by_fj1", "hiv_msu_to_mia_by_fj2", "hiv_msu_to_mia_by_fj3", "hiv_msu_to_mia_by_fj4", "hiv_msu_to_mia_by_ft1", "hiv_msu_to_mia_by_ft2", "hiv_msu_to_mia_by_ft3", "hiv_msu_to_mia_by_ft4", "hiv_msu_to_mia_by_fa1", "hiv_msu_to_mia_by_fa2", "hiv_msu_to_mia_by_fa3", "hiv_msu_to_mia_by_fa4", "hiv_msu_to_d", "hiv_mspc_to_msch", "hiv_mspc_to_mia_by_miah", "hiv_mspc_to_mia_by_mia", "hiv_mspc_to_mia_by_mi1", "hiv_mspc_to_mia_by_mi2", "hiv_mspc_to_mia_by_mi3", "hiv_mspc_to_mia_by_mi4", "hiv_mspc_to_mia_by_mj1", "hiv_mspc_to_mia_by_mj2", "hiv_mspc_to_mia_by_mj3", "hiv_mspc_to_mia_by_mj4", "hiv_mspc_to_mia_by_mt1", "hiv_mspc_to_mia_by_mt2", "hiv_mspc_to_mia_by_mt3", "hiv_mspc_to_mia_by_mt4", "hiv_mspc_to_mia_by_ma1", "hiv_mspc_to_mia_by_ma2", "hiv_mspc_to_mia_by_ma3", "hiv_mspc_to_mia_by_ma4", "hiv_mspc_to_mia_by_fia", "hiv_mspc_to_mia_by_fi1", "hiv_mspc_to_mia_by_fi2", "hiv_mspc_to_mia_by_fi3", "hiv_mspc_to_mia_by_fi4", "hiv_mspc_to_mia_by_fj1", "hiv_mspc_to_mia_by_fj2", "hiv_mspc_to_mia_by_fj3", "hiv_mspc_to_mia_by_fj4", "hiv_mspc_to_mia_by_ft1", "hiv_mspc_to_mia_by_ft2", "hiv_mspc_to_mia_by_ft3", "hiv_mspc_to_mia_by_ft4", "hiv_mspc_to_mia_by_fa1", "hiv_mspc_to_mia_by_fa2", "hiv_mspc_to_mia_by_fa3", "hiv_mspc_to_mia_by_fa4", "hiv_mspc_to_d", "hiv_msch_to_msc", "hiv_msch_to_miah_by_miah", "hiv_msch_to_miah_by_mia", "hiv_msch_to_miah_by_mi1", "hiv_msch_to_miah_by_mi2", "hiv_msch_to_miah_by_mi3", "hiv_msch_to_miah_by_mi4", "hiv_msch_to_miah_by_mj1", "hiv_msch_to_miah_by_mj2", "hiv_msch_to_miah_by_mj3", "hiv_msch_to_miah_by_mj4", "hiv_msch_to_miah_by_mt1", "hiv_msch_to_miah_by_mt2", "hiv_msch_to_miah_by_mt3", "hiv_msch_to_miah_by_mt4", "hiv_msch_to_miah_by_ma1", "hiv_msch_to_miah_by_ma2", "hiv_msch_to_miah_by_ma3", "hiv_msch_to_miah_by_ma4", "hiv_msch_to_miah_by_fia", "hiv_msch_to_miah_by_fi1", "hiv_msch_to_miah_by_fi2", "hiv_msch_to_miah_by_fi3", "hiv_msch_to_miah_by_fi4", "hiv_msch_to_miah_by_fj1", "hiv_msch_to_miah_by_fj2", "hiv_msch_to_miah_by_fj3", "hiv_msch_to_miah_by_fj4", "hiv_msch_to_miah_by_ft1", "hiv_msch_to_miah_by_ft2", "hiv_msch_to_miah_by_ft3", "hiv_msch_to_miah_by_ft4", "hiv_msch_to_miah_by_fa1", "hiv_msch_to_miah_by_fa2", "hiv_msch_to_miah_by_fa3", "hiv_msch_to_miah_by_fa4", "hiv_msch_to_d", "hiv_msc_to_mia_by_miah", "hiv_msc_to_mia_by_mia", "hiv_msc_to_mia_by_mi1", "hiv_msc_to_mia_by_mi2", "hiv_msc_to_mia_by_mi3", "hiv_msc_to_mia_by_mi4", "hiv_msc_to_mia_by_mj1", "hiv_msc_to_mia_by_mj2", "hiv_msc_to_mia_by_mj3", "hiv_msc_to_mia_by_mj4", "hiv_msc_to_mia_by_mt1", "hiv_msc_to_mia_by_mt2", "hiv_msc_to_mia_by_mt3", "hiv_msc_to_mia_by_mt4", "hiv_msc_to_mia_by_ma1", "hiv_msc_to_mia_by_ma2", "hiv_msc_to_mia_by_ma3", "hiv_msc_to_mia_by_ma4", "hiv_msc_to_mia_by_fia", "hiv_msc_to_mia_by_fi1", "hiv_msc_to_mia_by_fi2", "hiv_msc_to_mia_by_fi3", "hiv_msc_to_mia_by_fi4", "hiv_msc_to_mia_by_fj1", "hiv_msc_to_mia_by_fj2", "hiv_msc_to_mia_by_fj3", "hiv_msc_to_mia_by_fj4", "hiv_msc_to_mia_by_ft1