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popbio

popbio is an R package for modeling population growth rates using age- or stage-classified matrix models. The package consists mainly of methods described in Hal Caswell's Matrix Population Models (2001) and Morris and Doak's Quantitative Conservation Biology (2002). The R code was first submitted to CRAN in 2007.

See the wiki for more details.

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Version

Install

install.packages('popbio')

Monthly Downloads

2,335

Version

2.4.4

License

GPL-3

Maintainer

Chris Stubben

Last Published

May 3rd, 2018

Functions in popbio (2.4.4)

Annual census data for Aquilegia in the southwestern US

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

Converted Matlab functions from Morris and Doak (2002)

Create a projection matrix for Aquilegia

fundamental.matrix

Fundamental matrix and age-specific survival

Life Table Response Experiment

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

generation.time

Generation time

Annual transition data for Aquilegia in the southwestern US

Projection matrices for a tropical understory herb

boot.transitions

Bootstrap observed census transitions

01.Introduction

Introduction to the popbio Package

Generate beta-distributed random numbers

Projection matrices for mountain golden heather

Converted Matlab functions from Caswell (2001)

Correlation matrices for Hudsonia vital rates

Best Kendall estimates of Hudsonia vital rate means and variances

Matrix definition program for Hudsonia vital rates

Eigenvalue and eigenvector analysis of a projection matrix

Square matrices

net.reproductive.rate

Net reproductive rate

Elasticity analysis of a projection matrix

Plot a simple guide to colors

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

Population sizes of grizzly bears in Yellowstone from 1959-1997

stoch.projection

Simulate stochastic growth from a sequence of matrices

Return the first and last part of a matrix or dataframe

stoch.quasi.ext

Calculate quasi-extinction threshold

Count-based extinction probabilities and bootstrap confidence intervals

Projection matrix for teasel

Count-based extinction time cumulative distribution function

stage.vector.plot

Plot stage vector projections

stoch.growth.rate

Calculate log stochastic growth rate

Census data for hypothetical plant

Display a matrix image

Population growth rate

Plot logistic regression

Generate random lognormal values for fertility rates

Calculate population growth rates by projection

projection.matrix

Construct projection matrix models using transition frequency tables

Projection matrices for desert tortoise

Incorporate demographic stochasticity into population projections

Population densities for the sugarbeet cyst nematode

Calculate a variance matrix

Survirvorship data for adult and juvenile Acorn Woodpeckers

Split a projection matrix into separate T and F matrices

Stable stage distribution

reproductive.value

Stable stage distribution

Resample a projection matrix

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

Projection matrix for killer whale

Generate stretched beta-distributed random numbers

Calculate mean matrix

Projection matrices for monkeyflower

Sensitivity analysis of a projection matrix

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

Vital rate sensitivities and elasticities