Package: REffectivePred 1.0.1
REffectivePred: Pandemic Prediction Model in an SIRS Framework
A suite of methods to fit and predict case count data using a compartmental SIRS (Susceptible – Infectious – Recovered – Susceptible) model, based on an assumed specification of the effective reproduction number. The significance of this approach is that it relates epidemic progression to the average number of contacts of infected individuals, which decays as a function of the total susceptible fraction remaining in the population. The main functions are pred.curve(), which computes the epidemic curve for a set of parameters, and estimate.mle(), which finds the best fitting curve to observed data. The easiest way to pass arguments to the functions is via a config file, which contains input settings required for prediction, and the package offers two methods, navigate_to_config() which points the user to the configuration file, and re_predict() for starting the fit-predict process. The main model was published in Razvan G. Romanescu et al. <doi:10.1016/j.epidem.2023.100708>.
Authors:
REffectivePred_1.0.1.tar.gz
REffectivePred_1.0.1.tar.gz(r-4.5-noble)REffectivePred_1.0.1.tar.gz(r-4.4-noble)
REffectivePred_1.0.1.tgz(r-4.4-emscripten)REffectivePred_1.0.1.tgz(r-4.3-emscripten)
REffectivePred.pdf |REffectivePred.html✨
REffectivePred/json (API)
# Install 'REffectivePred' in R: |
install.packages('REffectivePred', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 11 days agofrom:3fa466aeb3. Checks:OK: 2. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Nov 13 2024 |
R-4.5-linux | OK | Nov 13 2024 |
Exports:c_helperci.curveestimate.mlefind_endsfind_startsload_configlog_lklhnavigate_to_configplot_outputspred.curveranges_to_wavesre_predictrt_empiricalwaves_1d_list
Readme and manuals
Help Manual
Help page | Topics |
---|---|
Contact rate function. | c_helper |
Confidence bands | ci.curve |
Fit the Model | estimate.mle |
Detect end of waves | find_ends |
Detect start of waves | find_starts |
Load configuration file | load_config |
The likelihood function | log_lklh |
Navigate to the config file | navigate_to_config |
Plotting function | plot_outputs |
Epidemic Curve Model | pred.curve |
Utility function for range manipulation | ranges_to_waves |
Demo of main functions | re_predict |
Empirical estimate of R_t | rt_empirical |
Serial interval | serial.helper |
Utility function for range manipulation | waves_1d_list |