- Fixed bugs in draw_one_set_of_ancestries resulting from incorrect lengths and an undefined variable (issue #92) (#93, @jstockwin)
- Fixed incorrect quantiles (issue #88) (#89, @jstockwin)

- Plotting no longer displays TableGrob output (#87, @zkamvar).

This release contains various spelling fixes for CRAN maintenance.

`sample_posterior_R()`

samples values of R from the posterior distribution of an`estimate_R`

object (#70, @acori)

- Added a
`NEWS.md`

file to track changes to the package. (#74, @zkamvar) - Added tests for plotting with vdiffr. (#74, @zkamvar)
- Remove un-used dependencies that were added during hackout3: plyr, grid, and plotly (#74, @zkamvar)
- Remove compare package from suggests and use test_that version. (#74, @zkamvar)
- Bump minimum required version of coarseDataTools to 0.6-4 (#71, @zkamvar)
- Incidence objects are now handled appropriately with accessors (#65, @zkamvar)

- Changed function names to snake_case (only exception is that R remains capital letter to avoid confusion between the reproduction number R and the growth rate r) and to be more explicit; so
`EstimateR`

becomes`estimate_R`

,`OverallInfectivity`

becomes`oberall_infectivity`

,`WT`

becomes`wallinga_teunis`

, and`DiscrSI`

becomes`discr_si`

. Names of arguments to these functions have also changed to snake_case. Note that compatibility functions have been added so that the old functions as written in EpiEstim 1.1-0 should still work but throw a warning pointing to the newest functions. - Compatibility with
`incidence`

package: in the function`estimate_R`

, the first argument, i.e. the incidence from which the reproduction number is calculated, can now be, either a vector of case counts (as in version 1.1-0) or an`incidence`

object (see R package`incidence`

). - Accounting for imported cases: in the function
`estimate_R`

, the first argument, i.e. the incidence from which the reproduction number can now provide information about known imported cases: by specifying the first argument as either a dataframe with columns “local” and “imported”, or an`incidence`

object with two groups (local and imported, see R package`incidence`

). This new feature is described in Thompson et al. Epidemics 2019 (currently in review). - Additional methods available for function
`estimate_R`

: in addition to`non_parametric_si`

,`parametric_si`

and`uncertain_si`

, which were already available in EpiEstim 1.1-0, two new methods have been added:`si_from_data`

or`si_from_sample`

. These allow feeding function`estimate_R`

data on observed serial intervals (method`si_from_data`

) or posterior samples of serial interval distributions obtained from such data (method`si_from_sample`

). These new features are described in Thompson et al. Epidemics 2019 (currently in review). - No more plotting option inside of
`estimate_R`

: estimate_R now generates on object of class`estimate_R`

, which can be plotted separately by using the new`estimate_R_plots`

function, which also now allows to plot several R estimates on a single plot. - New argument
`config`

for`estimate_R`

function: this is meant to minimise the number of arguments to function`estimate_R`

; so arguments`method`

,`t_start`

,`t_end`

,`n1`

,`n2`

,`mean_si`

,`std_si`

,`std_mean_si`

,`min_mean_si`

,`max_mean_si`

,`std_std_si`

,`min_std_si`

,`max_std_si`

,`si_distr`

,`mean_prior`

,`std_prior`

, and`cv_posterior`

are now specified as a group under this new`config`

argument. Such a`config`

argument must be of class`estimate_R_config`

and can be obtained as a results of the new`make_config`

function. - New function
`make_config`

, which defines settings for function`estimate_R`

, and sets defaults where arguments are missing. In particular, if argument`incid`

is not`NULL`

, by default`config$t_start`

and`config$t_end`

will be set so that, when the configuration is used inside`estimate_R`

function, the reproduction number is estimated by default on sliding weekly windows (in EpiEstim 1.1-0 there was no default for the time window of estimation of R). - Added a vignette to illustrate main features of the package.

`flu_2009_NYC_school`

`mers_2014_15`

,`MockRotavirus`

`stats`

(to use the gamma distribution; it was already used in EpiEstim 1.1-0 but making the dependency explicit)`coarseDataTools`

,`fitdistrplus`

,`coda`

(used for the new methods`si_from_data`

and`si_from_sample`

in`estimate_R`

function to estimate the serial interval from data).`incidence`

(so that`estimate_R`

can take an`incidence`

object as first argument)`graphics`

,`reshape2`

,`ggplot2`

,`gridExtra`

,`scales`

,`grDevices`

(to make new plots of outputs of`estimate_R`

and`wallinga_teunis`

functions)