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DESCRIPTION
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DESCRIPTION
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Package: SIMPLEGEN
Type: Package
Title: Simulating Plasmodium Epidemiological and Genetic Data
Version: 0.2.0
Authors@R: as.person(c(
"Bob Verity <[email protected]> [aut, cre]",
"Shazia Ruybal [aut]",
"Isobel Routledge [aut]",
"Sophie Berube [aut]",
"Daniel Larremore [aut]"
))
Description: Forwards-in time simulation of Plasmodium falciparum genetic data can be
computationally intensive, as many genotypes are tracked but ultimately lost. SIMPLEGEN
avoids this problem by splitting simulation into three steps - first, simulating
transmission under a simple individual-based model, second, pruning the infection history
to focus on nodes that contribute to the final sample, and third, simulating genetic data.
A secondary advantage is that any third-party epidemiological simulator can be used for
the first step as long as it outputs in the correct format. The major limitation of SIMPLEGEN
is that assumes the epidemiological and genetic processes are seperable, and hence is limited
to neutral variation, and cannot model selection.
BugReports: https://github.com/mrc-ide/SIMPLEGEN/issues
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.2.3
Imports:
data.table,
dplyr,
dust,
ggplot2,
magrittr,
Rdpack
Suggests:
testthat (>= 2.1.0),
covr,
knitr,
rmarkdown,
devtools
VignetteBuilder: knitr
LinkingTo:
cpp11,
dust
SystemRequirements: C++11
Depends:
R (>= 3.5.0)
RdMacros: Rdpack