Package: Pv3Rs
Title: Estimate the Cause of Recurrent Vivax Malaria using Genetic Data
Version: 1.0.0.9000
Authors@R: c(
    person("Aimee", "Taylor", email = "aimee.taylor@pasteur.fr", 
    role = c("aut", "cre"), 
    comment = c(ORCID = "0000-0002-2337-8992")),
    person("Yong See", "Foo", role = "aut", 
    comment = c(ORCID = "0000-0003-3010-9106")),
    person("Tymoteusz", "Kwiecinski", role = "com", comment = "compiled included macros.Rd"), 
    person("Duncan", "Murdoch", role = "ctb", comment = "author of included macros.Rd"),
    person("Mans", "Magnusson", role = "ctb", comment = "author of included msg_progress_bar.R"),
    person("Institut Pasteur", role = "cph"),
    person("European Union, Project 101110393", role = "fnd")
  )
Description: Plot malaria parasite genetic data on two or more
        episodes. Compute per-person posterior probabilities that each
        Plasmodium vivax (Pv) recurrence is a recrudescence, relapse,
        or reinfection (3Rs) using per-person P. vivax genetic data on
        two or more episodes and a statistical model described in
        Taylor, Foo and White (2022) <doi:10.1101/2022.11.23.22282669>.
        Plot per-recurrence posterior probabilities.
License: GPL (>= 3)
URL: https://aimeertaylor.github.io/Pv3Rs/,
        https://github.com/aimeertaylor/Pv3Rs
BugReports: https://github.com/aimeertaylor/Pv3Rs/issues
Depends: R (>= 3.5)
Imports: dplyr, fields, grDevices, igraph, matrixStats, methods,
        multicool, partitions, purrr, RColorBrewer
Suggests: codetools, gtools, knitr, Matrix, plyr, R.rsp, rmarkdown,
        testthat (>= 3.0.0), tictoc, utils
VignetteBuilder: knitr
Config/Needs/website: rmarkdown
Config/testthat/edition: 3
Encoding: UTF-8
LazyData: true
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
Config/pak/sysreqs: libglpk-dev libgmp3-dev libxml2-dev
Repository: https://plasmogenepi.r-universe.dev
Date/Publication: 2026-05-22 14:28:35 UTC
RemoteUrl: https://github.com/aimeertaylor/Pv3Rs
RemoteRef: HEAD
RemoteSha: 680b4c5a23b2f8e6ced0bcb5209ec82ff5b36243
NeedsCompilation: no
Packaged: 2026-06-21 09:56:06 UTC; root
Author: Aimee Taylor [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-2337-8992>),
  Yong See Foo [aut] (ORCID: <https://orcid.org/0000-0003-3010-9106>),
  Tymoteusz Kwiecinski [com] (compiled included macros.Rd),
  Duncan Murdoch [ctb] (author of included macros.Rd),
  Mans Magnusson [ctb] (author of included msg_progress_bar.R),
  Institut Pasteur [cph],
  European Union, Project 101110393 [fnd]
Maintainer: Aimee Taylor <aimee.taylor@pasteur.fr>