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MetaLandSim

Metapopulations Persistence and Range Expansion Simulation MetaLandSim is intended to provide a virtual environment, enabling the experimentation and simulation of processes at two scales: landscape and range. The simulation approach, taken by MetaLandSim, presents several advantages, like allowing the test of several alternatives and the knowledge of the full system. The role of simulation in landscape ecology is fundamental due to the spatial and temporal scale of the studied phenomena, which frequently hinders experimentation.

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Version

Install

install.packages('MetaLandSim')

Monthly Downloads

311

Version

1.0.10

License

GPL (>= 2)

Maintainer

Frederico Mestre

Last Published

June 30th, 2022

Functions in MetaLandSim (1.0.10)

accept.calculate

Calculate acceptance rates in MCMC chains

Create files for use with R-package coda.

Function for mode estimation of a continuous variable

Combines two chains into a single chain.

Add a given number of patches to a landscape

Classify patches in clusters

Modified patch occupancy data of Cabrera vole

Delivers the number of patches per cluster

components.graph

Number of components of a landscape

Convert data frame to landscape

Class 'expansion'

MetaLandSim.GUI

Graphic User Interface

MetaLandSim-package

Landscape And Range Expansion Simulation

create.parameter.df

Create parameter data frame

Import a shapefile

Extract landscape from span.graph generated list

ifm.robust.MCMC

Estimate the robust design incidence function model

Estimate the naive design incidence function model

ifm.missing.MCMC

Estimate the 'missing' design incidence function model

Produce an edge (links) data frame

landscape_change

Landscape loosing 5% of patches per time step

Returning a matrix with information on connections between patches

Returning information on a dynamic landscape list

manage_expansion_sim

Simulate range expansion simulation

manage_landscape_sim

Batch landscape simulation

Simulate landscape series occupation

Class 'landscape'

Graphical display of the expansion

Graphical display of the landscape

Computes landscape connectivity metrics

Computes topological distance

MetaLandSim-internal

Internal functions for the MetaLandSim package.

Class 'metapopulation'

Sample landscape with one simulated occupancy snapshot

Sample landscape with 10 simulated occupancy snapshots

Modified patch occupancy data of Cabrera vole as a data frame

parameter.estimate

Estimate parameters

Sample parameter data frame number 1

Sample parameter data frame number 2

Plot one landscape of the list created by span.graph

range_expansion

Produce a range expansion model

Probability of occupancy, dispersal model

Remove a given number of patches from the landscape

Remove the species occupancy from the landscape

Array corresponding to nsites x nyears x nvisits

Distance matrix between sampling sites (nsite x nsite).

Creates random landscape graph

summary_landscape

Summarize 'landscape' class objects

Stochastic Patch Occupancy Model

summary_metapopulation

Summarize 'metapopulation' class objects

Occupancy data generated with perfect detection with approximately 20% of data missing at random.

Occupancy data generated with perfect detection.

Occupancy data containing false absences

Simulate landscape dynamics over a number of time steps

Simulate landscape occupation

List with range.expansion output

Random landscape

Simulate species occupancy in one dynamic landscape

Vector of the areas for each site; here, 100 sites

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