popbio: Construction and Analysis of Matrix Population Models

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

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

All documentation is copyright its authors; we didn't write any of that.