nosoi

A Forward Agent-Based Transmission Chain Simulator

The aim of 'nosoi' (pronounced no.si) is to provide a flexible agent-based stochastic transmission chain/epidemic simulator (Lequime et al. in prep). It is named after the daimones of plague, sickness and disease that escaped Pandora's jar in the Greek mythology. 'nosoi' is able to take into account the influence of multiple variable on the transmission process (e.g. dual-host systems (such as arboviruses), within-host viral dynamics, transportation, population structure), alone or taken together, to create complex but relatively intuitive epidemiological simulations.

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Description file content

Package
nosoi
Type
Package
Title
A Forward Agent-Based Transmission Chain Simulator
Version
1.0.0
Description
The aim of 'nosoi' (pronounced no.si) is to provide a flexible agent-based stochastic transmission chain/epidemic simulator (Lequime et al. in prep). It is named after the daimones of plague, sickness and disease that escaped Pandora's jar in the Greek mythology. 'nosoi' is able to take into account the influence of multiple variable on the transmission process (e.g. dual-host systems (such as arboviruses), within-host viral dynamics, transportation, population structure), alone or taken together, to create complex but relatively intuitive epidemiological simulations.
URL
Language
en-US
License
GPL-3
Encoding
UTF-8
LazyData
true
RoxygenNote
6.1.1
biocViews
Depends
data.table (>= 1.12.0), R (>= 3.5.0)
Imports
utils (>= 3.5.2), stats (>= 3.5.2), methods (>= 3.5.2), dplyr (>= 0.8.0), magrittr (>= 1.5), stringr (>= 1.4.0), reshape2 (>= 1.4.0), raster (>= 2.8-19)
Suggests
testthat (>= 2.1.0), knitr, rmarkdown, igraph, tidyverse, ggplot2, ggnetwork, intergraph, viridis, gganimate, gifski, png, ape (>= 5.3), tidytree (>= 0.2.4), treeio (>= 1.6.2), ggtree (>= 1.16.0)
VignetteBuilder
knitr
NeedsCompilation
no
Packaged
2019-12-18 22:06:53 UTC; slequime
Author
Sebastian Lequime [aut, cre] (), Paul Bastide [aut] (), Simon Dellicour [aut] (), Philippe Lemey [aut] (), Guy Baele [aut] ()
Maintainer
Sebastian Lequime
Repository
CRAN
Date/Publication
2020-01-14 10:30:05 UTC

install.packages('nosoi')

1.0.0

10 days ago

https://github.com/slequime/nosoi

Sebastian Lequime

GPL-3

Depends on

data.table (>= 1.12.0), R (>= 3.5.0)

Imports

utils (>= 3.5.2), stats (>= 3.5.2), methods (>= 3.5.2), dplyr (>= 0.8.0), magrittr (>= 1.5), stringr (>= 1.4.0), reshape2 (>= 1.4.0), raster (>= 2.8-19)

Suggests

testthat (>= 2.1.0), knitr, rmarkdown, igraph, tidyverse, ggplot2, ggnetwork, intergraph, viridis, gganimate, gifski, png, ape (>= 5.3), tidytree (>= 0.2.4), treeio (>= 1.6.2), ggtree (>= 1.16.0)

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