Man pages for phac-nml-phrsd/wem
Wastewater Epidemic Model
| add_obs_string | helper function |
| broken_line | Piecewise linear function |
| build_data | Create a data object from dataframes. |
| build_data_csv | Create a data object from CSV files. |
| calc.all | Calculate total numbers per epidemiological states by summing... |
| calc_concen | calculate average daily deposited RNA concentration |
| calc_delayed_concen | Estimate RNA/day received at sampling site after decay and... |
| calc_Reff_from_post | Calculate Rt from Posteriors |
| calc_R_from_model | Estimate Effective Reproduction Number |
| calc_WWreport | turnaround time from sampling to result |
| check_prior_name_scalar | Check if prior's name exist |
| define_abc_prms | Define parameters for Appoximate Bayesian Computation (ABC)... |
| define_fit_priors | Prior distributions for fitted model parameters. |
| dot-plottype | Type of Datasource for plotting |
| err_fct | Calculate error for ABC fitting |
| estimate_Rt | Estimate Effective Reproduction Number. |
| fcst | Forecast from a fit object. |
| fcst_from_post | Forecast based on a fitted object. |
| find_col | find_col(ts, comp) finds columns for a specific compartment... |
| fit | Fitting Data to Model |
| fit_abc | Fitting ABC function (internal use) |
| fit_abc_unit | Perform fitting for one iteration |
| fit_recent | Fitting model to recent data only, using existing fit on past... |
| generate_obs_noise | Generate observation noise |
| load_prm | Load all baseline model parameters |
| load_prm_fit | FITTING - Load all baseline parameters |
| model_prm_example | Example of model parameters |
| now_string | Return current date and time with a friendly file name... |
| overwrite_vectors | Find the names that define an overwrite of vector elements... |
| plot_abc_err | Visualize Fitting Errors |
| plot_all | Plot all compartments of the model |
| plot_dashboard_prm | Visualize model parameters |
| plot_epidemic | Plot time series of main epidemiological variables. |
| plot_fcst | Plot forecasts |
| plot_fit_abc_vs_obs | Visualize fitting performance versus obsrvational data |
| plot_fit_result | Visualize Fitting Results and Statistics |
| plot_multvec | Plot Transmission Rate (Beta) |
| plot_obs_simulation | Plot Observational and Simulated Data |
| plot_post_distrib_abc | Visualize posterior distribution |
| plot_Rt | Plot the Effective Reproduction Number |
| plot_simobs_beta | Visualize observational data, simulated epidemic and... |
| post_ss_abc | Estimate statistical values after fiiting |
| prm_scalar_vec | Identify scalar and vector pramaters |
| read_prm_list | Read parameters from a dataframe and convert into a list |
| remove.fut.inference | Remove future reference im parameters. |
| report_cases | Reporting of clinical cases |
| run_from_posteriors | Run Simulation from Porsterios |
| sample_priors | Randomly sample from priors for fitting process |
| seir | SEIR compartmental model with 'nI' I, 'nIH' IH, 'nA' A, 'nH'... |
| simul | Simulate an epidemic |
| simul_from_post | Simulate epidemic from posterior distributions. |
| step_line | Step line function. |
| unpack_data | Helper function |
