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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.
Health stats visible at Monitor.