API for MingweiWilliamTang/LNAphyloDyn
Bayesian inference on coalescent-based phylodynamics using linear noise approximation
| Global functions | |
|---|---|
| CI_Curve | Source code |
| CI_Curve3 | Source code |
| CI_Curve_eff | Source code |
| CI_Curve_eff2 | Source code |
| Convert_R0 | Source code |
| DeathMX | Source code |
| DegenerateDet3 | Source code |
| ESlice | Man page Source code Source code |
| ESlice2 | Source code |
| ESlice2_log | Source code |
| ESlice_SIRS | Source code |
| ESlice_SIR_BD | Source code |
| ESlice_change_points | Source code |
| ESlice_general | Source code |
| ESlice_general2 | Source code |
| ESlice_general_NC | Source code |
| ESlice_general_NC_Structural | Source code |
| ESlice_par | Source code |
| ESlice_par_General | Source code |
| General_IntSigmaF | Source code |
| General_KOM_Filter | Source code |
| General_MCMC | Source code |
| General_MCMC2 | Source code |
| General_MCMC_cont | Source code |
| General_MCMC_with_ESlice | Source code |
| General_ODE_rk45 | Source code |
| Geweke_S1_S2_Traj | Source code |
| Geweke_S1_Traj_lambda | Source code |
| Geweke_S2_Traj | Source code |
| InitializeData | Source code |
| InitializeMCMC | Source code |
| KF_param | Source code |
| KF_param_chol | Source code |
| Like_Free | Man page |
| LogTraj | Source code |
| MCMC_initialize | Man page |
| MCMC_initialize2 | Source code |
| MCMC_initialize_BD | Source code |
| MCMC_initialize_SIRS | Source code |
| MCMC_initialize_general | Source code |
| MCMC_initialize_log | Source code |
| MCMC_initialize_stuctural | Source code |
| MCMC_setup | Source code |
| MCMC_setup_general | Source code |
| MCMC_setup_log | Source code |
| MCMC_setup_standard | Source code |
| MCMC_setup_structural | Source code |
| MigrationMx | Source code |
| NP_plot | Source code |
| New_Param_List | Source code |
| ODE | Source code |
| ODE2 | Source code |
| ODE_SEIR_one | Source code |
| ODE_SIRS_one | Source code |
| ODE_SIR_one | Source code |
| ODE_general_one | Source code |
| ODE_rk45 | Source code |
| ODE_rk45_stop | Source code |
| Ode_Coarse_Slicer | Source code |
| Param_Slice_update | Source code |
| Param_Slice_update_all | Source code |
| Param_Slice_update_all2 | Source code |
| Prevalence_Stan_Initialize | Source code |
| Prevalence_Stan_data | Source code |
| PseudoInverse | Source code |
| SEIR2_F | Source code |
| SEIR2_h | Source code |
| SEIR_F | Source code |
| SEIR_general_MCMC_Structural | Source code |
| SEIR_h | Source code |
| SEIR_simu_tree | Source code |
| SIRS2_period_SDE | Source code |
| SIRS_F | Source code |
| SIRS_IntSigma | Source code |
| SIRS_KOM_Filter | Source code |
| SIRS_LNA_MCMC_standard | Source code |
| SIRS_ODE | Source code |
| SIR_BD_Fm_LNA | Source code |
| SIR_BD_IntSigma | Source code |
| SIR_BD_KOM_Filter | Source code |
| SIR_BD_LNA_MCMC | Source code |
| SIR_BD_ODE | Source code |
| SIR_BD_PMCMC | Source code |
| SIR_BD_SDE | Source code |
| SIR_BD_SMC | Source code |
| SIR_BD_period_ODE_one | Source code |
| SIR_BD_period_ODE_one2 | Source code |
| SIR_BD_period_SDE | Source code |
| SIR_F | Source code |
| SIR_LNA_ESlice_MCMC | Man page Source code |
| SIR_LNA_ESlice_MCMC2 | Man page Source code |
| SIR_LNA_ESlice_MCMC4 | Man page |
| SIR_LNA_MCMC_log | Source code |
| SIR_LNA_MCMC_standard | Source code |
| SIR_ODE | Source code |
| SIR_ODE2 | Source code |
| SIR_h | Source code |
| SIR_log_KOM_Filter2 | Source code |
| SI_traj_initialize_stan | Source code |
| SI_traj_initialize_stan2 | Source code |
| SampleWithReplace | Source code |
| SigmaF | Source code |
| SigmaFirst2 | Source code |
| StateSpace_Like | Source code |
| StateSpace_Period_Like2 | Source code |
| Structural_Coal_lik | Source code |
| TFGY_list | Source code |
| TFGY_list2 | Source code |
| Traj_sim | Source code |
| Traj_sim_SIRS | Source code |
| Traj_sim_SIRS_ez | Source code |
| Traj_sim_SIR_BD | Source code |
| Traj_sim_SIR_BD_ez | Source code |
| Traj_sim_ez | Source code |
| Traj_sim_ezG | Source code |
| Traj_sim_ezG2 | Source code |
| Traj_sim_ezG_NC | Source code |
| Traj_sim_general | Source code |
