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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

2.7

License

GPL-3

Maintainer

Chris Stubben

Last Published

February 1st, 2020

Functions in popbio (2.7)

countCDFxt

Count-based extinction probabilities and bootstrap confidence intervals
extCDF

Count-based extinction time cumulative distribution function
eigen.analysis

Eigenvalue and eigenvector analysis of a projection matrix
aq.matrix

Create a projection matrix for Aquilegia
damping.ratio

Damping ratio
hudmxdef

Matrix definition program for Hudsonia vital rates
image2

Display a matrix image
elasticity

Elasticity analysis of a projection matrix
net.reproductive.rate

Net reproductive rate
nematode

Population densities for the sugarbeet cyst nematode
hudvrs

Best Kendall estimates of Hudsonia vital rate means and variances
hudsonia

Projection matrices for mountain golden heather
projection.matrix

Construct projection matrix models using transition frequency tables
resample

Resample a projection matrix
fundamental.matrix

Fundamental matrix and age-specific survival
grizzly

Population sizes of grizzly bears in Yellowstone from 1959-1997
pfister.plot

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

Generation time
lnorms

Generate random lognormal values for fertility rates
lambda

Population growth rate
pop.projection

Calculate population growth rates by projection
stoch.growth.rate

Log stochastic growth rate
head2

Return the first and last part of a matrix or dataframe
boot.transitions

Bootstrap observed census transitions
vitalsens

Vital rate sensitivities and elasticities
vitalsim

Stochastic vital rate simulations
stoch.projection

Project stochastic growth from a sequence of matrices
secder

Second derivatives of the dominant eigenvalue
test.census

Census data for hypothetical plant
tortoise

Projection matrices for desert tortoise
mean.list

Mean matrix
matrix2

Square matrices
reproductive.value

Reproductive value
calathea

Projection matrices for a tropical understory herb
hudcorrs

Correlation matrices for Hudsonia vital rates
logi.hist.plot

Plot logistic regression
splitA

Split a projection matrix into separate T and F matrices
sensitivity

Sensitivity analysis of a projection matrix
whale

Projection matrix for killer whale
stoch.sens

Stochastic growth rate sensitivity
stoch.quasi.ext

Quasi-extinction threshold
woodpecker

Survirvorship data for adult and juvenile Acorn Woodpeckers
matplot2

Plot a matrix
var2

Variance matrix
varEst

Estimate the variance of beta-binomial vital rates
multiresultm

Incorporate demographic stochasticity into population projections
stable.stage

Stable stage distribution
monkeyflower

Projection matrices for monkeyflower
stretchbetaval

Stretched beta-distributed random numbers
stage.vector.plot

Plot stage vector projections
teasel

Projection matrix for teasel
LTRE

Life Table Response Experiment
aq.census

Annual census data for Aquilegia chrysantha
betaval

Generate beta-distributed random numbers
Kendall

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

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

Introduction to the popbio Package
aq.trans

Annual transition data for Aquilegia chrysantha
02.Caswell

Converted Matlab functions from Caswell (2001)
03.Morris

Converted Matlab functions from Morris and Doak (2002)