Measurement of Biodiversity

[Up] [Top]

Documentation for package ‘mobr’ version 3.0.0

Help Pages

mobr-package Measurement of Biodiversity in R
avg_nn_dist Compute average nearest neighbor distance
calc_beta_div Calculate beta diversity from sites by species table.
calc_chao1 Estimation of species richness
calc_comm_div Calculate biodiversity statistics from sites by species table.
calc_C_target Calculate the recommended target coverage value for the computation of beta_C
calc_div Compute various diversity indices from a vector of species abundances (i.e., one row of a community matrix)
calc_PIE Calculate probability of interspecific encounter (PIE)
calc_SPIE Calculate S_PIE
calc_S_C Calculate species richness for a given coverage level.
Chat Calculate expected sample coverage C_hat
compare_samp_rarefaction Compare all sample-based curves (random, spatially constrained-k-NN, spatially constrained-k-NCN)
fire_comm Fire data set
fire_plot_attr Fire data set
get_delta_stats Conduct the MoB tests on drivers of biodiversity across scales.
get_mob_stats A now obsolete function that used to calculate sample based and group based biodiversity statistics.
get_null_comm Generate a null community matrix
invChat Number of individuals corresponding to a desired coverage (inverse C_hat)
inv_comm Invasive plants dataset
inv_plot_attr Invasive plants dataset
kNCN_average Construct spatially constrained sample-based rarefaction (sSBR) curve using the k-Nearest-Centroid-neighbor (k-NCN) algorithm
make_mob_in Create the 'mob_in' object.
mobr Measurement of Biodiversity in R
plot.mob_out Plot the multiscale MoB analysis output generated by 'get_delta_stats'.
plot.mob_stats Obsolete function that used to plot alpha- and gamma-scale biodiversity statistics for a MoB analysis
plot_abu Plot distributions of species abundance
plot_comm_div Plot alpha-, beta-, and gamma-scale biodiversity statistics for a MoB analysis
plot_N Plot the relationship between the number of plots and the number of individuals
plot_rarefaction Plot rarefaction curves for each treatment group
rarefaction Rarefied Species Richness
subset.mob_in Subset the rows of the mob data input object
tank_comm Cattle tank data set
tank_plot_attr Cattle tank data set