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  20160401 10:11:19 
Maintainer  Chris Stubben <stubben@lanl.gov> 
License  GPL3 
Version  2.4.3 
Package repository  View on CRAN 
Installation  Install the latest version of this package by entering the following in R:

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 betadistributed random numbers  
boot.transitions: Bootstrap observed census transitions  
calathea: Projection matrices for a tropical understory herb  
countCDFxt: Countbased 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: Countbased extinction time cumulative distribution function  
fundamental.matrix: Fundamental matrix and agespecific 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 loglog 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 quasiextinction threshold  
stoch.sens: stoch.sens  
stretchbetaval: Generate stretched betadistributed 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 betabinomial 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 
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