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MetaLandSim (version 1.0.4)

Landscape and Range Expansion Simulation

Description

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).

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Version

Install

install.packages('MetaLandSim')

Monthly Downloads

311

Version

1.0.4

License

GPL (>= 2)

Maintainer

Frederico Mestre

Last Published

June 17th, 2018

Functions in MetaLandSim (1.0.4)

accept.calculate

Calculate acceptance rates in MCMC chains
import.shape

Import a shapefile
convert.graph

Convert data frame to landscape
iterate.graph

Simulate landscape series occupation
metapopulation

Class 'metapopulation'
MetaLandSim-internal

Internal functions for the MetaLandSim package.
metrics.graph

Computes landscape connectivity metrics
plot_expansion

Graphical display of the expansion
landscape

Class 'landscape'
min_distance

Computes topological distance
plot_graph

Graphical display of the landscape
range_expansion

Produce a range expansion model
remove.species

Remove the species occupancy from the landscape
coda.create

Create files for use with R-package coda.
cabrera

Modified patch occupancy data of Cabrera vole
range_raster

Probability of occupancy, dispersal model
calcmode

Function for mode estimation of a continuous variable
combine.chains

Combines two chains into a single chain.
ifm.missing.MCMC

Estimate the 'missing' design incidence function model
removepoints

Remove a given number of patches from the landscape
MetaLandSim.GUI

Graphic User Interface
summary_landscape

Summarize 'landscape' class objects
MetaLandSim-package

Landscape And Range Expansion Simulation
create.parameter.df

Create parameter data frame
extract.graph

Extract landscape from span.graph generated list
expansion

Class 'expansion'
ifm.naive.MCMC

Estimate the naive design incidence function model
matrix.graph

Returning a matrix with information on connections between patches
edge.graph

Produce an edge (links) data frame
manage_expansion_sim

Simulate range expansion simulation
summary_metapopulation

Summarize 'metapopulation' class objects
manage_landscape_sim

Batch landscape simulation
param1

Sample parameter data frame number 1
mc_df

Modified patch occupancy data of Cabrera vole as a data frame
landscape_change

Landscape loosing 5% of patches per time step
param2

Sample parameter data frame number 2
parameter.estimate

Estimate parameters
plotL.graph

Plot one landscape of the list created by span.graph
list.stats

Returning information on a dynamic landscape list
occ.landscape2

Sample landscape with 10 simulated occupancy snapshots
occ.landscape

Sample landscape with one simulated occupancy snapshot
span.graph

Simulate landscape dynamics over a number of time steps
rland.graph

Creates random landscape graph
simulate_graph

Simulate species occupancy in one dynamic landscape
simulatedifm

Set of simulated data to use with the IFM parameter estimation functions. The data were generated using the code provided in "details".
species.graph

Simulate landscape occupation
spom

Stochastic Patch Occupancy Model
rg_exp

List with range.expansion output
rland

Random landscape
cluster.graph

Delivers the number of patches per cluster
cluster.id

Classify patches in clusters
addpoints

Add a given number of patches to a landscape
components.graph

Number of components of a landscape
ifm.robust.MCMC

Estimate the robust design incidence function model