| Traj_sim_general3 | Source code |
| Traj_sim_general_noncentral | Source code |
| TransformTraj | Source code |
| TruncTree_Fun | Source code |
| Update_Param | Source code |
| Update_Param_each | Source code |
| Update_Param_each_Norm | Source code |
| as.DatePhylo | Source code |
| betaDyn | Source code |
| betaTs | Source code |
| betaf | Source code |
| betafs | Source code |
| birthMx | Source code |
| branching_sampling_times2 | Source code |
| check_list_eq | Source code |
| chols | Source code |
| coal_init_stan | Source code |
| coal_init_stan_changepoint | Source code |
| coal_lik_init | Source code Source code |
| coal_like_fast | Source code |
| coal_loglik | Source code |
| coal_loglik2 | Source code |
| coal_loglik3 | Source code |
| coal_loglik_hom | Source code |
| coalsim_thin_sir | Source code |
| coalsim_thin_sir_Hom | Source code |
| colik2cpp | Source code |
| covtocor | Source code |
| effpopPlot | Source code |
| effpopfun | Source code Source code |
| expM | Source code |
| forwardSimulateODE_RST_core | Source code |
| general_F | Source code |
| histwithCI | Source code |
| inv2 | Source code |
| log_like_traj | Source code |
| log_like_traj2 | Source code |
| log_like_trajSIRS | Source code |
| log_like_trajSIR_BD | Source code |
| log_like_traj_general | Source code |
| log_like_traj_general2 | Source code |
| log_like_traj_general_adjust | Source code |
| log_like_traj_general_ez | Source code |
| medianCur | Source code |
| mvrnormArma | Source code |
| mvrnormArma2 | Source code |
| para_init_stan | Source code |
| para_init_stan_changepoint | Source code |
| para_init_stan_changepoint2 | Source code |
| param_transform | Source code |
| partocov | Source code |
| plot3 | Source code |
| prob_Eval | Source code |
| randomR0_traj | Source code |
| randomR0_traj_V | Source code |
| randomR0s | Source code |
| random_effpoptraj_line | Source code |
| random_trajectory | Source code |
| random_trajectory3D | Source code |
| random_trajectory_line | Source code |
| simuSEIR | Source code |
| simuSEIRt | Source code |
| simuSIR | Source code |
| simuSIRS | Source code |
| simuSIRt | Source code |
| sourceAttribMultiDemeCpp | Source code |
| stan_res_convert | Source code |
| stan_res_convert0 | Source code |
| stan_res_convertC0 | Source code |
| tauDist | Source code |
| updateAlphas | Source code |
| updateAlphas_BD | Source code |
| updateAlphas_General | Source code |
| updateAlphas_SIRS | Source code |
| updateAlphas_log | Source code |
| updateE_general_NC | Source code |
| updateLambda | Source code |
| updateLambdaGeneral | Source code |
| updateLambdaUnifProp | Source code |
| updateLambda_SIRS | Source code |
| updateLambda_SIR_BD | Source code |
| updateR0_general | Source code |
| updateR0_general_NC | Source code |
| updateR0gamma_general | Source code |
| updateR0gamma_general_NC | Source code |
| updateReSus_SIRS | Source code |
| updateReSus_SIR_BD | Source code |
| updateS1 | Source code |
| updateS1S2_SIR_BD | Source code |
| updateS1S2_log | Source code |
| updateS1_SIRS | Source code |
| updateS1_SIR_BD | Source code |
| updateS2 | Source code |
| updateS2_SIRS | Source code |
| updateS2_SIR_BD | Source code |
| updateTraj | Source code Source code |
| updateTraj_BD | Source code |
| updateTraj_general | Source code |
| updateTraj_general_NC | Source code |
| updateTraj_log | Source code |
| update_All_general_NC | Source code |
| update_All_general_NC_Adaptive | Source code |
| update_ChangePoint_ESlice | Source code Source code |
| update_ChangePoint_general | Source code |
| update_ChangePoint_general_NC | Source code |
| update_Par_ESlice | Source code |
| update_Par_ESlice_combine | Source code |
| update_Param_joint | Source code |
| update_Scale_SIRS | Source code |
| update_Scale_SIR_BD | Source code |
| update_hyper | Source code |
| updategamma_general | Source code |
| updategamma_general_NC | Source code |
| vlineCI | Source code |
| volz_loglik | Source code |
| volz_loglik_nh | Source code |
| volz_loglik_nh2 | Source code |
| volz_loglik_nh3 | Source code |
| volz_thin_sir | Source code |
