IPMpack: Builds and analyses Integral Projection Models (IPMs).

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IPMpack takes demographic vital rates and (optionally) environmental data to build integral projection models. A number of functional forms for growth and survival can be incorporated, as well as a range of reproductive strategies. The package also includes a suite of diagnostic routines, provides classic matrix model output (e.g., lambda, elasticities, sensitivities), and produces post-hoc metrics (e.g., passage time and life expectancy).

Author
CJE Metcalf, SM McMahon, R Salguero-Gomez, E Jongejans, C Merow
Date of publication
2015-01-29 19:11:29
Maintainer
Sean McMahon <ipmpack@gmail.com>
License
GPL
Version
2.1

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Man pages

addPdfGrowthPic
Adds probability density functions of density function of...
coerceGrowthObj
Function to coerce growth or survival objects, i.e., impose...
convergeIPM
Iterates until obtaining the number of bins required so that...
convertIncrement
Convert size increment according to time elapsed between...
dataIPMpackCryptantha.csv
Cryptantha Perennial Dataset with Covariates
dataIPMpackHypericumCov.csv
Hypericum Perennial Dataset with covariates
dataIPMpackHypericum.csv
Hypericum Perennial Dataset
dataIPMpackSilwood.csv
Silwood Monocarp Dataset
dataIPMpackSuccisa2.csv
Succisa pratensis Dataset
dataIPMpackSuccisa.csv
Succisa pratensis Dataset
diagnosticsPmatrix
Creates a series of diagnostic graphs for a P matrix.
discreteTrans-class
Class '"discreteTrans"'
discreteTransInteger-class
Class '"discreteTransInteger"'
elas
Estimates matrix element sensitivities and elasticities.
envMatrix-class
Class "envMatrix"
fecObj-class
Class "fecObj"
fecObjInteger-class
Class "fecObjInteger"
generateData
Generates random data in the form used by IPMpack.
growSurv
Combines growth and survival.
growth
Estimates growth probabilities.
growthCum
Models growth allowing for cumulative bin estimation.
growthCum-methods
~~ Methods for Function 'growthCum' ~~
growth-methods
~~ Methods for Function 'growth' ~~
growthModelComp
Compares growth and survival objects built from different...
growthObj-class
Class "growthObj"
growthObjDeclineVar-class
Class "growthObjDeclineVar"
growthObjHossfeld-class
Class "growthObjHossfeld"
growthObjIncr-class
Class "growthObjIncr"
growthObjIncrDeclineVar-class
Class "growthObjIncrDeclineVar"
growthObjLogIncr-class
Class '"growthObjLogIncr"'
growthObjLogIncrDeclineVar-class
Class '"growthObjLogIncrDeclineVar"'
growthObjNegBin-class
Class "growthObjNegBin"
growthObjPois
Class "growthObjPois"
growthObjTruncIncr-class
Class '"growthObjTruncIncr"'
Hossfeld
Creates a Hossfeld function defining growth.
IPMmatrix-class
Class '"IPMmatrix"'
IPMpack-internal
Internal IPMpack objects.
IPMpackNews
Show a text file containing package news and updates.
IPMpack-package
Construction and analysis of integral projection models and...
largeMatrixCalc
Calculates population growth rate (lambda) and stable stage...
logit
Implements an inverse of the logistic transform.
makeClonalObj
Function to build clonal reproduction objects
makeCompoundCmatrix
Builds a compound C matrix.
makeCompoundFmatrix
Builds a compound F matrix.
makeCompoundPmatrix
Builds a compound P matrix.
makeDiscreteTrans
Builds matrix for transitions between discrete (e.g....
makeDiscreteTransInteger
Builds matrix for transitions between discrete (e.g....
makeEnvObj
Builds environmental transition objects.
makeFecObj
Function to build fecundity objects
makeFecObjInteger
Function to build fecundity objects
makeGrowthObj
Function to build growth objects
makeGrowthObjHossfeld
Function to make a Hossfeld Growth Object
makeIntegerFmatrix
Builds P and F matrices built off regressions fitted to...
makeIPMCmatrix
Builds C matrices.
makeIPMFmatrix
Builds F matrices.
makeIPMmatrix
Builds IPM matrices.
makeIPMPmatrix
Builds P matrices.
makeOffspringObj
Function to build offspring objects
makeSurvObj
Functions to build survival objects
meanLifeExpect
Calculates the mean life expectancy.
passageTime
Defines passage time to a chosen continuous stage.
picGrow
Makes pictures of data with growth models
picSurv
Makes pictures of survival.
plotGrowthModelComp
Plots compared models built with 'growthModelComp' and...
predictFutureDistribution
Predicts continuous (e.g. size) stage distribution in the...
R0Calc
Calculates net reproductive rate (R0) from an IPM.
sampleIPM
Builds list of IPMs or P matrices from list growth, survival,...
sampleIPMOutput
Gets IPM output from a list of P matrices (only survival and...
sampleSequentialIPMs
Makes a list of IPMs where there is a discrete covariate.
sampleVitalRateObj
Calculates growth objects reflecting distribution of...
sensParams
Estimates sensitivity and elasticity of lambda (or R0, or...
simulateCarlina
Generates random data in the form used by IPMpack based on...
sizeToAge
Estimates size/stage to age relationships
stochGrowthRateManyCov
Estimates stochastic population growth rates (lambda_s) or...
stochGrowthRateSampleList
Estimating the stochastic population growth rate (lambda_s)...
stochPassageTime
Estimates passage time in a discretely varying environment.
surv
Survival
survivorship
Estimates survivorship between two time censuses.
surv-methods
~~ Methods for Function surv ~~
survObj-class
Class "survObj"
survObjOverDisp-class
Class '"survObjOverDisp"'
timeToSize
Projects how long it takes to get from a starting...
varLifeExpect
Calculates variation in life expectancy in a discretely...
varPassageTime
Estimates variation in passage time.
wrapHossfeld
Fitting Hossfeld growth function.

