Construction and Analysis of Matrix Population Models

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Documentation for package ‘popbio’ version 2.8

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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