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_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)