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).

AuthorFrederico Mestre, Fernando Canovas, Ricardo Pita, Antonio Mira, Pedro Beja.
Date of publication2017-01-19 18:31:21
MaintainerFrederico Mestre <mestre.frederico@gmail.com>
LicenseGPL (>= 2)
Version0.5.5

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

Functions

addpoints Man page
cabrera Man page
cluster.graph Man page
cluster.id Man page
components.graph Man page
convert.graph Man page
create.parameter.df Man page
edge.graph Man page
expansion Man page
extract.graph Man page
import.shape Man page
iterate.graph Man page
landscape Man page
landscape_change Man page
list.stats Man page
manage_expansion_sim Man page
manage_landscape_sim Man page
matrix.graph Man page
mc_df Man page
merge_order Man page
MetaLandSim Man page
MetaLandSim.GUI Man page
MetaLandSim-package Man page
metapopulation Man page
metrics.graph Man page
min_distance Man page
occ.landscape Man page
occ.landscape2 Man page
param1 Man page
param2 Man page
parameter.estimate Man page
plot_expansion Man page
plot_graph Man page
plotL.graph Man page
range_expansion Man page
range_raster Man page
removepoints Man page
remove.species Man page
rg_exp Man page
rland Man page
rland.graph Man page
simulate_graph Man page
span.graph Man page
species.graph Man page
spom Man page
summary_landscape Man page
summary_metapopulation Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.