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popbio (version 2.4.3)

Construction and Analysis of Matrix Population Models

Description

Construct and analyze projection matrix models from a demography study of marked individuals classified by age or stage. The package covers methods described in Matrix Population Models by Caswell (2001) and Quantitative Conservation Biology by Morris and Doak (2002).

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Version

Install

install.packages('popbio')

Monthly Downloads

1,640

Version

2.4.3

License

GPL-3

Maintainer

Chris Stubben

Last Published

April 1st, 2016

Functions in popbio (2.4.3)

Generate beta-distributed random numbers

Stable stage distribution

Calculate population growth rates by projection

Generate random lognormal values for fertility rates

Square matrices

Count-based extinction probabilities and bootstrap confidence intervals

Find the best Kendall's estimates of mean and environmental variance for beta-binomial vital rates.

Calculate a variance matrix

Converted Matlab functions from Caswell (2001)

net.reproductive.rate

Net reproductive rate

Create a projection matrix for Aquilegia

Estimate the variance of beta-binomial vital rates using approximation method of Akcakaya

Sensitivity analysis of a projection matrix

01.Introduction

Introduction to the popbio Package

Best Kendall estimates of Hudsonia vital rate means and variances

Return the first and last part of a matrix or dataframe

Calculate stochastic growth rate and extinction time CDF using vital rates with within-year, auto-, and cross-correlations

stoch.growth.rate

Calculate log stochastic growth rate

Correlation matrices for Hudsonia vital rates

Converted Matlab functions from Morris and Doak (2002)

Projection matrices for mountain golden heather

Eigenvalue and eigenvector analysis of a projection matrix

Projection matrices for desert tortoise

Population growth rate

fundamental.matrix

Fundamental matrix and age-specific survival

Projection matrix for teasel

Build a projection matrix from a time series of individuals (or densities) per stage.

boot.transitions

Bootstrap observed census transitions

Incorporate demographic stochasticity into population projections

Generate stretched beta-distributed random numbers

Population sizes of grizzly bears in Yellowstone from 1959-1997

Display a matrix image

Plot logistic regression

Census data for hypothetical plant

generation.time

Generation time

Split a projection matrix into separate T and F matrices

Projection matrices for monkeyflower

Create log-log plots of variance vs. sensitivity and CV vs. elasticity

Annual census data for Aquilegia in the southwestern US

Elasticity analysis of a projection matrix

Count-based extinction time cumulative distribution function

Life Table Response Experiment

projection.matrix

Construct projection matrix models using transition frequency tables

Calculate mean matrix

stage.vector.plot

Plot stage vector projections

Resample a projection matrix

stoch.projection

Simulate stochastic growth from a sequence of matrices

Matrix definition program for Hudsonia vital rates

Projection matrices for a tropical understory herb

stoch.quasi.ext

Calculate quasi-extinction threshold

Annual transition data for Aquilegia in the southwestern US

Survirvorship data for adult and juvenile Acorn Woodpeckers

Projection matrix for killer whale

Population densities for the sugarbeet cyst nematode

reproductive.value

Stable stage distribution

Vital rate sensitivities and elasticities