", "hiv_msc_to_mia_by_ft2", "hiv_msc_to_mia_by_ft3", "hiv_msc_to_mia_by_ft4", "hiv_msc_to_mia_by_fa1", "hiv_msc_to_mia_by_fa2", "hiv_msc_to_mia_by_fa3", "hiv_msc_to_mia_by_fa4", "hiv_msc_to_d", "hiv_miah_to_mia", "hiv_miah_to_d", "hiv_mia_to_mi1", "hiv_mia_to_mi2", "hiv_mia_to_mi3", "hiv_mia_to_mi4", "hiv_mia_to_d", "hiv_mi1_to_mi2", "hiv_mi1_to_mj1", "hiv_mi1_to_d", "hiv_mi2_to_mi3", "hiv_mi2_to_mj2", "hiv_mi2_to_d", "hiv_mi3_to_mi4", "hiv_mi3_to_mj3", "hiv_mi3_to_d", "hiv_mi4_to_mj4", "hiv_mi4_to_d", "hiv_mj1_to_mj2", "hiv_mj1_to_mt1", "hiv_mj1_to_d", "hiv_mj2_to_mj3", "hiv_mj2_to_mt2", "hiv_mj2_to_d", "hiv_mj3_to_mj4", "hiv_mj3_to_mt3", "hiv_mj3_to_d", "hiv_mj4_to_mt4", "hiv_mj4_to_d", "hiv_mt1_to_mi1", "hiv_mt1_to_mt2", "hiv_mt1_to_ma1", "hiv_mt1_to_d", "hiv_mt2_to_mi2", "hiv_mt2_to_mt3", "hiv_mt2_to_ma2", "hiv_mt2_to_d", "hiv_mt3_to_mi3", "hiv_mt3_to_mt4", "hiv_mt3_to_ma3", "hiv_mt3_to_d", "hiv_mt4_to_mi4", "hiv_mt4_to_ma4", "hiv_mt4_to_d", "hiv_ma1_to_mi1", "hiv_ma1_to_ma2", "hiv_ma1_to_d", "hiv_ma2_to_mi2", "hiv_ma2_to_ma3", "hiv_ma2_to_d", "hiv_ma3_to_mi3", "hiv_ma3_to_ma4", "hiv_ma3_to_d", "hiv_ma4_to_mi4", "hiv_ma4_to_d", "hiv_fs_to_fia_by_miah", "hiv_fs_to_fia_by_mia", "hiv_fs_to_fia_by_mi1", "hiv_fs_to_fia_by_mi2", "hiv_fs_to_fia_by_mi3", "hiv_fs_to_fia_by_mi4", "hiv_fs_to_fia_by_mj1", "hiv_fs_to_fia_by_mj2", "hiv_fs_to_fia_by_mj3", "hiv_fs_to_fia_by_mj4", "hiv_fs_to_fia_by_mt1", "hiv_fs_to_fia_by_mt2", "hiv_fs_to_fia_by_mt3", "hiv_fs_to_fia_by_mt4", "hiv_fs_to_fia_by_ma1", "hiv_fs_to_fia_by_ma2", "hiv_fs_to_fia_by_ma3", "hiv_fs_to_fia_by_ma4", "hiv_fs_to_fia_by_fia", "hiv_fs_to_fia_by_fi1", "hiv_fs_to_fia_by_fi2", "hiv_fs_to_fia_by_fi3", "hiv_fs_to_fia_by_fi4", "hiv_fs_to_fia_by_fj1", "hiv_fs_to_fia_by_fj2", "hiv_fs_to_fia_by_fj3", "hiv_fs_to_fia_by_fj4", "hiv_fs_to_fia_by_ft1", "hiv_fs_to_fia_by_ft2", "hiv_fs_to_fia_by_ft3", "hiv_fs_to_fia_by_ft4", "hiv_fs_to_fia_by_fa1", "hiv_fs_to_fia_by_fa2", "hiv_fs_to_fia_by_fa3", "hiv_fs_to_fia_by_fa4", "hiv_fs_to_d", "hiv_fia_to_fi1", "hiv_fia_to_fi2", "hiv_fia_to_fi3", "hiv_fia_to_fi4", "hiv_fia_to_d", "hiv_fi1_to_fi2", "hiv_fi1_to_fj1", "hiv_fi1_to_d", "hiv_fi2_to_fi3", "hiv_fi2_to_fj2", "hiv_fi2_to_d", "hiv_fi3_to_fi4", "hiv_fi3_to_fj3", "hiv_fi3_to_d", "hiv_fi4_to_fj4", "hiv_fi4_to_d", "hiv_fj1_to_fj2", "hiv_fj1_to_ft1", "hiv_fj1_to_d", "hiv_fj2_to_fj3", "hiv_fj2_to_ft2", "hiv_fj2_to_d", "hiv_fj3_to_fj4", "hiv_fj3_to_ft3", "hiv_fj3_to_d", "hiv_fj4_to_ft4", "hiv_fj4_to_d", "hiv_ft1_to_fi1", "hiv_ft1_to_ft2", "hiv_ft1_to_fa1", "hiv_ft1_to_d", "hiv_ft2_to_fi2", "hiv_ft2_to_ft3", "hiv_ft2_to_fa2", "hiv_ft2_to_d", "hiv_ft3_to_fi3", "hiv_ft3_to_ft4", "hiv_ft3_to_fa3", "hiv_ft3_to_d", "hiv_ft4_to_fi4", "hiv_ft4_to_fa4", "hiv_ft4_to_d", "hiv_fa1_to_fi1", "hiv_fa1_to_fa2", "hiv_fa1_to_d", "hiv_fa2_to_fi2", "hiv_fa2_to_fa3", "hiv_fa2_to_d", "hiv_fa3_to_fi3", "hiv_fa3_to_fa4", "hiv_fa3_to_d", "hiv_fa4_to_fi4", "hiv_fa4_to_d"],

