Man pages for jameshay218/virosolver
Infer epidemic dynamics using viral load data
| calculate_gr_ct_relationships | Calculate GR CT relationship for one R0 |
| calculate_gr_ct_relationships_R0s | Calculate GR CT relationship for multiple R0s |
| compare_tsi_dist_at_gr | Compare TSI vs. GR |
| create_posterior_func | Creates the posterior function to be used in the MCMC... |
| create_posterior_func_detectable | Creates the posterior function used in the MCMC framework for... |
| create_post_func_seeirr | Creates the posterior function used in the MCMC framework for... |
| create_post_func_seeirr_combined | Creates the posterior function used in the MCMC framework for... |
| detectable_SEEIRRModel | Detectable SEEIRR model |
| detectable_SEIRModel | Detectable SEIR model |
| example_ct_data | Example Ct value data |
| example_epi_data | Example epidemic data |
| example_gp_partab | Example Gaussian Process prior parameter table |
| example_seir_incidence | True simulated SEIR incidence |
| example_seir_partab | Example SEIR model parameter table |
| exponential_growth_model | Exponential growth model |
| gaussian_process_model | Gaussian process model |
| generate_viable_start_pars | Function to generate random starting parameter values that... |
| likelihood_cpp_wrapper | Wrapper function for the likelihood code, which is written in... |
| likelihood_detectable | Likelihood for using proportion detectable only |
| likelihood_pos_R | Likelihood for using proportion detectable only (R version) |
| likelihood_R | Likelihood (R version) |
| p_a | Function that gives the probability of observing Ct value x... |
| plot_distribution_fits | Plot distribution fits |
| plot_posterior_density | Plot posterior density |
| plot_prob_infection | Plot probability of infection |
| pred_dist_wrapper | This function calculates predicted Ct value densities for... |
| predicted_distribution_fits | Predicted distribution fits |
| prob_detectable_curve | Probability curve of detectable Ct values. |
| prop_detectable | Proportion still detectable (range of times) |
| prop_detectable_single | Proportion still detectable (single time) |
| reverse_gp_model | Reverse Gaussian process model |
| SEEIRRModel | SEEIRR Model |
| simulate_detectable_wrapper | Simulate binary PCR results (detectables) for the line list... |
| simulate_infection_times | Simulate infection times |
| simulate_observations_wrapper | Simulate full line list data |
| simulate_reporting | Simulate reporting |
| simulate_seir_process | Simulate SEIR model |
| simulate_seir_wrapper | Wrapper for SEIR model simulation, deterministic or... |
| simulate_viral_loads | Simulate viral loads |
| simulate_viral_loads_example | This function simulates N Ct values per age in ages and... |
| simulate_viral_loads_example_symptoms | Simulate N Ct values under symptom-based surveillance and... |
| simulate_viral_loads_wrapper | Simulate observed Ct values for the line list dataset |
| solveSEEIRRModel_rlsoda | Solve SEEIRR model with rlsoda |
| solveSEEIRRModel_rlsoda_wrapper | Wrapper function for the solveSEIRRModel_rlsoda code, which... |
| solveSEIRModel_lsoda | Solve SEIR Model with lsoda |
| solveSEIRModel_lsoda_wrapper | Wrapper function for the solveSEIRmodel_lsoda code, which is... |
| solveSEIRModel_rlsoda | Solve SEIR model with rlsoda |
| solveSEIRModel_rlsoda_wrapper | Wrapper function for the solveSEIRmodel_rlsoda code, which is... |
| solveSEIRswitch_rlsoda | Solve SEIR switch model with rlsoda |
| solveSEIRswitch_rlsoda_wrapper | Wrapper function for the solveSEIRswitch_rlsoda code, which... |
| vignette_data1 | Simulated SEIR incidence for vignettes |
| vignette_data2 | Simulated Ct values for vignettes |
| viral_load_func | This function returns modal Ct values or viral load values,... |
