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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

2,290

Version

2.8

License

GPL-3

Maintainer

Last Published

March 28th, 2024

Functions in popbio (2.8)

Population growth rate

Count-based extinction time cumulative distribution function

Return the first and last part of a matrix or dataframe

Best Kendall estimates of Hudsonia vital rate means and variances

Generate random lognormal values for fertility rates

net.reproductive.rate

Net reproductive rate

Population densities for the sugarbeet cyst nematode

Display a matrix image

Incorporate demographic stochasticity into population projections

Stochastic growth rate sensitivity

Projection matrices for monkeyflower

stoch.quasi.ext

Quasi-extinction threshold

Second derivatives of the dominant eigenvalue

Resample a projection matrix

Eigenvalue and eigenvector analysis of a projection matrix

Correlation matrices for Hudsonia vital rates

Estimate the variance of beta-binomial vital rates

Vital rate sensitivities and elasticities

stage.vector.plot

Plot stage vector projections

Elasticity analysis of a projection matrix

Square matrices

Stable stage distribution

Matrix definition program for Hudsonia vital rates

Stretched beta-distributed random numbers

Variance matrix

Plot logistic regression

Survirvorship data for adult and juvenile Acorn Woodpeckers

Projection matrix for killer whale

projection.matrix

Construct projection matrix models using transition frequency tables

Sensitivity analysis of a projection matrix

reproductive.value

Reproductive value

Projection matrices for mountain golden heather

Stochastic vital rate simulations

Projection matrix for teasel

Split a projection matrix into separate T and F matrices

Calculate population growth rates by projection

stoch.growth.rate

Log stochastic growth rate

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

Census data for hypothetical plant

stoch.projection

Project stochastic growth from a sequence of matrices

Projection matrices for desert tortoise

Annual census data for Aquilegia chrysantha

Life Table Response Experiment

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

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

Generate beta-distributed random numbers

Create a projection matrix for Aquilegia

boot.transitions

Bootstrap observed census transitions

generation.time

Generation time

Count-based extinction probabilities and bootstrap confidence intervals

Annual transition data for Aquilegia chrysantha

Converted Matlab functions from Caswell (2001)

Converted Matlab functions from Morris and Doak (2002)

Population sizes of grizzly bears in Yellowstone from 1959-1997

01.Introduction

Introduction to the popbio Package

Projection matrices for a tropical understory herb

fundamental.matrix

Fundamental matrix and age-specific survival