Package: popbio 2.8

Chris Stubben

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).

Authors:Chris Stubben, Brook Milligan, Patrick Nantel

popbio_2.8.tar.gz
popbio_2.8.tar.gz(r-4.5-noble)popbio_2.8.tar.gz(r-4.4-noble)
popbio_2.8.tgz(r-4.4-emscripten)popbio_2.8.tgz(r-4.3-emscripten)
popbio.pdf |popbio.html✨
popbio/json (API)

# Install 'popbio' in R:
install.packages('popbio', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:
  • aq.census - Annual census data for Aquilegia chrysantha
  • aq.trans - Annual transition data for Aquilegia chrysantha
  • calathea - Projection matrices for a tropical understory herb
  • grizzly - Population sizes of grizzly bears in Yellowstone from 1959-1997
  • hudcorrs - Correlation matrices for Hudsonia vital rates
  • hudsonia - Projection matrices for mountain golden heather
  • hudvrs - Best Kendall estimates of Hudsonia vital rate means and variances
  • monkeyflower - Projection matrices for monkeyflower
  • nematode - Population densities for the sugarbeet cyst nematode
  • teasel - Projection matrix for teasel
  • test.census - Census data for hypothetical plant
  • tortoise - Projection matrices for desert tortoise
  • whale - Projection matrix for killer whale
  • woodpecker - Survirvorship data for adult and juvenile Acorn Woodpeckers

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

42 exports 4.89 score 0 dependencies 3 dependents 51 mentions 908 scripts 972 downloads

Last updated 6 months agofrom:9befad8eea. Checks:OK: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKAug 26 2024
R-4.5-linuxOKAug 26 2024

Exports:aq.matrixbetavalboot.transitionscountCDFxtdamping.ratioeigen.analysiselasticityextCDFfundamental.matrixgeneration.timehead2hudmxdefimage2Kendalllambdalnormslogi.hist.plotLTREmatplot2matrix2multiresultmnet.reproductive.ratepfister.plotpop.projectionprojection.matrixQPmatreproductive.valueresamplesecdersensitivitysplitAstable.stagestage.vector.plotstoch.growth.ratestoch.projectionstoch.quasi.extstoch.sensstretchbetavalvar2varEstvitalsensvitalsim

Dependencies:

Readme and manuals

Help Manual

Help pageTopics
Introduction to the popbio Package01.Introduction popbio
Converted Matlab functions from Caswell (2001)02.Caswell Caswell
Converted Matlab functions from Morris and Doak (2002)03.Morris Morris
Annual census data for Aquilegia chrysanthaaq.census
Create a projection matrix for Aquilegiaaq.matrix
Annual transition data for Aquilegia chrysanthaaq.trans
Generate beta-distributed random numbersbetaval
Bootstrap observed census transitionsboot.transitions
Projection matrices for a tropical understory herbcalathea
Count-based extinction probabilities and bootstrap confidence intervalscountCDFxt
Damping ratiodamping.ratio
Eigenvalue and eigenvector analysis of a projection matrixeigen.analysis
Elasticity analysis of a projection matrixelasticity
Count-based extinction time cumulative distribution functionextCDF
Fundamental matrix and age-specific survivalfundamental.matrix
Generation timegeneration.time
Population sizes of grizzly bears in Yellowstone from 1959-1997grizzly
Return the first and last part of a matrix or dataframehead2
Correlation matrices for Hudsonia vital rateshudcorrs
Matrix definition program for Hudsonia vital rateshudmxdef
Projection matrices for mountain golden heatherhudsonia
Best Kendall estimates of Hudsonia vital rate means and varianceshudvrs
Display a matrix imageimage2
Find the best Kendall's estimates of mean and environmental variance for beta-binomial vital ratesKendall
Population growth ratelambda
Generate random lognormal values for fertility rateslnorms
Plot logistic regressionlogi.hist.plot
Life Table Response ExperimentLTRE
Plot a matrixmatplot2
Square matricesmatrix2
Mean matrixmean.list
Projection matrices for monkeyflowermonkeyflower
Incorporate demographic stochasticity into population projectionsmultiresultm
Population densities for the sugarbeet cyst nematodenematode
Net reproductive ratenet.reproductive.rate
Create log-log plots of variance vs. sensitivity and CV vs. elasticitypfister.plot
Calculate population growth rates by projectionpop.projection
Construct projection matrix models using transition frequency tablesprojection.matrix
Build a projection matrix from a time series of individuals (or densities) per stageQPmat
Reproductive valuereproductive.value
Resample a projection matrixresample
Second derivatives of the dominant eigenvaluesecder
Sensitivity analysis of a projection matrixsensitivity
Split a projection matrix into separate T and F matricessplitA
Stable stage distributionstable.stage
Plot stage vector projectionsstage.vector.plot
Log stochastic growth ratestoch.growth.rate
Project stochastic growth from a sequence of matricesstoch.projection
Quasi-extinction thresholdstoch.quasi.ext
Stochastic growth rate sensitivitystoch.sens
Stretched beta-distributed random numbersstretchbetaval
Projection matrix for teaselteasel
Census data for hypothetical planttest.census
Projection matrices for desert tortoisetortoise
Variance matrixvar2
Estimate the variance of beta-binomial vital ratesvarEst
Vital rate sensitivities and elasticitiesvitalsens
Stochastic vital rate simulationsvitalsim
Projection matrix for killer whalewhale
Survirvorship data for adult and juvenile Acorn Woodpeckerswoodpecker