Spatial Simulation and Scale-Dependent Analysis of Biodiversity Changes

Tools for the simulation, analysis and sampling of spatial biodiversity data (May et al. 2017) . 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.


The goal of the package is to facilitate understanding of scale-dependent biodiversity changes.

The package includes functions to simulate species distributions in space with controlled abundance distributions as well as controlled intraspecific aggregation. For analysis there are functions for species rarefaction and accumulation curves, species-area relationships, endemics-area relationships and th distance-decay of community similarity.

Installation

Sometimes the function devtools::install_github() does not install dependencies correctly. To be save it is better to install the dependencies of mobsim first.

install.packages("Rcpp","vegan","sads","rmarkdown","spatstat","testthat","knitr")

You can install mobsim from github with:

devtools::install_github("MoBiodiv/mobsim", build_vignettes = TRUE)

Getting help

You can get an overview of the available functions in mobsim:

?mobsim

Or have a look at tutorials in the vignette:

browseVignettes("mobsim")

Example

Here is an example of how to simulate two communities, which just differ in their spatial aggregation of species, but have the same species abundance distribution and the same total number of individuals.

Simulation of communities

library(mobsim)
comm_rand <- sim_poisson_community(s_pool = 30, n_sim = 300)
comm_agg <- sim_thomas_community(s_pool = 30, n_sim = 300, sigma = 0.05, mother_points = 1)
par(mfrow = c(1,2))
plot(comm_rand)
plot(comm_agg)

Analysis of spatially-explicit community data

mobsim mobsim offer functions to analyse spatially-explicit community data. For example the species-area relationship of a community can be easily evaluated.

sar_rand <- divar(comm_rand)
sar_agg <- divar(comm_agg)
plot(m_species ~ prop_area, data = sar_rand, type = "b", log = "xy",
     xlab = "Proportion of area sampled",ylab = "No. of species",
     ylim = c(3,30))
lines(m_species ~ prop_area, data = sar_agg, type = "b", col = 2)
legend("bottomright", c("Random","Aggregated"), col = 1:2, lwd = 2)

Sampling of communities

Simulated or observed communities can be also sampled inorder to test whether biodiversity changes are correctly detected and revealed by any sampling design.

par(mfrow = c(1,2))
samples_rand <- sample_quadrats(comm_rand, avoid_overlap = TRUE)
samples_agg <- sample_quadrats(comm_agg, avoid_overlap = TRUE)

News

Reference manual

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install.packages("mobsim")

0.1.0 by Felix May, a year ago


http://github.com/MoBiodiv/mobsim


Report a bug at https://github.com/MoBiodiv/mobsim


Browse source code at https://github.com/cran/mobsim


Authors: Felix May [aut, cre]


Documentation:   PDF Manual  


GPL-3 license


Imports Rcpp, vegan, sads, grDevices, utils, graphics, stats

Suggests rmarkdown, spatstat, testthat, knitr

Linking to Rcpp


See at CRAN