popbio: Construction and Analysis of Matrix Population Models

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Construct and analyze projection matrix models from a demography study of marked individuals classified by age or stage. The package covers methods described in Matrix Population Models by Caswell (2001) and Quantitative Conservation Biology by Morris and Doak (2002).

Author
Chris Stubben, Brook Milligan, Patrick Nantel
Date of publication
2016-04-01 10:11:19
Maintainer
Chris Stubben <stubben@lanl.gov>
License
GPL-3
Version
2.4.3

View on CRAN

Man pages

01Introduction
Introduction to the popbio Package
02Caswell
Converted Matlab functions from Caswell (2001)
03Morris
Converted Matlab functions from Morris and Doak (2002)
aq.census
Annual census data for Aquilegia in the southwestern US
aq.matrix
Create a projection matrix for Aquilegia
aq.trans
Annual transition data for Aquilegia in the southwestern US
betaval
Generate beta-distributed random numbers
boot.transitions
Bootstrap observed census transitions
calathea
Projection matrices for a tropical understory herb
countCDFxt
Count-based extinction probabilities and bootstrap confidence...
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...
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...
image2
Display a matrix image
Kendall
Find the best Kendall's estimates of mean and environmental...
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
Calculate mean matrix
monkeyflower
Projection matrices for monkeyflower
multiresultm
Incorporate demographic stochasticity into population...
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....
pop.projection
Calculate population growth rates by projection
projection.matrix
Construct projection matrix models using transition frequency...
QPmat
Build a projection matrix from a time series of individuals...
reproductive.value
Stable stage distribution
resample
Resample a projection matrix
secder
secder
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
Calculate log stochastic growth rate
stoch.projection
Simulate stochastic growth from a sequence of matrices
stoch.quasi.ext
Calculate quasi-extinction threshold
stoch.sens
stoch.sens
stretchbetaval
Generate stretched beta-distributed random numbers
teasel
Projection matrix for teasel
test.census
Census data for hypothetical plant
tortoise
Projection matrices for desert tortoise
var2
Calculate a variance matrix
varEst
Estimate the variance of beta-binomial vital rates using...
vitalsens
Vital rate sensitivities and elasticities
vitalsim
Calculate stochastic growth rate and extinction time CDF...
whale
Projection matrix for killer whale
woodpecker
Survirvorship data for adult and juvenile Acorn Woodpeckers

Files in this package

popbio
popbio/inst
popbio/inst/CITATION
popbio/inst/ChangeLog
popbio/NAMESPACE
popbio/demo
popbio/demo/fillmore.R
popbio/demo/Caswell.R
popbio/demo/00Index
popbio/demo/stage.classify.R
popbio/data
popbio/data/whale.rda
popbio/data/aq.census.rda
popbio/data/hudvrs.rda
popbio/data/hudcorrs.rda
popbio/data/calathea.rda
popbio/data/tortoise.rda
popbio/data/nematode.rda
popbio/data/test.census.tab.gz
popbio/data/aq.trans.rda
popbio/data/teasel.rda
popbio/data/woodpecker.rda
popbio/data/grizzly.rda
popbio/data/monkeyflower.tab.gz
popbio/data/hudsonia.rda
popbio/R
popbio/R/QPmat.R
popbio/R/stoch.growth.rate.R
popbio/R/image2.R
popbio/R/eigen.analysis.R
popbio/R/splitA.R
popbio/R/stable.stage.R
popbio/R/vitalsim.R
popbio/R/head2.R
popbio/R/pfister.plot.R
popbio/R/countCDFxt.R
popbio/R/stoch.quasi.ext.R
popbio/R/fundamental.matrix.R
popbio/R/matplot2.R
popbio/R/resample.R
popbio/R/stoch.projection.R
popbio/R/lambda.R
popbio/R/aq.matrix.R
popbio/R/logi.hist.plot.R
popbio/R/reproductive.value.R
popbio/R/pop.projection.R
popbio/R/mean.list.R
popbio/R/Kendall.R
popbio/R/damping.ratio.R
popbio/R/boot.transitions.R
popbio/R/net.reproductive.rate.R
popbio/R/stretchbetaval.R
popbio/R/vitalsens.R
popbio/R/var2.R
popbio/R/elasticity.R
popbio/R/betaval.R
popbio/R/LTRE.R
popbio/R/secder.R
popbio/R/sensitivity.R
popbio/R/lnorms.R
popbio/R/stoch.sens.R
popbio/R/multiresultm.R
popbio/R/extCDF.R
popbio/R/varEst.R
popbio/R/matrix2.R
popbio/R/generation.time.R
popbio/R/projection.matrix.R
popbio/R/stage.vector.plot.R
popbio/R/hudmxdef.R
popbio/MD5
popbio/DESCRIPTION
popbio/man
popbio/man/grizzly.Rd
popbio/man/fundamental.matrix.Rd
popbio/man/varEst.Rd
popbio/man/reproductive.value.Rd
popbio/man/03Morris.Rd
popbio/man/woodpecker.Rd
popbio/man/var2.Rd
popbio/man/image2.Rd
popbio/man/sensitivity.Rd
popbio/man/extCDF.Rd
popbio/man/nematode.Rd
popbio/man/head2.Rd
popbio/man/multiresultm.Rd
popbio/man/teasel.Rd
popbio/man/02Caswell.Rd
popbio/man/elasticity.Rd
popbio/man/aq.census.Rd
popbio/man/lnorms.Rd
popbio/man/hudcorrs.Rd
popbio/man/LTRE.Rd
popbio/man/boot.transitions.Rd
popbio/man/whale.Rd
popbio/man/splitA.Rd
popbio/man/test.census.Rd
popbio/man/generation.time.Rd
popbio/man/hudvrs.Rd
popbio/man/vitalsim.Rd
popbio/man/stage.vector.plot.Rd
popbio/man/lambda.Rd
popbio/man/matplot2.Rd
popbio/man/stoch.sens.Rd
popbio/man/resample.Rd
popbio/man/damping.ratio.Rd
popbio/man/stretchbetaval.Rd
popbio/man/matrix2.Rd
popbio/man/monkeyflower.Rd
popbio/man/tortoise.Rd
popbio/man/net.reproductive.rate.Rd
popbio/man/hudmxdef.Rd
popbio/man/aq.matrix.Rd
popbio/man/logi.hist.plot.Rd
popbio/man/mean.list.Rd
popbio/man/stoch.projection.Rd
popbio/man/stoch.growth.rate.Rd
popbio/man/stable.stage.Rd
popbio/man/aq.trans.Rd
popbio/man/QPmat.Rd
popbio/man/eigen.analysis.Rd
popbio/man/01Introduction.Rd
popbio/man/calathea.Rd
popbio/man/secder.Rd
popbio/man/projection.matrix.Rd
popbio/man/pop.projection.Rd
popbio/man/Kendall.Rd
popbio/man/vitalsens.Rd
popbio/man/betaval.Rd
popbio/man/hudsonia.Rd
popbio/man/countCDFxt.Rd
popbio/man/pfister.plot.Rd
popbio/man/stoch.quasi.ext.Rd