DESCRIPTION

Package: covidseir
Title: Bayesian SEIR Modelling for Multivariate COVID-19 Case
    Data
Version: 0.0.1.9001
Authors@R: 
    c(person(given = c("Sean", "C."),
             family = "Anderson",
             role = c("aut", "cre"),
             email = "sean@seananderson.ca",
             comment = c(ORCID = "0000-0001-9563-1937")),
      person(given = c("Andrew", "M."),
             family = "Edwards",
             role = "aut"),
      person(given = "Madi",
             family = "Yerlanov",
             role = "aut"),
      person(given = "Nicola",
             family = "Mulberry",
             role = "aut"),
      person(given = c("Jessica", "E."),
             family = "Stockdale",
             role = "aut"),
      person(given = c("Rebeca", "C."),
             family = "Falcao",
             role = "aut"),
      person(given = c("Sarafa", "A."),
             family = "Iyaniwura",
             role = "aut"),
      person(given = c("Michael", "C."),
             family = "Otterstatter",
             role = "aut"),
      person(given = c("Michael", "A."),
             family = "Irvine",
             role = "aut"),
      person(given = c("Naveed", "Z."),
             family = "Janjua",
             role = "aut"),
      person(given = "Daniel",
             family = "Coombs",
             role = "aut"),
      person(given = "Caroline",
             family = "Colijn",
             role = "aut",
             comment = "Principal Investigator; <ccolijn@sfu.ca>"))
Description: Fits a Bayesian SEIR (Susceptible, Exposed,
    Infectious, Recovered) model to daily COVID-19 case data. The package
    focuses on estimating the fraction of the usual contact rate for
    individuals participating in physical distancing (social distancing).
    The model is coded in 'Stan'. The model can accommodate multiple types
    of case data at once (e.g., reported cases, hospitalizations, ICU
    admissions) and accounts for delays between symptom onset and case
    appearance. This model is a continuation of the models described in the
    preprints <doi:10.1101/2020.04.17.20070086> and 
    <doi:10.1101/2020.06.12.20129833>.
License: GPL-2
Depends: 
    R (>= 3.5.0)
Imports: 
    dplyr,
    furrr (>= 0.2.0),
    ggplot2,
    glue,
    MASS,
    magrittr,
    methods,
    purrr,
    Rcpp (>= 0.12.0),
    reshape2,
    rstan (>= 2.18.1),
    tibble,
    tidyr
Suggests:
    knitr,
    future,
    lubridate,
    mgcv,
    rmarkdown,
    rstantools (>= 2.0.0)
LinkingTo: 
    BH (>= 1.66.0),
    Rcpp (>= 0.12.0),
    RcppEigen (>= 0.3.3.3.0),
    rstan (>= 2.18.1),
    StanHeaders (>= 2.18.0)
VignetteBuilder: 
    knitr
Biarch: true
Encoding: UTF-8
LazyData: true
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.1.1.9000
SystemRequirements: GNU make