Man pages for timcdlucas/MetapopEpi
Functions to run multipathogen, metapopulation epidemiological simulations

adjMatrixDraw adjacency matrix between colonies
birthRCalculate birth rates for each colony.
checkIfGiantIs the network one giant component or multiple small separate...
circleColonyPlace colonies in a circle. Most good for viz when all...
coinfectionRCalculate coinfection rates for each colony.
deathRCalculate death rates for each colony.
dispersalRCalculate dispersal rates for each colony.
edgeListCreate a list of edges with a column of weights
equalPopCreate equal colony sizes.
exponentialPopCreate exponential colony size distribution.
findCoinfDistrCalculate coinfection disease distributions (how many...
findDisDistrCalculate mean disease distributions (how many individuals...
findDiseaseAddedMake vector of which disease is added for each coinfection...
infectionRCalculate infection rates for each colony.
infectionTransFind possible possible infection transitions.
initTransitionsBuild the transition data.frame which will have rates...
inverseKernInverse kernel for calculating a weight matrix from a...
linearKernLinear kernel for calculating a weight matrix from a distance...
makePopMake a new population
MetapopEpiA package containing functions to run multi pathogen,...
netDegreeFind the network degree of colonies
netStrengthFind the network strength of colonies
numComponentsCount the number of components in population network
pAllPlot something...
pClassPlot the total number of individuals in each disease class
pColPlot the number of individuals by number of infections and...
pDisPlot the total number of infected individuals with each...
pInfPlot the total number of infected individuals in each colony
plotColonyNetPlot the population network in space
poissonPopCreate colony sizes based on poisson distribution.
popHeatA nice heat map for weighted adjacency matrices
popMatrixCalculate a dispersal matrix
pPopPlot the total number of individuals in each colony
pSIPlot the total number of infected individuals and total...
pSIRPlot the total number of individuals in each disease class
pSusPlot the number of susceptible individuals in each colony
randEventPerform a random event
runSimRun simulation up to certain event number
seedPathogenAdd single individuals infected with a number of pathogens
sumIReturns an nColony x nPathogens matrix
transRatesCalculate new transition rates.
uniformColonyMake a matrix of N colony locations placed by a spatial...
unweightedKernUnweighted kernel for calculating a weight matrix from a...
waitingTimeTakes a number [0,1] (which is presumably random) and returns...
weightMatrixDraw weighted adjacency matrix between colonies
timcdlucas/MetapopEpi documentation built on May 27, 2017, 8:37 a.m.