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.

Readme

nosoi

nosoi (pronounced no.so.i) is a flexible agent-based stochastic transmission chain/epidemic simulator in R, named after the daimones of plague, sickness and disease that escaped Pandora's jar in Greek mythology. nosoi is able to take into account the impact of multiple variables 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.

Installation

To get the current released version from CRAN:

install.packages("nosoi")

To get the latest (and possibly unstable) version, you can use the devtools package:

install.packages("devtools")
devtools::install_github(repo = "slequime/nosoi")

Documentation

You can find package documentation, with reference, tutorials and examples here: http://slequime.github.io/nosoi/ (built with pkgdown).

Functions in nosoi

Name	Description
dualDiscrete	Dual-host pathogen in structured (discrete) hosts populations
getDynamic	Gets the current number of infected hosts for the full length of the simulation
singleDiscrete	Single-host pathogen in a structured (discrete) host population
iniTable	Generates initial table to start the simulation (internal function)
getCumulative	Gets the cumulative number of infected hosts for the full length of the simulation
moveFunction.discrete	Make Discrete Move function
get_state	Get State at sampling time
singleContinuous	Single-host pathogen in a structured (continuous) host population
moveFunction.continuous	Make Continuous Move function
CoreSanityChecks	Checks if the simulator can start
nosoiSimOneConstructor	nosoiSimOne Constructor
dualNone	Dual-host pathogen in homogeneous hosts populations
getPositionInfected	get Position Infected
getExitingMoving	Get Exiting or Moving individuals
get_other_count	Get host count from table
nosoiSimConstructor	nosoiSim Constructor
get_position	Get Position on branch
getTransmissionTree	Gets the full transmission tree (phylogenetic tree-like) from a nosoi simulation
RasterSanityChecks	Checks if the raster is properly formatted
MatrixSanityChecks	Checks if the matrix is properly formatted
cumulativeInfected	Cumulative number of infected hosts at time t
makeMoves	Make Move function
nosoiSim	Top-level function to use nosoi.
newLineState	Creates a new line to be added to the movement table when hosts moves (internal function)
getR0	Gets R0 from a nosoi simulation
keepState	Should we build the table.host table
sampleTransmissionTreeFromExiting	Sample the transmission tree (phylogenetic tree-like) among the exited hosts
numberInfectedBGW	Number of infected hosts at time t (BGW)
get_node	Get Node
FunctionSanityChecks	Checks if a function is properly formatted
drawBernouilli	Draw newly infected
endMessage	End message
singleNone	Single-host pathogen in a homogeneous host population
getHostData	Extracts specific data from a nosoiSim object
nosoiSummary	Summarizes the epidemiological features of a nosoi simulation
updateTableState	Update table state with exiting individuals
paramConstructor	Param concatenator
writeInfected	Write newly infected function
sampleTransmissionTree	Sample the transmission tree (phylogenetic tree-like)
numberInfected	Number of active infected hosts at time t
moveRotateContinuous	Rotates movement in 2D space
newLine	Creates a new line to be added to the table when new host is infected (internal function)
updateHostCount	Summarise position of hosts in a discrete or discretized (raster) space
progressMessage	Progress bar
meetTransmit	Meet Transmit function
getTableHosts	Extracts table.hosts from a nosoiSim object
applyFunctionToHosts	Apply a function to table.host
merge_host_tables	Merge Population Data
add_node_tip	Add one tip
parseFunction	Parse function for later use
getTableState	Extracts table.state from a nosoiSim object
iniTableState	Generates initial movement table to start the simulation (internal function)
keep.tip.treedata	Keep tips
dualContinuous	Dual-host pathogen in structured (continuous) hosts populations
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Name

