Package index
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MetaLandSim-packageMetaLandSim - Landscape And Range Expansion Simulation
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accept.calculate() - Calculate acceptance rates in MCMC chains
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addpoints() - Add a given number of patches to a landscape
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cabrera - Modified patch occupancy data of Cabrera vole
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calcmode() - Function for mode estimation of a continuous variable
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cluster.graph() - Delivers the number of patches per cluster
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cluster.id() - Classify patches in clusters
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coda.create() - Create files for use with R-package coda.
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combine.chains() - Combines two chains into a single chain.
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components.graph() - Number of components of a landscape
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convert.graph() - Convert data frame to landscape
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create.parameter.df() - Create parameter data frame
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edge.graph() - Produce an edge (links) data frame
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expansion - Class 'expansion'
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extract.graph() - Extract landscape from span.graph generated list
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ifm.missing.MCMC() - Estimate the 'missing' design incidence function model
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ifm.naive.MCMC() - Estimate the naive design incidence function model
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ifm.robust.MCMC() - Estimate the robust design incidence function model
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import.shape() - Import a shapefile
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iterate.graph() - Simulate landscape series occupation
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landscape - Class 'landscape'
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landscape_change - Landscape loosing 5% of patches per time step
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list.stats() - Returning information on a dynamic landscape list
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manage_expansion_sim() - Simulate range expansion simulation
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manage_landscape_sim() - Batch landscape simulation
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matrix.graph() - Returning a matrix with information on connections between patches
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mc_df - Modified patch occupancy data of Cabrera vole as a data frame
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merge_order - Internal functions for the MetaLandSim package.
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metapopulation - Class 'metapopulation'
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metrics.graph() - Computes landscape connectivity metrics
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min_distance() - Computes topological distance
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occ.landscape - Sample landscape with one simulated occupancy snapshot
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occ.landscape2 - Sample landscape with 10 simulated occupancy snapshots
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param1 - Sample parameter data frame number 1
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param1 - Sample parameter data frame number 2
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parameter.estimate() - Estimate parameters
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plotL.graph() - Plot one landscape of the list created by span.graph
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plot_expansion() - Graphical display of the expansion simulations
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plot_graph() - Graphical display of the landscape
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range_expansion() - Computes a range expansion model
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range_raster() - Probability of occupancy, dispersal model
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remove.species() - Remove the species occupancy from the landscape
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removepoints() - Remove a given number of patches from the landscape
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rg_exp - List with range.expansion output
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rland - Random landscape
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rland.graph() - Creates random landscape graph
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sim.area - Vector of the areas for each site; here, 100 sites
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sim.det.20 - Array corresponding to nsites x nyears x nvisits
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sim.distance - Distance matrix between sampling sites (nsite x nsite).
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simulate_graph() - Simulate species occupancy in one dynamic landscape
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simulatedifm - Set of simulated data to use with the IFM parameter estimation functions. The data were generated using the code provided in "details".
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span.graph() - Simulate landscape dynamics over a number of time steps
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species.graph() - Simulate landscape occupation
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spom() - Stochastic Patch Occupancy Model
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summary_landscape() - Summarize 'landscape' class objects
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summary_metapopulation() - Summarize 'metapopulation' class objects
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z.sim.20 - Occupancy data generated with perfect detection with approximately 20% of data missing at random.
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z.sim.20.fa - Occupancy data containing false absences
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z.sim - Occupancy data generated with perfect detection.