R: Construction and Analysis of Matrix Population Models

# Construction and Analysis of Matrix Population Models

## Documentation for package ‘popbio’ version 2.7

- DESCRIPTION file.
- Code demos. Use demo() to run them.

## Help Pages

01.Introduction | Introduction to the popbio Package
02.Caswell | Converted Matlab functions from Caswell (2001)
03.Morris | Converted Matlab functions from Morris and Doak (2002)
aq.census | Annual census data for Aquilegia chrysantha
aq.matrix | Create a projection matrix for Aquilegia
aq.trans | Annual transition data for Aquilegia chrysantha
betaval | Generate beta-distributed random numbers
boot.transitions | Bootstrap observed census transitions
calathea | Projection matrices for a tropical understory herb
Caswell | Converted Matlab functions from Caswell (2001)
countCDFxt | Count-based extinction probabilities and bootstrap confidence intervals
damping.ratio | Damping ratio
eigen.analysis | Eigenvalue and eigenvector analysis of a projection matrix
elasticity | Elasticity analysis of a projection matrix
extCDF | Count-based extinction time cumulative distribution function
fundamental.matrix | Fundamental matrix and age-specific survival
generation.time | Generation time
grizzly | Population sizes of grizzly bears in Yellowstone from 1959-1997
head2 | Return the first and last part of a matrix or dataframe
hudcorrs | Correlation matrices for Hudsonia vital rates
hudmxdef | Matrix definition program for Hudsonia vital rates
hudsonia | Projection matrices for mountain golden heather
hudvrs | Best Kendall estimates of Hudsonia vital rate means and variances
image2 | Display a matrix image
Kendall | Find the best Kendall's estimates of mean and environmental variance for beta-binomial vital rates
lambda | Population growth rate
lnorms | Generate random lognormal values for fertility rates
logi.hist.plot | Plot logistic regression
LTRE | Life Table Response Experiment
matplot2 | Plot a matrix
matrix2 | Square matrices
mean.list | Mean matrix
monkeyflower | Projection matrices for monkeyflower
Morris | Converted Matlab functions from Morris and Doak (2002)
multiresultm | Incorporate demographic stochasticity into population projections
nematode | Population densities for the sugarbeet cyst nematode
net.reproductive.rate | Net reproductive rate
pfister.plot | Create log-log plots of variance vs. sensitivity and CV vs. elasticity
pop.projection | Calculate population growth rates by projection
popbio | Introduction to the popbio Package
projection.matrix | Construct projection matrix models using transition frequency tables
QPmat | Build a projection matrix from a time series of individuals (or densities) per stage
reproductive.value | Reproductive value
resample | Resample a projection matrix
secder | Second derivatives of the dominant eigenvalue
sensitivity | Sensitivity analysis of a projection matrix
splitA | Split a projection matrix into separate T and F matrices
stable.stage | Stable stage distribution
stage.vector.plot | Plot stage vector projections
stoch.growth.rate | Log stochastic growth rate
stoch.projection | Project stochastic growth from a sequence of matrices
stoch.quasi.ext | Quasi-extinction threshold
stoch.sens | Stochastic growth rate sensitivity
stretchbetaval | Stretched beta-distributed random numbers
teasel | Projection matrix for teasel
test.census | Census data for hypothetical plant
tortoise | Projection matrices for desert tortoise
var2 | Variance matrix
varEst | Estimate the variance of beta-binomial vital rates
vitalsens | Vital rate sensitivities and elasticities
vitalsim | Stochastic vital rate simulations
whale | Projection matrix for killer whale
woodpecker | Survirvorship data for adult and juvenile Acorn Woodpeckers