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DESCRIPTION
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DESCRIPTION
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Package: wwinference
Title: Jointly infers infection dynamics from wastewater data and epidemiological indicators
Version: 0.1.0.99
Authors@R: c(
person(given = "Kaitlyn",
family = "Johnson",
role = c("aut", "cre"),
email = "[email protected]",
comment = c(ORCID = "0000-0001-8011-0012")),
person(given = "Dylan",
family = "Morris",
role = c("aut"),
email = "[email protected]",
comment = c(ORCID = "0000-0002-3655-406X")),
person(given = "Sam",
family = "Abbott",
role = c("aut"),
email = "[email protected]",
comment = c(ORCID = "0000-0001-8057-8037")),
person(given = "Christian",
family = "Bernal Zelaya",
role = c("aut"),
email = "[email protected]"),
person(given = "George",
family = "Vega Yon",
role = c("aut"),
email = "[email protected]",
comment = c(ORCID = "0000-0002-3171-0844")),
person(given = "Damon",
family = "Bayer",
role = c("aut"),
email = "[email protected]"),
person(given = "Andrew",
family = "Magee",
role = c("aut"),
email = "[email protected]"),
person(given = "Scott",
family = "Olesen",
role = c("aut"),
email = "[email protected]"),
person(given = "Adam",
family = "Howes",
role = c("ctb"),
email = "[email protected]",
comment = c(ORCID = "0000-0003-2386-4031")),
person(given = "Chirag",
family = "Kumar",
role = c("ctb"),
email = "[email protected]"),
person(given = "Alexander",
family = "Keyel",
role = c("ctb"),
email = "[email protected]",
comment = c(ORCID = "000-0001-5256-6274")),
person(given = "Hannah",
family = "Cohen",
role = c("ctb"),
email = "[email protected]")
)
Description: An implementation of a hierarchical semi-mechanistic renewal
approach jointly calibrating to multiple wastewater concentrations datasets from
subsets of a specified population and epidemioliogical indicators such as cases
or hospital admissions from the whole population. Our framework is an extension
of the widely used semi-mechanistic renewal framework EpiNow2, using a Bayesian
latent variable approach implemented in the probabilistic programming language
Stan. This package contains just the core components needed to fit these two
data sources and produce the following outputs-- estimated and forecasted
hospital admissions, estimated and forecasted wastewater concentrations,
global R(t) estimates, local R(t) estimates for the subpopulations
represented by each wastewater catchment area.
License: Apache License (>= 2)
URL: https://github.com/cdcgov/ww-inference-model/, https://cdcgov.github.io/ww-inference-model/
BugReports: https://github.com/cdcgov/ww-inference-model/issues/
Depends:
R (>= 4.1.0)
SystemRequirements: CmdStan (>=2.35.0)
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
Suggests:
testthat (>= 3.0.0),
bookdown,
knitr,
withr,
rcmdcheck
Config/testthat/edition: 3
LazyData: true
Imports:
fs,
dplyr,
lubridate,
glue,
RcppTOML,
cli,
tibble,
tidybayes,
tidyr,
purrr,
cmdstanr (>= 0.8.0),
rlang,
scales,
ggplot2,
posterior,
checkmate
Remotes:
stan-dev/cmdstanr
VignetteBuilder:
knitr