In KenLi93/CatchAll: Species Richness estimation with CatchAll

knitr::opts_chunk$set(echo = TRUE, warning = FALSE)

This package contains functions that estimate the species richness with finite exponential-mixed Poisson models (up to the three-component exponential mixed-Poisson model) and other state-of-art species richness estimators.

Installation

library(devtools)
install_github("KenLi93/CatchAll")

Basic Usage

library(CatchAll)
library(breakaway)
data(apples)

Poisson Model:

Poisson_model(apples, cutoff = 20)

Geometric model (or single exponential-mixed Poisson model):

geometric_model(apples, cutoff = 20)

Two- or three-component exponential mixture mixed Poisson model:

two_geometric_model(apples, cutoff = 50)

three_geometric_model(apples, cutoff = 70)

An integrated function for simultaneously viewing the results of all above models for different cut-off of species frequency counts.

apples_results <- all_parametric_model(apples)
head(apples_results, 10)

The richness estimates in CatchAll are displayed as follows:

apples_best_models <- catch_all(apples)
apples_best_models

KenLi93/CatchAll documentation built on May 7, 2019, 3:59 a.m.