| 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 |
