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).

Author
Frederico Mestre, Fernando Canovas, Ricardo Pita, Antonio Mira, Pedro Beja.
Date of publication
2016-10-04 00:06:32
Maintainer
Frederico Mestre <mestre.frederico@gmail.com>
License
GPL (>= 2)
Version
0.5.4

View on CRAN

Man pages

addpoints
Add a given number of patches to a landscape
cabrera
Modified patch occupancy data of Cabrera vole
cluster.graph
Delivers the number of patches per cluster
cluster.id
Classify patches in clusters
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
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...
mc_df
Modified patch occupancy data of Cabrera vole as a data frame
merge_order
Internal functions for the MetaLandSim package.
MetaLandSim.GUI
Graphic User Interface
MetaLandSim-package
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
plot_expansion
Graphical display of the expansion
plot_graph
Graphical display of the landscape
plotL.graph
Plot one landscape of the list created by span.graph
range_expansion
Produce a range expansion model
range_raster
Probability of occupancy, dispersal model
removepoints
Remove a given number of patches from the landscape
remove.species
Remove the species occupancy from the landscape
rg_exp
List with range.expansion output
rland
Random landscape
rland.graph
Creates random landscape graph
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

Files in this package

MetaLandSim
MetaLandSim/inst
MetaLandSim/inst/examples
MetaLandSim/inst/examples/presences.asc
MetaLandSim/inst/examples/landmask.asc.aux.xml
MetaLandSim/inst/examples/landmask.asc
MetaLandSim/inst/examples/presences.asc.aux.xml
MetaLandSim/inst/CITATION
MetaLandSim/inst/doc
MetaLandSim/inst/doc/parametrization.R
MetaLandSim/inst/doc/range_expansion.Rnw
MetaLandSim/inst/doc/range_expansion.R
MetaLandSim/inst/doc/range_expansion.pdf
MetaLandSim/inst/doc/parametrization.pdf
MetaLandSim/inst/doc/landscape_simulation.pdf
MetaLandSim/inst/doc/parametrization.Rnw
MetaLandSim/inst/doc/landscape_simulation.R
MetaLandSim/inst/doc/MetaLandSim.pdf
MetaLandSim/inst/doc/landscape_simulation.Rnw
MetaLandSim/inst/logo
MetaLandSim/inst/logo/logo.gif
MetaLandSim/inst/logo/logo2.gif
MetaLandSim/NAMESPACE
MetaLandSim/data
MetaLandSim/data/occ.landscape2.rda
MetaLandSim/data/rland.rda
MetaLandSim/data/occ.landscape.rda
MetaLandSim/data/param2.rda
MetaLandSim/data/datalist
MetaLandSim/data/rg_exp.rda
MetaLandSim/data/param1.rda
MetaLandSim/data/mc_df.rda
MetaLandSim/data/landscape_change.rda
MetaLandSim/data/cabrera.rda
MetaLandSim/R
MetaLandSim/R/parameter.estimate.R
MetaLandSim/R/extract.graph.R
MetaLandSim/R/min_distance.R
MetaLandSim/R/metrics.graph.R
MetaLandSim/R/remove.species.R
MetaLandSim/R/simulate_graph.R
MetaLandSim/R/attr_age_unique_landscape.R
MetaLandSim/R/manage_landscape_sim.R
MetaLandSim/R/cluster.id.R
MetaLandSim/R/manage_expansion_sim.R
MetaLandSim/R/range_expansion.R
MetaLandSim/R/convert.graph.R
MetaLandSim/R/species.graph.R
MetaLandSim/R/import.shape.R
MetaLandSim/R/list.stats.R
MetaLandSim/R/rland.graph.R
MetaLandSim/R/iterate.graph.R
MetaLandSim/R/removepoints.R
MetaLandSim/R/patch_age.R
MetaLandSim/R/addpoints.R
MetaLandSim/R/summary_metapopulation.R
MetaLandSim/R/plotL.graph.R
MetaLandSim/R/summary_landscape.R
MetaLandSim/R/merge_order.R
MetaLandSim/R/cluster.graph.R
MetaLandSim/R/plot_expansion.R
MetaLandSim/R/range_raster.R
MetaLandSim/R/spom.R
MetaLandSim/R/span.graph.R
MetaLandSim/R/MetaLandSim.GUI.R
MetaLandSim/R/matrix.graph.R
MetaLandSim/R/components.graph.R
MetaLandSim/R/create.parameter.df.R
MetaLandSim/R/plot_graph.R
MetaLandSim/R/edge.graph.R
MetaLandSim/vignettes
MetaLandSim/vignettes/range_expansion.Rnw
MetaLandSim/vignettes/succ.png
MetaLandSim/vignettes/parametrization.Rnw
MetaLandSim/vignettes/it1.png
MetaLandSim/vignettes/rg2.png
MetaLandSim/vignettes/landscape_simulation.Rnw
MetaLandSim/vignettes/rg1.png
MetaLandSim/MD5
MetaLandSim/build
MetaLandSim/build/vignette.rds
MetaLandSim/DESCRIPTION
MetaLandSim/man
MetaLandSim/man/expansion.Rd
MetaLandSim/man/range_raster.Rd
MetaLandSim/man/remove.species.Rd
MetaLandSim/man/summary_landscape.Rd
MetaLandSim/man/plotL.graph.Rd
MetaLandSim/man/extract.graph.Rd
MetaLandSim/man/import.shape.Rd
MetaLandSim/man/plot_graph.Rd
MetaLandSim/man/simulate_graph.Rd
MetaLandSim/man/removepoints.Rd
MetaLandSim/man/min_distance.Rd
MetaLandSim/man/occ.landscape2.Rd
MetaLandSim/man/cluster.graph.Rd
MetaLandSim/man/list.stats.Rd
MetaLandSim/man/MetaLandSim-package.Rd
MetaLandSim/man/convert.graph.Rd
MetaLandSim/man/param1.Rd
MetaLandSim/man/create.parameter.df.Rd
MetaLandSim/man/mc_df.Rd
MetaLandSim/man/metrics.graph.Rd
MetaLandSim/man/iterate.graph.Rd
MetaLandSim/man/span.graph.Rd
MetaLandSim/man/rland.graph.Rd
MetaLandSim/man/spom.Rd
MetaLandSim/man/addpoints.Rd
MetaLandSim/man/summary_metapopulation.Rd
MetaLandSim/man/cluster.id.Rd
MetaLandSim/man/rland.Rd
MetaLandSim/man/species.graph.Rd
MetaLandSim/man/merge_order.Rd
MetaLandSim/man/rg_exp.Rd
MetaLandSim/man/parameter.estimate.Rd
MetaLandSim/man/cabrera.Rd
MetaLandSim/man/manage_expansion_sim.Rd
MetaLandSim/man/components.graph.Rd
MetaLandSim/man/matrix.graph.Rd
MetaLandSim/man/occ.landscape.Rd
MetaLandSim/man/param2.Rd
MetaLandSim/man/edge.graph.Rd
MetaLandSim/man/metapopulation.Rd
MetaLandSim/man/landscape.Rd
MetaLandSim/man/plot_expansion.Rd
MetaLandSim/man/landscape_change.Rd
MetaLandSim/man/MetaLandSim.GUI.Rd
MetaLandSim/man/range_expansion.Rd
MetaLandSim/man/manage_landscape_sim.Rd