The fourth minor release of the {epiparameter} focuses on splitting the code and data, with the data being moved into a separate R package: {epiparameterDB}. There are also some minor additional improvements focusing on printing and plotting.
parameters.json) has been removed from the {epiparameter}
package and moved to the {epiparameterDB} R package which is taken on as
a dependency. The {epiparameter} package is licensed solely as MIT with
dual licensing with CC0 removed (#415).data_dictionary.json) and JSON
validation workflow (validate-json.yaml) have been removed
from the package (#415).epiparameter_db() (#417).print() and format() methods for the
<epiparameter> class have been improved to show the
units of parameter estimates, as well as summary statistics, if
available, for unparameterised <epiparameter> objects
(#419).on.exit() is no longer called in plotting functions to
allow user-specified graphical parameters to not be overwritten
(#420).plot() method for the
<multi_epiparameter> class is added. This enables a
list of <epiparameter> objects with continuous
distributions to be compared on a single plot (#425).lines() method for the
<epiparameter> class is added (#425).is_continuous() causing it to incorrectly
returning FALSE for <epiparameter>
objects with normal distributions is fixed (#422).The third minor release of the {epiparameter} R package contains a range of updates and improvements to the package. The principal aim of this release is to simplify, clarify and enhance the classes and class methods when working with epidemiological parameters in R.
The are a large number of breaking changes in this release, primarily functions and function arguments being renamed or restructured, see the Breaking changes section for an overview.
c() method has been added for
<epiparameter> and
<multi_epiparameter> objects (#368).aggregate() method has been added for
<multi_epiparameter> to enable consensus
distributions to be built utilising the mixture distribution class from
{distributional}
(#388).convert_summary_stats_to_params() can now convert from
median and dispersion for a lognormal distribution (#378).data_dictionary.json has been enhanced to improve
validation of the library of epidemiological parameters
(parameters.json) (#379).<epiparameter> S3 methods has been added to the
design_principles.Rmd vignette (#383).data_from_epireview.Rmd article has been improved
and updated with new changes from {epireview} (@CarmenTamayo & @cm401 & @kellymccain28, #305
& #373).parameters.json) and to the $metadata
element in <epiparameter> objects. The
create_metadata() function now has a units
argument to construct metadata lists (#391).database.Rmd vignette by adding a short
citation to the reference column (@jamesmbaazam, #348).family() method for
<epiparameter> has been improved to allow access to
distribution names for transformed (e.g. mixture and
truncated distributions) and untransformed
(e.g. gamma and lognormal) distributions with
a new argument base_dist and a new internal function
.distributional_family() (#398).as_epiparameter() can now work with the SARS parameters
from {epireview} (#407).<epidist> class has been renamed
<epiparameter> to avoid confusion with the similar R
package {epidist}
(#360).epidist in their names have
been renamed to use epiparameter due to the renaming of the
class (#360).epiparameter() and
new_epiparameter() functions (previously
epidist() and new_epidist()) have been updated
to collapse the prob_dist, prob_dist_params,
discretise and truncation arguments into
prob_distribution, which accepts the output of
create_prob_distribution() (#381).epi_dist argument has been renamed
epi_name. This is to clarify that {epiparameter} can work
with epidemiological parameters that take a variety of forms (e.g. point
estimates, ranges, probability distributions, etc.) (#390).<vb_epidist> class and it’s methods have been
removed from the package. It was not being used and was increasing the
complexity and maintenance load of the package (#359).create_prob_dist() has been renamed to
create_prob_distribution() (#381).validate_epiparameter() (previously
validate_epidist()) has been renamed
assert_epiparameter(), and test_epiparameter()
has been added, with the aim to harmonise design with {contactmatrix}
and the messages and errors have been improved (#366 & #402).|>) in dependencies, and the
R-CMD-check workflow on GitHub actions now explicitly runs on the
minimum version of R stated in the DESCRIPTION (#384 &
#405).<epiparameter> (when
auto_calc_params = TRUE) (#381).epidist_db() has been deprecated. It is replaced by
epiparameter_db() (#360 & #399).The second release of the {epiparameter} R package focuses on interoperability with the {epireview} R package. Several functions have been refactored and enhanced.
This release benefited from feedback from the participants of an EpiParameter Community workshop hosted by the World Health Organisation.
The as_epidist() S3 generic has been added to the
package for the coercion of other R objects into
<epidist> objects. The
as_epidist.data.frame() method is added, as well as the
internal functions is_epireview() which determines if a
<data.frame> is from {epireview}, and
epireview_to_epidist() performs the conversion (#298, #334
& #335)
The epireview_core_cols.rda data is added to the
package. This is used to determine whether the input to
as_epidist.data.frame() is a parameter table from
{epireview} as these objects do not have a recognisable class attribute
(#298).
A new website only vignette (i.e. article)
data_from_epireview.Rmd is added that explains how to use
as_epidist() with data from {epireview} (#298 &
#335).
A new vignette database.Rmd is added to the package
to provide a web interface to the {epiparameter} library of
epidemiological parameters. Contributed by @sbfnk (#311).
The plotting method for <epidist> objects
(plot.epidist()) has been improved to better differentiate
continuous from discrete or discretised distributions (#315).
epidist_db(..., single_epidist = TRUE) now
prioritises parameter entries that account for right truncation
(#323).
create_epidist_prob_dist() (previously named
create_prob_dist()) is now exported and enables more
control of discretisation settings by allowing arguments to be passed to
distcrete::distcrete() via ...
(#324).
The <multi_epidist> print method
(print.multi_epidist()) has been improved to provides
object information in the print header, the first few elements of the
list or all elements if list is short, and some extra links and advice
in the print footer. The design of the print method follows the design
pattern of {pillar}
(#326).
<epidist> objects and functions that work with
<epidist> objects now work with exponential
distributions (#333).
The package now has an explicit data license: CC0
in the LICENSE file.
list_distributions() has been replaced by
parameter_tbl() which enhances the printing by leveraging
{pillar} (#321).
The <vb_epidist> plotting method
(plot.vb_epidist()) has been removed from the package. This
provided minimal functionality and was unnecessarily complicating the
function signature of plot.epidist() (#315).
Initial release of the {epiparameter} R package. {epiparameter} provides:
A library of epidemiological parameters extracted from the literature for a range of diseases.
Functions and classes (with class methods) to work with epidemiological parameters and distributions.
sysdata.rda, as
epiparameter::multi_epidist) or as internal data
(inst/extdata/parameters.json).epidist_db() function loads epidemiological
parameters from the library.convert_params_to_summary_stats() &
convert_summary_stats_to_params(), and
extract_param()).<epidist>. This class has S3 methods to aid users
easily work with these data structures. These include printing,
plotting, and distribution functions for PDF/PMF, CDF, random number
generation and distribution quantiles. The <epidist>
class has a constructor function, a validator function, accessors
(get_*()), checkers (is_*()). There is also a
<vb_epidist> S3 class for vector-borne parameters,
and an internal <multi_epidist> class for improved
printing of lists of <epidist> objects.list_distributions() is a helper function to provide
information from a list of <epidist> objects in
tabular form. calc_disc_dist_quantile() calculates the
quantiles of a probability distribution based on the vector of
probabilities and time data.epiparameter.Rmd), one as an
tutorial on converting and extracting parameters
(extract_convert.Rmd), one on the protocol used to collect
entries for the library of epidemiological parameters
(data_protocol.Rmd), a design vignette
(design_principles.Rmd), and a supplementary vignette which
quantifies the bias from using the parameter extraction
(extract_param()) from {epiparameter}
(extract-bias.Rmd).