            "dep": ["EndCriteria_GEMF", "TransmissionNodeSample_GEMF"]
        },

        "Instant": {
            "req": []
        },

        "PANGEA": {
            "req": ["Rscript_path", "pangea_yr.start", "pangea_yr.end", "pangea_seed", "pangea_s.INC.recent", "pangea_s.INC.recent.len", "pangea_s.PREV.min", "pangea_s.PREV.max", "pangea_s.PREV.base", "pangea_s.INTERVENTION.start", "pangea_s.INTERVENTION.mul", "pangea_s.ARCHIVAL.n", "pangea_s.MODEL", "pangea_s.PREV.max.n", "pangea_s.INTERVENTION.prop", "pangea_epi.model", "pangea_epi.acute", "pangea_epi.intervention", "pangea_epi.dt", "pangea_epi.import", "pangea_root.edge.fixed", "pangea_v.N0tau", "pangea_v.r", "pangea_v.T50", "pangea_wher.mu", "pangea_wher.sigma", "pangea_bwerm.mu", "pangea_bwerm.sigma", "pangea_er.gamma", "pangea_er.gtr", "pangea_sp.prop.of.sexactive", "pangea_report.prop.recent", "pangea_dbg.GTRparam", "pangea_dbg.rER", "pangea_index.starttime.mode", "pangea_startseq.mode", "pangea_seqtime.mode"],

