Functions to run multipathogen, metapopulation epidemiological simulations

adjMatrix | Draw adjacency matrix between colonies |

birthR | Calculate birth rates for each colony. |

checkIfGiant | Is the network one giant component or multiple small separate... |

circleColony | Place colonies in a circle. Most good for viz when all... |

coinfectionR | Calculate coinfection rates for each colony. |

deathR | Calculate death rates for each colony. |

dispersalR | Calculate dispersal rates for each colony. |

edgeList | Create a list of edges with a column of weights |

equalPop | Create equal colony sizes. |

exponentialPop | Create exponential colony size distribution. |

findCoinfDistr | Calculate coinfection disease distributions (how many... |

findDisDistr | Calculate mean disease distributions (how many individuals... |

findDiseaseAdded | Make vector of which disease is added for each coinfection... |

infectionR | Calculate infection rates for each colony. |

infectionTrans | Find possible possible infection transitions. |

initTransitions | Build the transition data.frame which will have rates... |

inverseKern | Inverse kernel for calculating a weight matrix from a... |

linearKern | Linear kernel for calculating a weight matrix from a distance... |

makePop | Make a new population |

MetapopEpi | A package containing functions to run multi pathogen,... |

netDegree | Find the network degree of colonies |

netStrength | Find the network strength of colonies |

numComponents | Count the number of components in population network |

pAll | Plot something... |

pClass | Plot the total number of individuals in each disease class |

pCol | Plot the number of individuals by number of infections and... |

pDis | Plot the total number of infected individuals with each... |

pInf | Plot the total number of infected individuals in each colony |

plotColonyNet | Plot the population network in space |

poissonPop | Create colony sizes based on poisson distribution. |

popHeat | A nice heat map for weighted adjacency matrices |

popMatrix | Calculate a dispersal matrix |

pPop | Plot the total number of individuals in each colony |

pSI | Plot the total number of infected individuals and total... |

pSIR | Plot the total number of individuals in each disease class |

pSus | Plot the number of susceptible individuals in each colony |

randEvent | Perform a random event |

runSim | Run simulation up to certain event number |

seedPathogen | Add single individuals infected with a number of pathogens |

sumI | Returns an nColony x nPathogens matrix |

transRates | Calculate new transition rates. |

uniformColony | Make a matrix of N colony locations placed by a spatial... |

unweightedKern | Unweighted kernel for calculating a weight matrix from a... |

waitingTime | Takes a number [0,1] (which is presumably random) and returns... |

weightMatrix | Draw weighted adjacency matrix between colonies |

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