popbio: Construction and Analysis of Matrix Population Models
Version 2.4.3

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).

AuthorChris Stubben, Brook Milligan, Patrick Nantel
Date of publication2016-04-01 10:11:19
MaintainerChris Stubben <stubben@lanl.gov>
LicenseGPL-3
Version2.4.3
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("popbio")

Popular man pages

eigen.analysis: Eigenvalue and eigenvector analysis of a projection matrix
grizzly: Population sizes of grizzly bears in Yellowstone from...
logi.hist.plot: Plot logistic regression
matplot2: Plot a matrix
pop.projection: Calculate population growth rates by projection
stoch.quasi.ext: Calculate quasi-extinction threshold
vitalsens: Vital rate sensitivities and elasticities
See all...

All man pages Function index File listing

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

Functions

Files

inst
inst/CITATION
inst/ChangeLog
NAMESPACE
demo
demo/fillmore.R
demo/Caswell.R
demo/00Index
demo/stage.classify.R
data
data/whale.rda
data/aq.census.rda
data/hudvrs.rda
data/hudcorrs.rda
data/calathea.rda
data/tortoise.rda
data/nematode.rda
data/test.census.tab.gz
data/aq.trans.rda
data/teasel.rda
data/woodpecker.rda
data/grizzly.rda
data/monkeyflower.tab.gz
data/hudsonia.rda
R
R/QPmat.R
R/stoch.growth.rate.R
R/image2.R
R/eigen.analysis.R
R/splitA.R
R/stable.stage.R
R/vitalsim.R
R/head2.R
R/pfister.plot.R
R/countCDFxt.R
R/stoch.quasi.ext.R
R/fundamental.matrix.R
R/matplot2.R
R/resample.R
R/stoch.projection.R
R/lambda.R
R/aq.matrix.R
R/logi.hist.plot.R
R/reproductive.value.R
R/pop.projection.R
R/mean.list.R
R/Kendall.R
R/damping.ratio.R
R/boot.transitions.R
R/net.reproductive.rate.R
R/stretchbetaval.R
R/vitalsens.R
R/var2.R
R/elasticity.R
R/betaval.R
R/LTRE.R
R/secder.R
R/sensitivity.R
R/lnorms.R
R/stoch.sens.R
R/multiresultm.R
R/extCDF.R
R/varEst.R
R/matrix2.R
R/generation.time.R
R/projection.matrix.R
R/stage.vector.plot.R
R/hudmxdef.R
MD5
DESCRIPTION
man
man/grizzly.Rd
man/fundamental.matrix.Rd
man/varEst.Rd
man/reproductive.value.Rd
man/03Morris.Rd
man/woodpecker.Rd
man/var2.Rd
man/image2.Rd
man/sensitivity.Rd
man/extCDF.Rd
man/nematode.Rd
man/head2.Rd
man/multiresultm.Rd
man/teasel.Rd
man/02Caswell.Rd
man/elasticity.Rd
man/aq.census.Rd
man/lnorms.Rd
man/hudcorrs.Rd
man/LTRE.Rd
man/boot.transitions.Rd
man/whale.Rd
man/splitA.Rd
man/test.census.Rd
man/generation.time.Rd
man/hudvrs.Rd
man/vitalsim.Rd
man/stage.vector.plot.Rd
man/lambda.Rd
man/matplot2.Rd
man/stoch.sens.Rd
man/resample.Rd
man/damping.ratio.Rd
man/stretchbetaval.Rd
man/matrix2.Rd
man/monkeyflower.Rd
man/tortoise.Rd
man/net.reproductive.rate.Rd
man/hudmxdef.Rd
man/aq.matrix.Rd
man/logi.hist.plot.Rd
man/mean.list.Rd
man/stoch.projection.Rd
man/stoch.growth.rate.Rd
man/stable.stage.Rd
man/aq.trans.Rd
man/QPmat.Rd
man/eigen.analysis.Rd
man/01Introduction.Rd
man/calathea.Rd
man/secder.Rd
man/projection.matrix.Rd
man/pop.projection.Rd
man/Kendall.Rd
man/vitalsens.Rd
man/betaval.Rd
man/hudsonia.Rd
man/countCDFxt.Rd
man/pfister.plot.Rd
man/stoch.quasi.ext.Rd
popbio documentation built on May 20, 2017, 12:05 a.m.

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