R: Landscape and Range Expansion Simulation

# Landscape and Range Expansion Simulation

## Documentation for package ‘MetaLandSim’ version 2.0.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package README

## Help Pages

MetaLandSim-package | Landscape And Range Expansion Simulation
accept.calculate | Calculate acceptance rates in MCMC chains
addpoints | Add a given number of patches to a landscape
cabrera | Modified patch occupancy data of Cabrera vole
calcmode | Function for mode estimation of a continuous variable
cluster.graph | Delivers the number of patches per cluster
cluster.id | Classify patches in clusters
coda.create | Create files for use with R-package coda.
combine.chains | Combines two chains into a single chain.
components.graph | Number of components of a landscape
convert.graph | Convert data frame to landscape
create.parameter.df | Create parameter data frame
edge.graph | Produce an edge (links) data frame
expansion | Class 'expansion'
extract.graph | Extract landscape from span.graph generated list
ifm.missing.MCMC | Estimate the 'missing' design incidence function model
ifm.naive.MCMC | Estimate the naive design incidence function model
ifm.robust.MCMC | Estimate the robust design incidence function model
import.shape | Import a shapefile
iterate.graph | Simulate landscape series occupation
landscape | Class 'landscape'
landscape_change | Landscape loosing 5% of patches per time step
list.stats | Returning information on a dynamic landscape list
manage_expansion_sim | Simulate range expansion simulation
manage_landscape_sim | Batch landscape simulation
matrix.graph | Returning a matrix with information on connections between patches
mc_df | Modified patch occupancy data of Cabrera vole as a data frame
merge_order | Internal functions for the MetaLandSim package.
MetaLandSim | Landscape And Range Expansion Simulation
metapopulation | Class 'metapopulation'
metrics.graph | Computes landscape connectivity metrics
min_distance | Computes topological distance
occ.landscape | Sample landscape with one simulated occupancy snapshot
occ.landscape2 | Sample landscape with 10 simulated occupancy snapshots
param1 | Sample parameter data frame number 1
param2 | Sample parameter data frame number 2
parameter.estimate | Estimate parameters
plotL.graph | Plot one landscape of the list created by span.graph
plot_expansion | Graphical display of the expansion simulations
plot_graph | Graphical display of the landscape
range_expansion | Computes a range expansion model
range_raster | Probability of occupancy, dispersal model
remove.species | Remove the species occupancy from the landscape
removepoints | Remove a given number of patches from the landscape
rg_exp | List with range.expansion output
rland | Random landscape
rland.graph | Creates random landscape graph
sim.area | Vector of the areas for each site; here, 100 sites
sim.det.20 | Array corresponding to nsites x nyears x nvisits
sim.distance | Distance matrix between sampling sites (nsite x nsite).
simulatedifm | Set of simulated data to use with the IFM parameter estimation functions. The data were generated using the code provided in "details".
simulate_graph | Simulate species occupancy in one dynamic landscape
span.graph | Simulate landscape dynamics over a number of time steps
species.graph | Simulate landscape occupation
spom | Stochastic Patch Occupancy Model
summary_landscape | Summarize 'landscape' class objects
summary_metapopulation | Summarize 'metapopulation' class objects
z.sim | Occupancy data generated with perfect detection.
z.sim.20 | Occupancy data generated with perfect detection with approximately 20% of data missing at random.
z.sim.20.fa | Occupancy data containing false absences