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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)NEWS.md file to track changes to the package.
(#74, @zkamvar)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.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).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).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).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.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.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).flu_2009_NYC_schoolmers_2014_15,MockRotavirusstats (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)These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.