Learn R Programming

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.

Copy Link

Version

Install

install.packages('MetaLandSim')

Monthly Downloads

311

Version

2.0.0

License

GPL (>= 2)

Maintainer

Frederico Mestre

Last Published

January 12th, 2023

Functions in MetaLandSim (2.0.0)

Estimate the naive design incidence function model

Extract landscape from span.graph generated list

Import a shapefile

Convert data frame to landscape

Class 'expansion'

Produce an edge (links) data frame

ifm.missing.MCMC

Estimate the 'missing' design incidence function model

create.parameter.df

Create parameter data frame

Class 'metapopulation'

Simulate landscape series occupation

Returning a matrix with information on connections between patches

manage_landscape_sim

Batch landscape simulation

manage_expansion_sim

Simulate range expansion simulation

Returning information on a dynamic landscape list

ifm.robust.MCMC

Estimate the robust design incidence function model

MetaLandSim-internal

Internal functions for the MetaLandSim package.

Computes topological distance

Modified patch occupancy data of Cabrera vole as a data frame

Computes landscape connectivity metrics

Graphical display of the landscape

range_expansion

Computes a range expansion model

Sample landscape with one simulated occupancy snapshot

Plot one landscape of the list created by span.graph

Sample landscape with 10 simulated occupancy snapshots

Creates random landscape graph

Graphical display of the expansion simulations

Sample parameter data frame number 1

Array corresponding to nsites x nyears x nvisits

Random landscape

Remove a given number of patches from the landscape

Simulate species occupancy in one dynamic landscape

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

List with range.expansion output

Simulate landscape dynamics over a number of time steps

summary_landscape

Summarize 'landscape' class objects

Class 'landscape'

Distance matrix between sampling sites (nsite x nsite).

Stochastic Patch Occupancy Model

Simulate landscape occupation

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

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

Occupancy data generated with perfect detection.

landscape_change

Landscape loosing 5% of patches per time step

Sample parameter data frame number 2

summary_metapopulation

Summarize 'metapopulation' class objects

parameter.estimate

Estimate parameters

Remove the species occupancy from the landscape

Probability of occupancy, dispersal model

Occupancy data containing false absences

components.graph

Number of components of a landscape

Combines two chains into a single chain.

Function for mode estimation of a continuous variable

accept.calculate

Calculate acceptance rates in MCMC chains

Classify patches in clusters

Delivers the number of patches per cluster

Add a given number of patches to a landscape

MetaLandSim-package

Landscape And Range Expansion Simulation

Modified patch occupancy data of Cabrera vole

Create files for use with R-package coda.