This is the first stable release providing core functionality for
producing probabilistic or point nowcasts from a dataframe with incident
case counts indexed by reference dates and report dates. It supports
doing so across multiple strata, either through creating
reporting_triangle objects for each strata and nowcasting
independently, or nowcasting directly from a dataframe containing
multiple strata. The reporting_triangle object allows users
to specify the unit of the delay, and provides helpful
print and summary S3 methods, as well as
functionality to truncate to a specific delay or a percentile of the
observed delays. A paper validating and evaluating the performance of
the methods is available at https://wellcomeopenresearch.org/articles/10-614/v1.
Package
fill_triangle() has been removed. Use
estimate_and_apply_delay() instead, which now supports
optional delay estimation via the delay_pmf parameter
(#334).
fill_triangles() has been removed. Use
estimate_and_apply_delays() instead (#334).
Rename truncate_triangle() to
truncate_to_row() and truncate_triangles() to
truncate_to_rows() to clarify that these functions truncate
by row count and distinguish them from other truncation utilities such
as truncate_to_quantile() and
truncate_to_delay() (#336).
Use the as_reporting_triangle and
baselinenowcast workflow in the vignette which walks
through a nowcasting example applied to syndromic surveillance data in
the U.S.
Add preprocess parameter to
estimate_delay() to control handling of negative values in
reporting triangles. Set to preprocess_negative_values by
default to redistribute negative values to earlier delays, or set to
NULL to preserve negative PMF entries. This allows the
method to work with reporting corrections that result in net downward
adjustments at specific delays (#278).
Export preprocess_negative_values() function to allow
users to manually handle negative values in reporting triangles by
redistributing them to earlier delays (#278).
Add a baselinenowcast.data.frame() method which ingests
a data.frame with one or more strata to nowcast and returns a
baselinenowcast_df object.
Add converters between reporting_triangle and
ChainLadder triangle formats via as_ChainLadder_triangle()
and as_reporting_triangle.triangle(), enabling use of
ChainLadder’s mature claims reserving methods alongside
baselinenowcast’s nowcasting functionality.
Add a baselinenowcast.reporting_triangle() method which
ingests a reporting_triangle object and produces a
baselinenowcast_df object which is a data.frame with
nowcasts and associated metadata.
Add a as_reporting_triangle() S3 method which ingests a
data.frame or matrix and returns a reporting_triangle
object, which will be used as an input to the eventual
baselinenowcast() function.
Add a vignette which demonstrates how to pre-process for nowcasting
syndromic surveillance system data using the U.S. National Syndromic
Surveillance Program (NSSP) data as a case study, and then use
baselinenowcast to nowcast cases of a specific syndromic
surveillance definition.
Add intermediate-level grouping functions to generate a point
nowcast from a reporting triangle and to take a point nowcast and
estimate and apply uncertainty.
Refactor estimate_uncertainty to take in an error model
function, an aggregator function for aggregating across reference times,
and an aggregator function for aggregating across delays.
Documentation
Add a vignette which walks through the low-level function interface
on the same nowcasting problem as in the Getting Started vignette.
Modify the Getting Started vignette to use the
baselinenowcast() wrapper function.
Improve PMF validation message to be more informative when the delay
PMF does not sum to approximately 1. The message now shows the actual
sum and clarifies that this may be expected when working with downward
corrections or incomplete data (#148, #278).
Include the pre-print as well as the package in the citation.
baselinenowcast 0.0.0.1.000
Package
Replace argument names with more complete versions where
possible.
Replace most function names with action-oriented function
naming.
Add a check to ensure that there are sufficient non-zero values in
the reporting triangle.
Add a check to ensure that sufficient n are specified
for the delay estimate.
Change the requirement so that the number of rows used for delay
estimation need not be greater than or equal to the number of columns,
but instead that at least one row contains a full set of
observations.
Add support for passing in a restricted set of functions to the
estimate_dispersion() function to transform the “target”
dataset across reference dates.
Implements a safe iterator in the step where retrospective point
nowcasts are generated from a list of retrospective reporting triangles,
ensuring that the iterations continue even if not all retrospective
point nowcasts can be generated.
Replace function named replace_lower_right_with_NA()
with generate_triangle().
Removes requirement that all elements of the reporting triangle are
integers.
Modify the method used to estimate dispersion. Instead of estimating
dispersion on individual elements of the nowcast matrix, we now estimate
dispersion on the predicted nowcasts summed across reporting dates as a
function of forecast horizon.
Standardises naming of objects that are matrices vs vectors and
objects that contain observations, point estimates, and probabilistic
draws.
Modifies functions that estimate a delay and generate a point
nowcast to ensure that they throw an error/warning if the first element
of the delay PMF is 0.
Adjusts function to estimate delay distribution to be able to handle
complete and partially complete reporting triangles.
Add function to convert a list of expected observed reporting
squares to a long tidy dataframe indexed by reference time, delay, and a
sample index.
Implement zero-handling in the bottom left of the reporting triangle
when applying the delay to generate a point nowcast.
Add function to generate a list of expected observed reporting
squares.
Add function to generate an expected observed reporting square from
a point nowcast and a vector of dispersion parameters.
Add function to estimate dispersion parameters from a match list of
nowcasts and observed reporting triangles.
Add functions to generate retrospective nowcasts from a single
reporting triangle.
Refactor uncertainty estimation to use a user-facing function to
generate retrospective reporting triangles.
Introduced function to estimate the uncertainty from a triangle to
be nowcasted and a delay distribution.
Introduced functions to get the delay estimate and apply the delay,
and used these in the Getting Started vignette.
Added package skeleton.
Documentation
Modify vignette to be consistent with the decided upon defaults for
the number of reference times used for delay estimation and
uncertainty.
Add new logo.
Methods write-up as a separate vignette.
Bug fixes
Fix internal checks that ensure there is sufficient data for the
specified target choice, using the number of NA rows rather than the
number of columns as a proxy for the number of horizons.
Bug fix to change the requirement so that the sum of the elements in
the structure vector must not be greater than the number of
columns.
Introduced function to estimate the uncertainty from a triangle to
be nowcasted and a delay distribution.
Introduced functions to get the delay estimate and apply the delay,
and used these in the Getting Started vignette.
Added package skeleton.
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