A tool to estimate time varying instantaneous reproduction number during epidemics
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annecori Interface revision (#41)
* ignore more files

* skeleton for compatibility function

* finalised compatibility function for estimate_r function

* replacing EstimateR by estimate_r everywhere

* added functions to process config ouside of estimate_r

* renaming EstimateR_func to estimate_r_func

* renaming internal function PosteriorFromSIDistr to be posterior_from_si_distr

* renamed function DiscrSI to be discr_si

* tidying code and examples for discr_si

* changing names of R scripts to snake_case

* edited discr_si function so it can be used with k a vector

* simplified calls to discr_si to use the vectorized version

* added compatibility function OverallInfectivity

* cosmetic changes to overall_infectivity

* added documentation to check_cdt_samples_convergence

* cosmetic changes to coarse2estim

* added documentation for init_MCMC_params

* cosmetic changes to overall_infectivity

* cosmetic changes to plots.R

* edited check_si_distr so error message is more explicit when si_distr is not specified as an argument. Should fix #21.

* moving a lot of the funciton estimte_r_func into separate check_config function now called by estimate_r rather than estimate_r_func

* removed a condition in uncertainty_si method which was imposing that the sd of each SI is <= mean SI; not sure why we had such condition and it sometimes made it very difficult to find pairs of sds, mean within the ranges specified which verified that condition. This should fix #22.

* moved check_config back to estimate_r

* fixing issue #23

* changed WT to wallinga_teunis, with a new config argument similar to that in esimate_R. Wrote a WT function to ensure compatibility with old versions of EpiEstim
fixes issue #34.

* cosmetic changes to wallinga_teunis

* fix #38

* changing init_MCMC_params to init_mcmc_params. Also made a few changes that were breaking checks

* changed cdtsamples argument of function check_cdt_samnples_convergence to be cdt_samples

* in estimate_r changed config.pars to be config

* changing I argument of estimate_r to be incid

* changing result of test4 which has changed because of modification to code solving issue #22

* changed deprecated EstimateR so argument match current CRAN version of package exactly

* changed deprecated WT function so argument match current CRAN version of package exactly

* edited compatibility function to pass the check

* added data files as in Thompson et al. (in prep). Also corrected issues where dic.fit.mcmc has argument called init.pars, not init_pars as mistakenly changed to yesterday

* setting version number to 2.0-0
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README.md

EpiEstim

A tool to estimate time varying instantaneous reproduction number during epidemics

This tool is described in the following paper:

A New Framework and Software to Estimate Time-Varying Reproduction Numbers During Epidemics Anne Cori, Neil M. Ferguson, Christophe Fraser and Simon Cauchemez American Journal of Epidemiology 2013.