Files in this package

IPMpack/DESCRIPTION
IPMpack/IPMpack.Rproj
IPMpack/NAMESPACE
IPMpack/R
IPMpack/R/IPMpack-Analyses.r
IPMpack/R/IPMpack-Classes_and_Methods.R
IPMpack/R/IPMpack-Hidden.r
IPMpack/R/IPMpack-Matrices.R
IPMpack/R/IPMpack-Util.r
IPMpack/R/IPMpack-Vital_Rate_Obj.r
IPMpack/TODO.txt
IPMpack/build
IPMpack/build/vignette.rds
IPMpack/data
IPMpack/data/dataIPMpackCryptantha.csv.gz
IPMpack/data/dataIPMpackHypericum.csv.gz
IPMpack/data/dataIPMpackHypericumCov.csv.gz
IPMpack/data/dataIPMpackSilwood.csv.gz
IPMpack/data/dataIPMpackSuccisa.csv.gz
IPMpack/data/dataIPMpackSuccisa2.csv.gz
IPMpack/inst
IPMpack/inst/doc
IPMpack/inst/doc/IPMpack_Vignette.R
IPMpack/inst/doc/IPMpack_Vignette.Rnw
IPMpack/inst/doc/IPMpack_Vignette.pdf
IPMpack/man
IPMpack/man/Hossfeld.Rd
IPMpack/man/IPMmatrix-class.Rd
IPMpack/man/IPMpack-internal.Rd
IPMpack/man/IPMpack-package.Rd
IPMpack/man/IPMpackNews.Rd
IPMpack/man/R0Calc.Rd
IPMpack/man/addPdfGrowthPic.Rd
IPMpack/man/coerceGrowthObj.Rd
IPMpack/man/convergeIPM.Rd
IPMpack/man/convertIncrement.Rd
IPMpack/man/dataIPMpackCryptantha.csv.Rd
IPMpack/man/dataIPMpackHypericum.csv.Rd
IPMpack/man/dataIPMpackHypericumCov.csv.Rd
IPMpack/man/dataIPMpackSilwood.csv.Rd
IPMpack/man/dataIPMpackSuccisa.csv.Rd
IPMpack/man/dataIPMpackSuccisa2.csv.Rd
IPMpack/man/diagnosticsPmatrix.Rd
IPMpack/man/discreteTrans-class.Rd
IPMpack/man/discreteTransInteger-class.Rd
IPMpack/man/elas.Rd
IPMpack/man/envMatrix-class.Rd
IPMpack/man/fecObj-class.Rd
IPMpack/man/fecObjInteger-class.Rd
IPMpack/man/generateData.Rd
IPMpack/man/growSurv.Rd
IPMpack/man/growth-methods.Rd
IPMpack/man/growth.Rd
IPMpack/man/growthCum-methods.Rd
IPMpack/man/growthCum.Rd
IPMpack/man/growthModelComp.Rd
IPMpack/man/growthObj-class.Rd
IPMpack/man/growthObjDeclineVar-class.Rd
IPMpack/man/growthObjHossfeld-class.Rd
