Landscape and Range Expansion Simulation
Calculate acceptance rates in MCMC chains
Add a given number of patches to a landscape
Function for mode estimation of a continuous variable
Delivers the number of patches per cluster
Classify patches in clusters
Create files for use with R-package coda.
Combines two chains into a single chain.
Number of components of a landscape
Convert data frame to landscape
Create parameter data frame
Produce an edge (links) data frame
Class 'expansion'
Extract landscape from span.graph generated list
Estimate the 'missing' design incidence function model
Estimate the naive design incidence function model
Estimate the robust design incidence function model
Import a shapefile
Simulate landscape series occupation
Class 'landscape'
Returning information on a dynamic landscape list
Simulate range expansion simulation
Batch landscape simulation
Returning a matrix with information on connections between patches
Internal functions for the MetaLandSim package.
Landscape And Range Expansion Simulation
Class 'metapopulation'
Computes landscape connectivity metrics
Computes topological distance
Estimate parameters
Graphical display of the expansion simulations
Graphical display of the landscape
Plot one landscape of the list created by span.graph
Computes a range expansion model
Probability of occupancy, dispersal model
Remove the species occupancy from the landscape
Remove a given number of patches from the landscape
Creates random landscape graph
Vector of the areas for each site; here, 100 sites
Array corresponding to nsites x nyears x nvisits
Distance matrix between sampling sites (nsite x nsite).
Simulate species occupancy in one dynamic landscape
Simulate landscape dynamics over a number of time steps
Simulate landscape occupation
Stochastic Patch Occupancy Model
Summarize 'landscape' class objects
Summarize 'metapopulation' class objects
Occupancy data containing false absences
Occupancy data generated with perfect detection with approximately 20%...
Occupancy data generated with perfect detection.
Tools to generate random landscape graphs, evaluate species occurrence in dynamic landscapes, simulate future landscape occupation and evaluate range expansion when new empty patches are available (e.g. as a result of climate change). References: Mestre, F., Canovas, F., Pita, R., Mira, A., Beja, P. (2016) <doi:10.1016/j.envsoft.2016.03.007>; Mestre, F., Risk, B., Mira, A., Beja, P., Pita, R. (2017) <doi:10.1016/j.ecolmodel.2017.06.013>; Mestre, F., Pita, R., Mira, A., Beja, P. (2020) <doi:10.1186/s12898-019-0273-5>.