Exposure-Lag-Response Modeling for Plant Disease Epidemiology
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Documentation for package ‘EpiExposure’ version 0.1.0
Help Pages
| binomial_data | Simulated binomial epidemiological dataset |
| build_design | Build an epidemic-level DLNM design matrix |
| check_identifiability | Diagnose identifiability and numerical stability of DLNM cross-basis designs |
| compare_exposures | Compare chronological exposure profiles |
| compare_periods | Compare period-specific DLNM effects |
| compare_predictions | Compare predicted outcomes between exposure scenarios |
| compute_eci | Compute Exposure Cumulative Impact |
| compute_ecilag | Compute lag-specific decomposition of Exposure Cumulative Impact (ECI) |
| define_exposures | Define DLNM exposure templates |
| define_periods | Define epidemiological lag periods |
| ensemble_bestfit | Create model and lag-contribution ensembles from best-fit DLNM models |
| epi_data | Simulated beta epidemiological dataset |
| epi_sensitivity | Compute sensitivity of exposure-response curves |
| find_bestfit | Find the best DLNM model structure using grouped validation |
| fit_epidlnm | Fit a harmonized DLNM inferential model |
| gamma_data | Simulated gamma epidemiological dataset |
| gaussian_data | Simulated gaussian epidemiological dataset |
| nb2_data | Simulated negative-binomial epidemiological dataset |
| plot_eci | Plot ECI and lag-specific contribution results |
| plot_effects | Plot lag-specific or period-specific effects |
| plot_losses | Plot simulated yield and economic losses |
| plot_performance | Plot out-of-fold model performance |
| plot_scenarios | Plot predictions across epidemiological scenarios |
| poisson_data | Simulated poisson epidemiological dataset |
| predict_outcomes | Predict outcomes from fitted EpiExposure DLNM models |
| prepare_response | Prepare and validate the epidemic-level response for modeling |
| reduce_effects | Reduce a fitted DLNM to a one-dimensional association |
| simulate_exposures | Simulate chronological exposure profiles |
| simulate_losses | Simulate yield and economic losses |
| simulate_ranges | Generate exposure-value scenarios across DLNM lag periods |
| simulate_scenarios | Simulate epidemiological exposure-profile scenarios |
| spatial_replicate | Simulated epidemiological data with independent spatial replicates |
| spatial_year | Simulated epidemiological data with independent spatial fields by year |
| st_poisson | Simulated spatial poisson epidemiological dataset |
| summarise_effects | Summarise DLNM exposure-lag effects on link and response scales |