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
General_IntSigmaF Source code
General_KOM_Filter Source code
General_MCMC Source code
General_MCMC2 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
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_Coarse_Slicer Source code
Param_Slice_update 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
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
StateSpace_Like Source code
StateSpace_Period_Like2 Source code
Structural_Coal_lik Source code
TFGY_list 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
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
colik.fgy Source code
colik2cpp Source code
colikcpp_prepare Source code
effpopPlot Source code
effpopfun Source code Source code
expM 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
plot3 Source code
randomR0_traj Source code
randomR0_traj_V Source code
random_effpoptraj_line Source code
random_trajectory Source code
random_trajectory3D Source code
random_trajectory_line Source code
simuSEIR Source code
simuSIR Source code
simuSIRS Source code
sourceAttribMultiDemeCpp Source code
stan_res_convert Source code
stan_res_convert0 Source code
stan_res_convertC0 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
update_ChangePoint_general Source code
update_ChangePoint_general_NC 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
MingweiWilliamTang/LNAphyloDyn documentation built on Dec. 6, 2017, 5:39 a.m.