diversityoccu: Calculates alpha diversity from multiple species occupancy data

Description

This function takes a data.frame with multiple presence absence-data from various species in different sites, covariates of each site to calculate occupancy, variables specific to sampling days to calculate probability of detection, and it calculates the alpha diversity for each site.

Usage

diversityoccu(pres, sitecov, obscov, spp, form, index = "shannon", dredge = FALSE)

Arguments

pres

a data.frame where rows are the sites and columns are a series of presence-absence observation from multiple species, every species needs to have the same number of observations.

sitecov

a data.frame where every row is a site, and every column is a measurement of that site, such as elevation or slope, this covariates are usually more constant.

obscov

a list where every element is a data frame with the daily covariates for each site, that is a measurement for each day, such as average temperature of a day, this covariates are usually very .

spp

the number of species in the pres data.frame

form

a formula in the format ~ obscov ~ sitcov, the first arguments will be used to calculate probability of detection and the second part the occupancy.

index

Diversity index, one of "shannon", "simpson" or "invsimpson".

dredge

default = FALSE, if TRUE, for each species, the best occupancy model will be determined by fitting all possible models and ranking by AICc.

Value

A list with the fitted models for each species, the calculated Alpha diversity for each site, and a dataframe with the abundance of each species and diversity.

Details

This function fits the latent abundance mixture model described in Royle and Nichols (2003), to calculate the abundance of every species in each site, the using that abundance it calculates the alpha diversity index for each site based on that abundance.

Examples

Run this code

## Not run: 
# #Load the data
# data("IslandBirds")
# data("Daily_Cov")
# data("siteCov")
# 
# #Model the abundance for  5 bird species and calculate alpha diversity from that
# 
# BirdDiversity <-diversityoccu(pres = IslandBirds, sitecov = siteCov,
# obscov = Daily_Cov,spp =  5, form = ~ Day + Wind + Time + Rain +
# Noise ~ Elev + AgroFo + SecVec + Wetland + Upland)
# 
# #To see the estimates and p values for each model:
# 
# BirdDiversity$models
# ## End(Not run)