Man pages for c97sr/learnidd
A collection of functions useful for the study of infectious disease dynamics
| adm.apply.seed | Assumes the existance of farmdf in an enclosing environment |
| adm.load.sheep.prep.sim | sets up data set for simulation |
| adm.plot.farm.and.seeds | Function to plot farms randomly near to the coast |
| adm.plot.gen | Function to plot the generations of the simulation |
| adm.seed.sheep | Function to see farms randomly near to the coast |
| adm.setup.aux.mat | creates distance matrix |
| adm.sheep.params | Function to setup a parameter object for the smv simulations |
| augment_data | function to augment data |
| calc_log_likelihood | calculate log likelihood of data given model prediction... |
| calc_prediction_accuracy | calculate proportion of prediction points which are within... |
| calculateLogLikCluster_incubation | calculate the contribution of a cluster to the log... |
| calculateLogLikCluster_transmission | calculate the contribution of a cluster to the log... |
| calculateLogLik_incubation | calculate log likelihood for the model of incubation only,... |
| comp_seir | Solves the SEIR model |
| DA_condition | function to decide whether data should be augmented for a... |
| extract_incidence | extracts the incidence data for a given country and year |
| extract_predicted_points | extract predicted points from linear regression object |
| extract_predicted_points_seir | extract predicted points for SEIR model |
| extract_subset_prediction | extract subset of prediction data frame containing... |
| extract_week_index | extract index of week number from week names |
| f.incub | calculate the probability density for a given incubation... |
| fit_seir | fit the SEIR model to data |
| h | calculate the cumulative hazard of infection at time t |
| H | calculate the cumulative hazard of infection at time t |
| likelihood_profile_seir | construct a likelihood profile for R_0 given data |
| linear_regression | performs linear regression for a given country and year |
| logRatioProposal_DA | function to return the log ratio of the proposal distribution... |
| plot_incidence | plots the incidence |
| plot_incidence_all | plots the incidence for a given country (all years) |
| plot_likelihood_profile | plot a likelihood profile for R_0 given data |
| run_MCMC | run MCMC algorithm to fit parameters to data |
| run_MCMC_DA | run MCMC with data augmentation to fit parameters to data |
| S | calculate the probability of having survived infection at... |
| solve_seir_model | solve SEIR model for incidence |
| solve_seir_wrapper | solve SEIR model for incidence, specifying default parameters... |
| subset_incidence_data | subset incidence data for weeks of interest |