IPMpack/man/growthObjIncr-class.Rd
IPMpack/man/growthObjIncrDeclineVar-class.Rd
IPMpack/man/growthObjLogIncr-class.Rd
IPMpack/man/growthObjLogIncrDeclineVar-class.Rd
IPMpack/man/growthObjNegBin-class.Rd
IPMpack/man/growthObjPois.Rd
IPMpack/man/growthObjTruncIncr-class.Rd
IPMpack/man/largeMatrixCalc.Rd
IPMpack/man/logit.Rd
IPMpack/man/makeClonalObj.Rd
IPMpack/man/makeCompoundCmatrix.Rd
IPMpack/man/makeCompoundFmatrix.Rd
IPMpack/man/makeCompoundPmatrix.Rd
IPMpack/man/makeDiscreteTrans.Rd
IPMpack/man/makeDiscreteTransInteger.Rd
IPMpack/man/makeEnvObj.Rd
IPMpack/man/makeFecObj.Rd
IPMpack/man/makeFecObjInteger.Rd
IPMpack/man/makeGrowthObj.Rd
IPMpack/man/makeGrowthObjHossfeld.Rd
IPMpack/man/makeIPMCmatrix.Rd
IPMpack/man/makeIPMFmatrix.Rd
IPMpack/man/makeIPMPmatrix.Rd
IPMpack/man/makeIPMmatrix.Rd
IPMpack/man/makeIntegerFmatrix.Rd
IPMpack/man/makeOffspringObj.Rd
IPMpack/man/makeSurvObj.Rd
IPMpack/man/meanLifeExpect.Rd
IPMpack/man/passageTime.Rd
IPMpack/man/picGrow.Rd
IPMpack/man/picSurv.Rd
IPMpack/man/plotGrowthModelComp.Rd
IPMpack/man/predictFutureDistribution.Rd
IPMpack/man/sampleIPM.Rd
IPMpack/man/sampleIPMOutput.Rd
IPMpack/man/sampleSequentialIPMs.Rd
IPMpack/man/sampleVitalRateObj.Rd
IPMpack/man/sensParams.Rd
IPMpack/man/simulateCarlina.Rd
IPMpack/man/sizeToAge.Rd
IPMpack/man/stochGrowthRateManyCov.Rd
IPMpack/man/stochGrowthRateSampleList.Rd
IPMpack/man/stochPassageTime.Rd
IPMpack/man/surv-methods.Rd
IPMpack/man/surv.Rd
IPMpack/man/survObj-class.Rd
IPMpack/man/survObjOverDisp-class.Rd
IPMpack/man/survivorship.Rd
IPMpack/man/timeToSize.Rd
IPMpack/man/varLifeExpect.Rd
IPMpack/man/varPassageTime.Rd
IPMpack/man/wrapHossfeld.Rd
IPMpack/vignettes
IPMpack/vignettes/IPMpack_Vignette-fig7.pdf
IPMpack/vignettes/IPMpack_Vignette.Rnw
IPMpack/vignettes/Rd.sty
IPMpack/vignettes/Sweave.sty