Package: epidemia
Title: Modeling of Epidemics using Hierarchical Bayesian Models
Version: 1.0.0
Authors@R: c(
    person(given = "James",
           family = "Scott",
           role = c("aut","cre"),
           email = "james.scott15@imperial.ac.uk",
           comment = c(ORCID = "0000-0003-0106-5618")
	   ),
    person(given = "Axel",
           family = "Gandy",
           role = c("aut"),
           email = "a.gandy@imperial.ac.uk",
           comment = c(ORCID = "0000-0002-6777-0451")
	   ),
    person(given = "Swapnil",
           family = "Mishra",
           role = c("aut"),
           email = "swapnilmishra.anu@gmail.com",
           comment = c(ORCID = "0000-0002-8759-5902")
	   ),
	person(given = "Juliette",
           family = "Unwin",
           role = c("aut"),
           email = "h.unwin@imperial.ac.uk",
           comment = c(ORCID = "0000-0002-9120-4003")
	   ),
    person(given = "Seth",
           family = "Flaxman",
           role = c("aut"),
           email = "s.flaxman@imperial.ac.uk",
           comment = c(ORCID = "0000-0002-2477-4217")
	   ),
    person(given = "Samir",
           family = "Bhatt",
           role = c("aut"),
           email = "s.bhatt@imperial.ac.uk",
           comment = c(ORCID = "0000-0002-0891-4611")
	   ),
    person(given = "Jonathan",
           family = "Ish-Horowicz",
           role = c("ctb"),
           email = "jonathan.ish-horowicz17@imperial.ac.uk",
           comment = c(ORCID = "0000-0002-5386-6620")
	   ),
    person(given = "Leon",
           family = "Wu",
           role = c("ctb"),
           email = "leon.wu16@imperial.ac.uk"
	   ),
    person(given = "Ben",
           family = "Goodrich",
           role = c("ctb"),
           email = "benjamin.goodrich@columbia.edu"
	   ),
    person(given = "Jonah",
           family = "Gabry",
           role = c("ctb"),
           email = "jsg2201@columbia.edu"
	   ),
    person(given = "Trustees of", 
            family = "Columbia University", 
            role = "cph", 
            comment = "R/helpers.R"),
    person(given = "Paul-Christian", 
            family = "Burkner", 
            email = "paul.buerkner@gmail.com", 
            role = "cph", 
            comment = "R/misc.R"),
    person(given = "Triad", 
            family = "Sou", 
            email = "triadsou@gmail.com", 
            role = "cph", 
            comment = "R/geom_stepribbon.R"),
    person(given = "Kengo", 
            family = "Nagashima",
            role = "cph", 
            comment = "R/geom_stepribbon.R")
	   )
Description: Flexibly specify and fit Bayesian statistical models for epidemics. 'epidemia' leverages Rs formula interface so 
    that users can parameterize reproduction numbers and ascertainment rates in terms of predictors. Infections are propagated over 
    time using self-exciting point processes. Multiple regions can be modeled simultaneously with multilevel models. The models and framework behind 
    the package are described in Bhatt et al. (2021) <arXiv:2012.00394>. The design of the package has been inspired by, and has borrowed from, 
    'rstanarm' (Goodrich et al., 2020) <https://mc-stan.org/rstanarm/>. 'rstan' (Stan Development Team, 2020) <https://mc-stan.org/> is used as 
    the back end for fitting models.
License: GPL-3
URL: https://github.com/ImperialCollegeLondon/epidemia/
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
Biarch: true
Depends: R (>= 3.5.0)
Imports: dplyr (>= 0.8.5), methods, Rcpp (>= 0.12.0), rstan (>=
        2.18.1), rstantools (>= 2.0.0), magrittr, rstanarm, lme4,
        ggplot2, Matrix, scales, Rdpack, stats, zoo, tidyr, rlang,
        bayesplot, hrbrthemes
LinkingTo: BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0),
        rstan (>= 2.18.1), StanHeaders (>= 2.18.0)
SystemRequirements: GNU make
Suggests: testthat, knitr, gridExtra, bookdown, EpiEstim, lubridate,
        kableExtra, extrafont
RdMacros: Rdpack
NeedsCompilation: yes
Packaged: 2021-10-23 13:26:11 UTC; jamesscott
Author: James Scott [aut, cre] (<https://orcid.org/0000-0003-0106-5618>),
  Axel Gandy [aut] (<https://orcid.org/0000-0002-6777-0451>),
  Swapnil Mishra [aut] (<https://orcid.org/0000-0002-8759-5902>),
  Juliette Unwin [aut] (<https://orcid.org/0000-0002-9120-4003>),
  Seth Flaxman [aut] (<https://orcid.org/0000-0002-2477-4217>),
  Samir Bhatt [aut] (<https://orcid.org/0000-0002-0891-4611>),
  Jonathan Ish-Horowicz [ctb] (<https://orcid.org/0000-0002-5386-6620>),
  Leon Wu [ctb],
  Ben Goodrich [ctb],
  Jonah Gabry [ctb],
  Trustees of Columbia University [cph] (R/helpers.R),
  Paul-Christian Burkner [cph] (R/misc.R),
  Triad Sou [cph] (R/geom_stepribbon.R),
  Kengo Nagashima [cph] (R/geom_stepribbon.R)
Maintainer: James Scott <james.scott15@imperial.ac.uk>
Repository: CRAN
Date/Publication: 2021-10-25 07:50:05 UTC
Built: R 4.0.5; x86_64-w64-mingw32; 2022-04-21 16:19:20 UTC; windows
Archs: i386, x64