Description

dualDiscrete

Dual-host pathogen in structured (discrete) hosts populations

getDynamic

Gets the current number of infected hosts for the full length of the simulation

singleDiscrete

Single-host pathogen in a structured (discrete) host population

iniTable

Generates initial table to start the simulation (internal function)

getCumulative

Gets the cumulative number of infected hosts for the full length of the simulation

moveFunction.discrete

Make Discrete Move function

get_state

Get State at sampling time

singleContinuous

Single-host pathogen in a structured (continuous) host population

moveFunction.continuous

Make Continuous Move function

CoreSanityChecks

Checks if the simulator can start

nosoiSimOneConstructor

nosoiSimOne Constructor

dualNone

Dual-host pathogen in homogeneous hosts populations

getPositionInfected

get Position Infected

getExitingMoving

Get Exiting or Moving individuals

get_other_count

Get host count from table

nosoiSimConstructor

nosoiSim Constructor

get_position

Get Position on branch

getTransmissionTree

Gets the full transmission tree (phylogenetic tree-like) from a nosoi simulation

RasterSanityChecks

Checks if the raster is properly formatted

MatrixSanityChecks

Checks if the matrix is properly formatted

cumulativeInfected

Cumulative number of infected hosts at time t

makeMoves

Make Move function

nosoiSim

Top-level function to use nosoi.

newLineState

Creates a new line to be added to the movement table when hosts moves (internal function)

getR0

Gets R0 from a nosoi simulation

keepState

Should we build the table.host table

sampleTransmissionTreeFromExiting

Sample the transmission tree (phylogenetic tree-like) among the exited hosts

numberInfectedBGW

Number of infected hosts at time t (BGW)

get_node

Get Node

FunctionSanityChecks

Checks if a function is properly formatted

drawBernouilli

Draw newly infected

endMessage

End message

singleNone

Single-host pathogen in a homogeneous host population

getHostData

Extracts specific data from a nosoiSim object

nosoiSummary

Summarizes the epidemiological features of a nosoi simulation

updateTableState

Update table state with exiting individuals

paramConstructor

Param concatenator

writeInfected

Write newly infected function

sampleTransmissionTree

Sample the transmission tree (phylogenetic tree-like)

numberInfected

Number of active infected hosts at time t

moveRotateContinuous

Rotates movement in 2D space

newLine

Creates a new line to be added to the table when new host is infected (internal function)

updateHostCount

Summarise position of hosts in a discrete or discretized (raster) space

progressMessage

Progress bar

meetTransmit

Meet Transmit function

getTableHosts

Extracts table.hosts from a nosoiSim object

applyFunctionToHosts

Apply a function to table.host

merge_host_tables

Merge Population Data

add_node_tip

Add one tip

parseFunction

Parse function for later use

getTableState

Extracts table.state from a nosoiSim object

iniTableState

Generates initial movement table to start the simulation (internal function)

keep.tip.treedata

Keep tips

dualContinuous

Dual-host pathogen in structured (continuous) hosts populations

No Results!

Vignettes of nosoi

Name
continuous.Rmd
discrete.Rmd
none.Rmd
nosoi.Rmd
output.Rmd
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Name

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Details

Type	Package
URL	https://github.com/slequime/nosoi
Language	en-US
License	GPL-3
Encoding	UTF-8
LazyData	true
RoxygenNote	6.1.1
biocViews
VignetteBuilder	knitr
NeedsCompilation	no
Packaged	2019-12-18 22:06:53 UTC; slequime
Repository	CRAN
Date/Publication	2020-01-14 10:30:05 UTC

suggests	ape (>= 5.3) , gganimate , ggnetwork , ggplot2 , ggtree (>= 1.16.0) , gifski , igraph , intergraph , knitr , png , rmarkdown , testthat (>= 2.1.0) , tidytree (>= 0.2.4) , tidyverse , treeio (>= 1.6.2) , viridis
depends	data.table (>= 1.12.0) , R (>= 3.5.0)
imports	dplyr (>= 0.8.0) , magrittr (>= 1.5) , methods (>= 3.5.2) , raster (>= 2.8-19) , reshape2 (>= 1.4.0) , stats (>= 3.5.2) , stringr (>= 1.4.0) , utils (>= 3.5.2)
Contributors	Paul Bastide, Simon Dellicour, Philippe Lemey, Guy Baele

nosoi v1.0.0