            "dep": ["ContactNetwork_PANGEA", "ContactNetworkGenerator_PANGEA", "EndCriteria_Instant", "NodeEvolution_PANGEA", "NodeSample_PANGEA", "NumBranchSample_All", "NumTimeSample_PANGEA", "SeedSelection_PANGEA", "SeedSequence_PANGEA", "SequenceEvolution_PANGEA", "SourceSample_PANGEA", "TimeSample_PANGEA", "TransmissionNodeSample_PANGEA", "TransmissionTimeSample_PANGEA", "TreeUnit_Same"]
        },

        "PangeaSim": {
            "req": [],

            "dep": ["ContactNetworkGenerator_PangeaSim", "EndCriteria_PangeaSim", "SeedSelection_PangeaSim", "TransmissionNodeSample_PangeaSim"]
        },

        "SAISGEMF": {
            "req": ["gemf_path", "end_time", "sais_beta_seed", "sais_beta_by_i", "sais_beta_a_seed", "sais_beta_a_by_i", "sais_kappa", "sais_delta"],

            "dep": ["EndCriteria_GEMF", "TransmissionNodeSample_GEMF"]
        },

        "SAAPPHIIREGEMF": {
            "req": ["gemf_path", "end_time", "saapphiire_freq_s", "saapphiire_freq_e", "saapphiire_freq_p1", "saapphiire_freq_p2", "saapphiire_freq_i1", "saapphiire_freq_i2", "saapphiire_freq_a1", "saapphiire_freq_a2", "saapphiire_freq_h", "saapphiire_freq_r", "saapphiire_s_to_e_seed", "saapphiire_e_to_p1", "saapphiire_p1_to_p2", "saapphiire_p2_to_i1", "saapphiire_p2_to_a1", "saapphiire_i1_to_i2", "saapphiire_i1_to_h", "saapphiire_i2_to_h", "saapphiire_i2_to_r", "saapphiire_a1_to_a2", "saapphiire_a2_to_r", "saapphiire_h_to_r", "saapphiire_s_to_e_by_e", "saapphiire_s_to_e_by_p1", "saapphiire_s_to_e_by_p2", "saapphiire_s_to_e_by_i1", "saapphiire_s_to_e_by_i2", "saapphiire_s_to_e_by_a1", "saapphiire_s_to_e_by_a2"], # TODO FINISH THESE

            "dep": ["EndCriteria_GEMF", "TransmissionNodeSample_GEMF"]
        },

        "SAPHIREGEMF": {
            "req": ["gemf_path", "end_time", "saphire_freq_s", "saphire_freq_e", "saphire_freq_p", "saphire_freq_i", "saphire_freq_a", "saphire_freq_h", "saphire_freq_r", "saphire_s_to_e_seed", "saphire_e_to_p", "saphire_p_to_i", "saphire_p_to_a", "saphire_i_to_h", "saphire_i_to_r", "saphire_a_to_r", "saphire_h_to_r", "saphire_s_to_e_by_e", "saphire_s_to_e_by_p", "saphire_s_to_e_by_i", "saphire_s_to_e_by_a"],

            "dep": ["EndCriteria_GEMF", "TransmissionNodeSample_GEMF"]
        },

        "SEIRGEMF": {
            "req": ["gemf_path", "end_time", "seir_beta_seed", "seir_beta_by_i", "seir_lambda", "seir_delta"],

            "dep": ["EndCriteria_GEMF", "TransmissionNodeSample_GEMF"]
        },

        "SI": {
            "req": ["infection_rate"],

            "dep": ["TransmissionNodeSample_SI"]
        },

        "SIGEMF": {
            "req": ["gemf_path", "end_time", "si_beta_seed", "si_beta_by_i"],

