The hardware and bandwidth for this mirror is donated by METANET, the Webhosting and Full Service-Cloud Provider.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]metanet.ch.
Maintainer is changing to @adamkucharski (#143).
The output column names severity_mean
and
ascertainment_mean
have been corrected to
severity_estimate
and ascertainment_estimate
.
This may break any workflows that rely on the previous column names
(#146).
This version of cfr includes changes to the severity estimation algorithms used in calculating a static severity measure, and may lead to small changes to some CFR values calculated using v0.1.0 (#129).
cfr_static()
:
Has more informative checks on intermediate values passed to
.estimate_severity()
.
Prints a message when CFR value cannot be determined or are unreliable.
cfr_rolling()
:
Prints a message explaining that this is a convenience function.
Has improved input checking.
Uses new .estimate_severity()
functionality based on
outbreak size and initial expectation of CFR (#129).
Prints a message when some rolling CFR values cannot be determined or are unreliable.
.estimate_severity()
:
Renamed with .
prefix to indicate internal
function.
Added parameter p_mid
for initial severity estimate,
which is used to determine the likelihood approximation method.
Selects from among Binomial, Poisson, and Normal approximation of
the likelihood depending on the outbreak size and p_mid
using the function .select_fun_likelihood()
; prints a
message with the selected method (#129).
Lowest possible severity estimate is reduced to \(10^{-4}\).
Severity estimates and confidence intervals stored as named
vectors rather than a <data.frame>
.
.select_func_likelihood()
: Internal function added
that chooses likelihood approximation function based on outbreak size
and p_mid
.
Binomial approximation used for small outbreaks with cumulative cases lower than the Poisson threshold.
Poisson approximation used for outbreaks above the Poisson
threshold and with p_mid
< 0.05.
Normal approximation used for outbreaks above the Poisson
threshold and with p_mid
> 0.05.
test_fn_req_args()
is updated to use
Reduce(f = "+")
and Map()
rather than
sum(mapply())
.
Added package level documentation.
Updated Readme with lifecycle (stable) and RepoStatus (Active) badges (#113), added DPG badge (#127), and updated the related projects section; corrected figure labelling (#114).
Updated _pkgdown.yaml
with a manual Bootstrap
version (#136) reference sections, added a software permissions vignette
(#125), and enabled development mode (#143).
Updated WORDLIST
.
Updated all function documentation files (#134).
Added section in distributions vignette on when it is acceptable to use continuous rather than discrete distributions.
Corrected explanation of estimate_outcomes()
in
static severity vignette and added explanations of profile likelihood
generation methods used in all severity vignettes (#143).
Corrected equations in vignettes (#133) and removed
.estimate_severity()
from vignettes (#132).
All snapshots are updated with severity values from new likelihood functions (#129).
Added session global state checker script and setup options script (#119).
All tests are updated to reflect that functions will sometimes throw informative messages.
Tests using incidence2 suppress warnings on missing
values (added in incidence2 v2.3.0) as filling missing values
is the subject of the test for prepare_data.incidence2()
(#143).
Added or updated GitHub Actions workflows for dependency changes, linting, updating the citation file, and updating the license year (#119, #137, #142).
Updated other GHA workflows and infrastructure files to match the
latest versions on epiverse-trace/packagetemplate
(#119).
Normalised DESCRIPTION
file.
Added tools/check.env
from
epiverse-trace/packagetemplate
to suppress specific checks
on package size, Rd cross references, GNU Make requirement, and
non-ASCII strings (#142).
Initial CRAN submission of cfr, an R package to estimate the severity of a disease and ascertainment of cases while correcting for delays in outcomes of reported cases being known.
This release includes:
<incidence2>
class from the incidence2
package,cfr v0.1.0 only includes functionality for static ascertainment calculations. The functionality for time-varying ascertainment is expected to be included in future versions, and an older implementation was removed just prior to release. The news section for cfr v0.1.0 has been updated to reflect this.
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.