Package: mobsim 0.3.2

Felix May

mobsim: Spatial Simulation and Scale-Dependent Analysis of Biodiversity Changes

Simulation, analysis and sampling of spatial biodiversity data (May, Gerstner, McGlinn, Xiao & Chase 2017) <doi:10.1111/2041-210x.12986>. In the simulation tools user define the numbers of species and individuals, the species abundance distribution and species aggregation. Functions for analysis include species rarefaction and accumulation curves, species-area relationships and the distance decay of similarity.

Authors:Felix May [aut, cre, cph], Alban Sagouis [aut], German Centre for Integrative Biodiversity Research Halle-Jena-Leipzig [fnd], Freie Universität Berlin [fnd]

mobsim_0.3.2.tar.gz
mobsim_0.3.2.zip(r-4.7)mobsim_0.3.2.zip(r-4.6)mobsim_0.3.2.zip(r-4.5)
mobsim_0.3.2.tgz(r-4.6-x86_64)mobsim_0.3.2.tgz(r-4.6-arm64)mobsim_0.3.2.tgz(r-4.5-x86_64)mobsim_0.3.2.tgz(r-4.5-arm64)
mobsim_0.3.2.tar.gz(r-4.7-arm64)mobsim_0.3.2.tar.gz(r-4.7-x86_64)mobsim_0.3.2.tar.gz(r-4.6-arm64)mobsim_0.3.2.tar.gz(r-4.6-x86_64)
mobsim_0.3.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
mobsim/json (API)

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

Bug tracker:https://github.com/mobiodiv/mobsim/issues

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

On CRAN:

Conda:

biodiversitymacroecologypoint-pattern-analysisrarefactionsimulationspeciesspecies-abundance-distributionscpp

7.21 score 21 stars 104 scripts 243 downloads 24 exports 20 dependencies

Last updated from:ef1e5ce9f9. Checks:13 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK168
linux-devel-x86_64OK175
source / vignettesOK224
linux-release-arm64OK163
linux-release-x86_64OK179
macos-release-arm64OK169
macos-release-x86_64OK372
macos-oldrel-arm64OK172
macos-oldrel-x86_64OK379
windows-develOK152
windows-releaseOK141
windows-oldrelOK124
wasm-releaseOK140

Exports:abund_rectcommunitycommunity_to_saddist_decaydist_decay_quadratsdiv_rand_rectdiv_rectdivarrare_curverThomas_rcppsample_quadratssampling_gridssampling_one_quadratsampling_random_bruteforcesampling_random_overlapsampling_random_spatstatsampling_transectssim_poisson_communitysim_poisson_coordssim_sadsim_thomas_communitysim_thomas_coordsspec_samplespec_sample_curve

Dependencies:bbmlebdsmatrixclusterGUILDSlatticeMASSMatrixmgcvmvtnormnlmenloptrnumDerivpermutepoilogpoweRlawpracmaRcppsadsveganVGAM

Changes of biodiversity components
Introduction | Change in total number of individuals | Change in the abundance distribution | Change in spatial distributions
Rendered fromBiodiversity_Changes.Rmdusingknitr::rmarkdown

Last update: 2024-03-21
Started: 2016-11-02

Introduction to mobsim
An example application of mobsim | Simulating communities | Analysis of spatially-explicit community data | Sampling spatially-explicit community data | Analysis of plot-based community data | Small scale analysis | Large scale analysis | Compare results across scales | Conclusion
Rendered fromIntroduction_mobsim.Rmdusingknitr::rmarkdown

Last update: 2024-03-21
Started: 2017-05-02

Sampling communities with mobsim
Random sampling | Transect sampling | Grid sampling
Rendered fromSampling_communities.Rmdusingknitr::rmarkdown

Last update: 2024-03-21
Started: 2017-09-27

Simulating communities with mobsim
Biodiversity components | Simulating species abundance distributions | Simulate spatial distributions | Random distributions | Aggregated positions | References
Rendered fromSimulating_communities.Rmdusingknitr::rmarkdown

Last update: 2024-03-21
Started: 2017-07-29

Analysis of biodiversity patterns
Simulate and explore data | Non-spatial patterns | Species abundance distribution (SAD) | Rarefaction curve | Spatial patterns | Species-accumulation curve | Diversity-area relationships | Distance decay of community similarity | References
Rendered fromBiodiversity_Patterns.Rmdusingknitr::rmarkdown

Last update: 2017-11-01
Started: 2016-11-02

Readme and manuals

Help Manual

Help pageTopics
-------------------------- Get local species abundance distributionabund_rect
Create spatial community objectcommunity
Get species abundance distribution from community objectcommunity_to_sad
Distance decay of similaritydist_decay
Distance decay of similarity with user-defined quadratsdist_decay_quadrats
Distribution of local diversity indicesdiv_rand_rect
Get local diversity indicesdiv_rect
Diversity-area relationshipsdivar
Plot spatial community objectplot.community
Plot distance decay of similarityplot.dist_decay
-------------------------- Plot diversity-area relationshipsplot.divar
Plot species abundance distributionsplot.sad
Plot species sampling curvesplot.spec_sample_curve
Species rarefaction curverare_curve
Thomas process individual distribution simulation for one speciesrThomas_rcpp
Plot-based samples from a spatially-explicit censussample_quadrats
Creates square quadrats aligned on a regular gridsampling_grids
Creates one square quadrat randomly located in the landscapesampling_one_quadrat
Creates coordinates (lower left corner of a quadrat) randomly distributed but without overlapping each othersampling_random_bruteforce
Creates coordinates (lower left corner of a quadrat) randomly distributed that may overlap each othersampling_random_overlap
Creates coordinates (lower left corner of a quadrat) randomly distributed but without overlapping each othersampling_random_spatstat
Creates square quadrats aligned along a transectsampling_transects
Simulate community with random spatial positions.sim_poisson_community
Simulate random spatial coordinatessim_poisson_coords
Simulate species abundance distributionssim_sad
Simulate community with clumped spatial positions.sim_thomas_community
Simulate clumped spatial coordinatessim_thomas_coords
Sample species richnessspec_sample
Non-spatial and spatially-explicit species sampling curvesspec_sample_curve
Print summary of spatial community objectsummary.community
Print summary of species abundance distribution objectsummary.sad