Package: mobsim 0.3.1

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]

mobsim_0.3.1.tar.gz
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mobsim.pdf |mobsim.html✨
mobsim/json (API)
NEWS

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

Peer review:

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

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

On CRAN:

biodiversitymacroecologypoint-pattern-analysisrarefactionsimulationspeciesspecies-abundance-distributions

7.75 score 20 stars 75 scripts 184 downloads 24 exports 20 dependencies

Last updated 6 months agofrom:7c66cdb333. Checks:OK: 1 ERROR: 8. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 20 2024
R-4.5-win-x86_64ERRORNov 20 2024
R-4.5-linux-x86_64ERRORNov 20 2024
R-4.4-win-x86_64ERRORNov 20 2024
R-4.4-mac-x86_64ERRORNov 20 2024
R-4.4-mac-aarch64ERRORNov 20 2024
R-4.3-win-x86_64ERRORNov 20 2024
R-4.3-mac-x86_64ERRORNov 20 2024
R-4.3-mac-aarch64ERRORNov 20 2024

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

Analysis of biodiversity patterns

Felix May

Rendered fromBiodiversity_Patterns.Rmdusingknitr::rmarkdownon Nov 20 2024.

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

Changes of biodiversity components

Felix May

Rendered fromBiodiversity_Changes.Rmdusingknitr::rmarkdownon Nov 20 2024.

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

Introduction to mobsim

Felix May

Rendered fromIntroduction_mobsim.Rmdusingknitr::rmarkdownon Nov 20 2024.

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

Sampling communities with mobsim

Felix May

Rendered fromSampling_communities.Rmdusingknitr::rmarkdownon Nov 20 2024.

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

Simulating communities with mobsim

Felix May

Rendered fromSimulating_communities.Rmdusingknitr::rmarkdownon Nov 20 2024.

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

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