            "dep": ["EndCriteria_GEMF", "TransmissionNodeSample_GEMF"]
        },

        "SIRGEMF": {
            "req": ["gemf_path", "end_time", "sir_beta_seed", "sir_beta_by_i", "sir_delta"],

            "dep": ["EndCriteria_GEMF", "TransmissionNodeSample_GEMF"]
        },

        "SISGEMF": {
            "req": ["gemf_path", "end_time", "sis_beta_seed", "sis_beta_by_i", "sis_delta"],

            "dep": ["EndCriteria_GEMF", "TransmissionNodeSample_GEMF"]
        },

        "SVITRGEMF": {
            "req": ["gemf_path", "end_time", "svitr_beta_seed", "svitr_beta_by_i", "svitr_beta_by_t", "svitr_delta", "svitr_s_to_v", "svitr_i_to_t", "svitr_t_to_r"],

            "dep": ["EndCriteria_GEMF", "TransmissionNodeSample_GEMF"]
        },

        "TransmissionFile": {
            "req": ["transmission_network_file"],

            "dep": ["EndCriteria_TransmissionFile", "SeedSelection_TransmissionFile", "TransmissionNodeSample_TransmissionFile"]
        }
    },

    "TreeNode": {
        "Simple": {
            "req": []
        }
    },

    "TreeUnit": {
        "AutocorrelatedConstantIncrement": {
            "req": ["tree_rate_p", "tree_rate_delta", "tree_rate_R0", "tree_rate_min", "tree_rate_max"]
        },

        "AutocorrelatedExponential": {
            "req": ["tree_rate_R0"]
        },

        "AutocorrelatedGamma": {
            "req": ["tree_rate_v", "tree_rate_R0"]
        },

        "AutocorrelatedLogNormal": {
            "req": ["tree_rate_v", "tree_rate_R0"]
        },

        "Beta": {
            "req": ["tree_rate_a", "tree_rate_b"]
        },

        "ChiSquared": {
            "req": ["tree_rate_df"]
        },

        "ConstantRate": {
            "req": ["tree_mutation_rate"]
        },

        "CoxIngersollRoss": {
            "req": ["tree_rate_a", "tree_rate_b", "tree_rate_sigma", "tree_rate_R0"]
        },

        "Dirichlet": {
            "req": ["tree_rate_alpha"]
        },

        "Exponential": {
            "req": ["tree_rate_scale"]
        },

        "F": {
            "req": ["tree_rate_dfnum", "tree_rate_dfden"]
        },

        "Gamma": {
            "req": ["tree_rate_shape", "tree_rate_scale"]
        },

        "Gumbel": {
            "req": ["tree_rate_loc", "tree_rate_scale"]
        },

        "InverseGaussian": {
            "req": ["tree_rate_mean", "tree_rate_shape"]
        },

        "Logistic": {
            "req": ["tree_rate_loc", "tree_rate_scale"]
        },

        "LogNormal": {
            "req": ["tree_rate_mean", "tree_rate_stdev"]
        },

        "NoncentralChiSquared": {
            "req": ["tree_rate_df", "tree_rate_lambda"]
        },

        "NoncentralF": {
            "req": ["tree_rate_dfnum", "tree_rate_dfden", "tree_rate_lambda"]
        },

        "Normal": {
            "req": ["tree_rate_mean", "tree_rate_stdev"]
        },

        "Pareto": {
            "req": ["tree_rate_shape"]
        },

        "Power": {
            "req": ["tree_rate_shape"]
        },

        "Rayleigh": {
            "req": ["tree_rate_scale"]
        },

        "Same": {
            "req": []
        },

        "Triangular": {
            "req": ["tree_rate_left", "tree_rate_mode", "tree_rate_right"]
        },

        "TruncatedNormal": {
            "req": ["tree_rate_loc", "tree_rate_scale", "tree_rate_min", "tree_rate_max"]
        },

        "Uniform": {
            "req": ["tree_rate_min", "tree_rate_max"]
        },

        "Weibull": {
            "req": ["tree_rate_shape", "tree_rate_scale"]
        }
    }
}