Package: metaRange 1.1.4

Stefan Fallert

metaRange: Framework to Build Mechanistic and Metabolic Constrained Species Distribution Models

Build spatially and temporally explicit process-based species distribution models, that can include an arbitrary number of environmental factors, species and processes including metabolic constraints and species interactions. The focus of the package is simulating populations of one or multiple species in a grid-based landscape and studying the meta-population dynamics and emergent patterns that arise from the interaction of species under complex environmental conditions. It provides functions for common ecological processes such as negative exponential, kernel-based dispersal (see Nathan et al. (2012) <doi:10.1093/acprof:oso/9780199608898.003.0015>), calculation of the environmental suitability based on cardinal values ( Yin et al. (1995) <doi:10.1016/0168-1923(95)02236-Q>, simplified by Yan and Hunt (1999) <doi:10.1006/anbo.1999.0955> see eq: 4), reproduction in form of an Ricker model (see Ricker (1954) <doi:10.1139/f54-039> and Cabral and Schurr (2010) <doi:10.1111/j.1466-8238.2009.00492.x>), as well as metabolic scaling based on the metabolic theory of ecology (see Brown et al. (2004) <doi:10.1890/03-9000> and Brown, Sibly and Kodric-Brown (2012) <doi:10.1002/9781119968535.ch>).

Authors:Stefan Fallert [aut, cre, cph], Lea Li [aut, cph], Juliano Sarmento Cabral [aut, cph, ths], Tyler Morgan-Wall [ctb, cph], Bavarian Ministry of Science and Arts [fnd], Deutsche Bundesstiftung Umwelt [fnd]

metaRange_1.1.4.tar.gz
metaRange_1.1.4.tar.gz(r-4.5-noble)metaRange_1.1.4.tar.gz(r-4.4-noble)
metaRange_1.1.4.tgz(r-4.4-emscripten)metaRange_1.1.4.tgz(r-4.3-emscripten)
metaRange.pdf |metaRange.html
metaRange/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/metarange/metarange/issues

Pkgdown:https://metarange.github.io

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3

openblascpp

4.00 score 11 scripts 182 downloads 16 exports 6 dependencies

Last updated 10 months agofrom:b40940b651. Checks:OK: 2. Indexed: no.

TargetResultDate
Doc / VignettesOKDec 06 2024
R-4.5-linux-x86_64OKDec 06 2024

Exports:calculate_dispersal_kernelcalculate_normalization_constantcalculate_suitabilitycreate_simulationdispersalmetabolic_scalingmetaRangeEnvironmentmetaRangePriorityQueuemetaRangeProcessmetaRangeSimulationmetaRangeSpeciesnegative_exponential_functionricker_allee_reproduction_modelricker_reproduction_modelsave_speciesset_verbosity

Dependencies:backportscheckmateR6RcppRcppArmadilloterra

01: Introduction to metaRange

Rendered fromA01_intro.Rmdusingknitr::rmarkdownon Dec 06 2024.

Last update: 2024-02-10
Started: 2023-11-24

02: Multiple species

Rendered fromA02_multiple_species.Rmdusingknitr::rmarkdownon Dec 06 2024.

Last update: 2024-02-10
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03: Niche suitability

Rendered fromA03_niche_suitability.Rmdusingknitr::rmarkdownon Dec 06 2024.

Last update: 2024-02-10
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04: Dispersal

Rendered fromA04_dispersal.Rmdusingknitr::rmarkdownon Dec 06 2024.

Last update: 2024-02-10
Started: 2023-11-24

05: Species interactions

Rendered fromA05_species_interactions.Rmdusingknitr::rmarkdownon Dec 06 2024.

Last update: 2024-02-10
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06: Metabolic scaling

Rendered fromA06_metabolic_scaling.Rmdusingknitr::rmarkdownon Dec 06 2024.

Last update: 2024-02-10
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07: Age structured populations

Rendered fromA07_age_structured_populations.Rmdusingknitr::rmarkdownon Dec 06 2024.

Last update: 2024-02-10
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08: Advanced options

Rendered fromA08_advanced_options.Rmdusingknitr::rmarkdownon Dec 06 2024.

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09: Troubleshooting / caveats

Rendered fromA09_troubleshooting_and_caveats.Rmdusingknitr::rmarkdownon Dec 06 2024.

Last update: 2024-02-10
Started: 2023-11-24

Readme and manuals

Help Manual

Help pageTopics
Calculate 2D dispersal kernel.calculate_dispersal_kernel
Normalization constant calculationcalculate_normalization_constant
Calculate (estimate) environmental suitabilitycalculate_suitability
Create a simulationcreate_simulation
Dispersal processdispersal
Metabolic scalingmetabolic_scaling
metaRangeEnvironment objectmetaRangeEnvironment
Process priority queuemetaRangePriorityQueue
metaRangeProcess objectmetaRangeProcess
metaRangeSimulation objectmetaRangeSimulation
metaRangeSpecies objectmetaRangeSpecies
Negative Exponential kernelnegative_exponential_function
Plotting functionplot.metaRangeEnvironment
Plotting functionplot.metaRangeSimulation
Plotting functionplot.metaRangeSpecies
Print traits or globalsprint.metaRangeVariableStorage
Ricker reproduction model with Allee effectsricker_allee_reproduction_model
Ricker reproduction modelricker_reproduction_model
Save functionsave_species
Set verbosity of metaRange simulationset_verbosity
Summary for metaRange simulationsummary.metaRangeSimulation
Summary for metaRange speciessummary.metaRangeSpecies