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).

Install the latest version of this package by entering the following in R:
install.packages("popbio")
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

Functions

01.Introduction Man page
02.Caswell Man page
03.Morris Man page
aq.census Man page
aq.matrix Man page
aq.trans Man page
betaval Man page
boot.transitions Man page
calathea Man page
Caswell Man page
countCDFxt Man page
damping.ratio Man page
eigen.analysis Man page
elasticity Man page
extCDF Man page
fundamental.matrix Man page
generation.time Man page
grizzly Man page
head2 Man page
hudcorrs Man page
hudmxdef Man page
hudsonia Man page
hudvrs Man page
image2 Man page
Kendall Man page
lambda Man page
lnorms Man page
logi.hist.plot Man page
LTRE Man page
matplot2 Man page
matrix2 Man page
mean.list Man page
monkeyflower Man page
Morris Man page
multiresultm Man page
nematode Man page
net.reproductive.rate Man page
pfister.plot Man page
popbio Man page
pop.projection Man page
projection.matrix Man page
QPmat Man page
reproductive.value Man page
resample Man page
secder Man page
sensitivity Man page
splitA Man page
stable.stage Man page
stage.vector.plot Man page
stoch.growth.rate Man page
stoch.projection Man page
stoch.quasi.ext Man page
stoch.sens Man page
stretchbetaval Man page
teasel Man page
test.census Man page
tortoise Man page
var2 Man page
varEst Man page
vitalsens Man page
vitalsim Man page
whale Man page
woodpecker Man page

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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