Package: MetaLandSim 2.0.0

MetaLandSim: Landscape and Range Expansion Simulation

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). References: Mestre, F., Canovas, F., Pita, R., Mira, A., Beja, P. (2016) <doi:10.1016/j.envsoft.2016.03.007>; Mestre, F., Risk, B., Mira, A., Beja, P., Pita, R. (2017) <doi:10.1016/j.ecolmodel.2017.06.013>; Mestre, F., Pita, R., Mira, A., Beja, P. (2020) <doi:10.1186/s12898-019-0273-5>.

Authors:Frederico Mestre, Fernando Canovas, Benjamin Risk, Ricardo Pita, Antonio Mira, Pedro Beja.

MetaLandSim_2.0.0.tar.gz
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MetaLandSim.pdf |MetaLandSim.html✨
MetaLandSim/json (API)

# Install 'MetaLandSim' in R:
install.packages('MetaLandSim', repos = c('https://fmestre1.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/fmestre1/metalandsim/issues

Datasets:
  • cabrera - Modified patch occupancy data of Cabrera vole
  • landscape_change - Landscape loosing 5% of patches per time step
  • mc_df - Modified patch occupancy data of Cabrera vole as a data frame
  • 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
  • rg_exp - List with range.expansion output
  • rland - Random landscape
  • 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).
  • 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

On CRAN:

biogeographyecologymetapopulationspecies

5.10 score 3 stars 28 scripts 596 downloads 39 exports 35 dependencies

Last updated 2 years agofrom:0bb7922ce6. Checks:OK: 3 NOTE: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 13 2024
R-4.5-winNOTENov 13 2024
R-4.5-linuxNOTENov 13 2024
R-4.4-winNOTENov 13 2024
R-4.4-macNOTENov 13 2024
R-4.3-winOKNov 13 2024
R-4.3-macOKNov 13 2024

Exports:accept.calculateaddpointscalcmodecluster.graphcluster.idcoda.createcombine.chainscomponents.graphconvert.graphcreate.parameter.dfedge.graphextract.graphifm.missing.MCMCifm.naive.MCMCifm.robust.MCMCimport.shapeiterate.graphlist.statsmanage_expansion_simmanage_landscape_simmatrix.graphmerge_ordermetrics.graphmin_distanceparameter.estimateplot_expansionplot_graphplotL.graphrange_expansionrange_rasterremove.speciesremovepointsrland.graphsimulate_graphspan.graphspecies.graphspomsummary_landscapesummary_metapopulation

Dependencies:classclicodacpp11deldire1071evaluategluegoogleVishighrigraphjsonliteknitrlatticelifecyclemagrittrMASSMatrixminpack.lmpkgconfigpolyclipproxyRcpprlangspspatstat.dataspatstat.geomspatstat.randomspatstat.univarspatstat.utilsterravctrsxfunyamlzipfR

Landscape Occupation Simulation in Dynamic Landscapes

Rendered fromlandscape_simulation-knitr.Rnwusingutils::Sweaveon Nov 13 2024.

Last update: 2018-01-03
Started: 2017-12-21

Model Parametrization

Rendered fromparameter_estimation-knitr.Rnwusingutils::Sweaveon Nov 13 2024.

Last update: 2018-01-03
Started: 2017-12-21

Range Expansion Simulation

Rendered fromrange_expansion-knitr.Rnwusingutils::Sweaveon Nov 13 2024.

Last update: 2023-01-12
Started: 2017-12-21

Readme and manuals

Help Manual

Help pageTopics
Landscape And Range Expansion SimulationMetaLandSim-package MetaLandSim
Calculate acceptance rates in MCMC chainsaccept.calculate
Add a given number of patches to a landscapeaddpoints
Modified patch occupancy data of Cabrera volecabrera
Function for mode estimation of a continuous variablecalcmode
Delivers the number of patches per clustercluster.graph
Classify patches in clusterscluster.id
Create files for use with R-package coda.coda.create
Combines two chains into a single chain.combine.chains
Number of components of a landscapecomponents.graph
Convert data frame to landscapeconvert.graph
Create parameter data framecreate.parameter.df
Produce an edge (links) data frameedge.graph
Class 'expansion'expansion
Extract landscape from span.graph generated listextract.graph
Estimate the 'missing' design incidence function modelifm.missing.MCMC
Estimate the naive design incidence function modelifm.naive.MCMC
Estimate the robust design incidence function modelifm.robust.MCMC
Import a shapefileimport.shape
Simulate landscape series occupationiterate.graph
Class 'landscape'landscape
Landscape loosing 5% of patches per time steplandscape_change
Returning information on a dynamic landscape listlist.stats
Simulate range expansion simulationmanage_expansion_sim
Batch landscape simulationmanage_landscape_sim
Returning a matrix with information on connections between patchesmatrix.graph
Modified patch occupancy data of Cabrera vole as a data framemc_df
Internal functions for the MetaLandSim package.merge_order
Class 'metapopulation'metapopulation
Computes landscape connectivity metricsmetrics.graph
Computes topological distancemin_distance
Sample landscape with one simulated occupancy snapshotocc.landscape
Sample landscape with 10 simulated occupancy snapshotsocc.landscape2
Sample parameter data frame number 1param1
Sample parameter data frame number 2param2
Estimate parametersparameter.estimate
Graphical display of the expansion simulationsplot_expansion
Graphical display of the landscapeplot_graph
Plot one landscape of the list created by span.graphplotL.graph
Computes a range expansion modelrange_expansion
Probability of occupancy, dispersal modelrange_raster
Remove the species occupancy from the landscaperemove.species
Remove a given number of patches from the landscaperemovepoints
List with range.expansion outputrg_exp
Random landscaperland
Creates random landscape graphrland.graph
Vector of the areas for each site; here, 100 sitessim.area
Array corresponding to nsites x nyears x nvisitssim.det.20
Distance matrix between sampling sites (nsite x nsite).sim.distance
Simulate species occupancy in one dynamic landscapesimulate_graph
Set of simulated data to use with the IFM parameter estimation functions. The data were generated using the code provided in "details".simulatedifm
Simulate landscape dynamics over a number of time stepsspan.graph
Simulate landscape occupationspecies.graph
Stochastic Patch Occupancy Modelspom
Summarize 'landscape' class objectssummary_landscape
Summarize 'metapopulation' class objectssummary_metapopulation
Occupancy data generated with perfect detection.z.sim
Occupancy data generated with perfect detection with approximately 20% of data missing at random.z.sim.20
Occupancy data containing false absencesz.sim.20.fa