IPMpack: Builds and analyses Integral Projection Models (IPMs).
Version 2.1

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).

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AuthorCJE Metcalf, SM McMahon, R Salguero-Gomez, E Jongejans, C Merow
Date of publication2015-01-29 19:11:29
MaintainerSean McMahon <ipmpack@gmail.com>
LicenseGPL
Version2.1
Package repositoryView on R-Forge
InstallationInstall the latest version of this package by entering the following in R:
install.packages("IPMpack", repos="http://R-Forge.R-project.org")

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.

Functions

.getIPMoutput Man page
.getIPMoutputDirect Man page
.getListRegObjects Man page
.getListRegObjectsFec Man page
.makeListIPMs Man page
.makeListPmatrix Man page
.requireCachedGenerics Man page
Hossfeld Man page Source code
IPMmatrix-class Man page
IPMpack Man page
IPMpack-package Man page
IPMpackNews Man page Source code
R0Calc Man page Source code
addPdfGrowthPic Man page Source code
alteredFit Source code
coerceGrowthObj Man page Source code
coerceSurvObj Man page Source code
convergeIPM Man page Source code
convergeLambda Source code
convergeLifeExpectancy Source code
convergeR0 Source code
convertIncrement Man page Source code
createCompoundCmatrix Man page
createCompoundFmatrix Man page
createCompoundPmatrix Man page
createFecObj Source code
createGrowthObj Source code
createIPMCmatrix Man page Source code
createIPMFmatrix Man page Source code
createIPMPmatrix Man page Source code
createIntegerFmatrix Man page Source code
createIntegerPmatrix Man page Source code
createSurvObj Source code
dataIPMpackCryptantha Man page
dataIPMpackHypericum Man page
dataIPMpackHypericumCov Man page
dataIPMpackSilwood Man page
dataIPMpackSuccisa Man page
dataIPMpackSuccisa2 Man page
deathDataAugment Source code
dentifyPossibleYearsCarlina Source code
diagnosticsPmatrix Man page Source code
discreteTrans-class Man page
discreteTransInteger-class Man page
elas Man page Source code
envMatrix-class Man page
fecObj-class Man page
fecObjInteger-class Man page
fecPostCensus Source code
fecPostCensusInteger Source code
fecPreCensus Source code
fecPreCensusInteger Source code
fecRaw Source code
generateData Man page Source code
generateDataDiscrete Source code
generateDataStoch Source code
getIPMoutput Source code
getIPMoutputDirect Source code
getListRegObjects Source code
getListRegObjectsFec Source code
growSurv Man page Source code
growth Man page
growth,numeric,numeric,data.frame,growthObj-method Man page
growth,numeric,numeric,data.frame,growthObjDeclineVar-method Man page
growth,numeric,numeric,data.frame,growthObjHossfeld-method Man page
growth,numeric,numeric,data.frame,growthObjIncr-method Man page
growth,numeric,numeric,data.frame,growthObjIncrDeclineVar-method Man page
growth,numeric,numeric,data.frame,growthObjLogIncr-method Man page
growth,numeric,numeric,data.frame,growthObjLogIncrDeclineVar-met Man page
growth,numeric,numeric,data.frame,growthObjNegBin-method Man page
growth,numeric,numeric,data.frame,growthObjPois-method Man page
growth,numeric,numeric,data.frame,growthObjTruncIncr-method Man page
growth,numeric,numeric,numeric,growthObjDeclineVar-method Man page
growth,numeric,numeric,numeric,growthObjHossfeld-method Man page
growth,numeric,numeric,numeric,growthObjIncr-method Man page
growth,numeric,numeric,numeric,growthObjIncrDeclineVar-method Man page
growth,numeric,numeric,numeric,growthObjLogIncr-method Man page
growth,numeric,numeric,numeric,growthObjTruncIncr-method Man page
growth-methods Man page
growthCum Man page
growthCum,numeric,numeric,data.frame,growthObj-method Man page
growthCum,numeric,numeric,data.frame,growthObjDeclineVar-method Man page
growthCum,numeric,numeric,data.frame,growthObjHossfeld-method Man page
growthCum,numeric,numeric,data.frame,growthObjIncr-method Man page
growthCum,numeric,numeric,data.frame,growthObjIncrDeclineVar-met Man page
growthCum,numeric,numeric,data.frame,growthObjLogIncr-method Man page
growthCum,numeric,numeric,data.frame,growthObjLogIncrDeclineVar- Man page
growthCum,numeric,numeric,data.frame,growthObjTruncIncr-method Man page
growthCum,numeric,numeric,numeric,growthObjLogIncr-method Man page
growthCum,numeric,numeric,numeric,growthObjTruncIncr-method Man page
growthCum-methods Man page
growthIntegrate,numeric,numeric,numeric,numeric,growthObjHossfel Man page
growthModelComp Man page Source code
growthObj-class Man page
growthObjDeclineVar-class Man page
growthObjHossfeld-class Man page
growthObjIncr-class Man page
growthObjIncrDeclineVar-class Man page
growthObjLogIncr-class Man page
growthObjLogIncrDeclineVar-class Man page
growthObjNegBin-class Man page
growthObjPois-class Man page
growthObjTruncIncr-class Man page
invLogit Man page Source code
largeMatrixCalc Man page Source code
makeClonalObj Man page Source code
makeClonalObjInteger Man page Source code
makeCompoundCmatrix Man page Source code Source code
makeCompoundFmatrix Man page Source code
makeCompoundPmatrix Man page Source code
makeCovDf Source code
makeDiscreteTrans Man page Source code
makeDiscreteTransInteger Man page Source code
makeEnvObj Man page Source code
makeFecObj Man page Source code
makeFecObjInteger Man page Source code
makeGrowthObj Man page Source code
makeIPMCmatrix Man page Source code
makeIPMFmatrix Man page Source code
makeIPMPmatrix Man page Source code
makeIPMmatrix Man page Source code
makeIntegerFmatrix Man page Source code
makeIntegerPmatrix Man page Source code
makeListFmatrix Source code
makeListIPMs Source code
makeListPmatrix Source code
makeOffspringObj Man page Source code
makeSurvObj Man page Source code
makegrowthObjHossfeld Man page Source code
meanLifeExpect Man page Source code
offspringCum Source code
passageTime Man page Source code
picGrow Man page Source code
picSurv Man page Source code
plotGrowthModelComp Man page Source code
plotResultsStochStruct Source code
plotSurvModelComp Man page Source code
predictFutureDistribution Man page Source code
predictMuX Source code
sampleIPM Man page Source code
sampleIPMOutput Man page Source code
sampleSequentialIPMs Man page Source code
sampleVitalRateObj Man page Source code
sens Man page Source code
sensParams Man page Source code
sensParamsDiscrete Source code
simulateCarlina Man page Source code
sizeToAge Man page Source code
stochGrowthRateManyCov Man page Source code
stochGrowthRateSampleList Man page Source code
stochLifeExpect Source code
stochPassageTime Man page Source code
stochPassageTime,numeric,IPMmatrix,envMatrix-method Man page
surv Man page
surv,numeric,data.frame,survObj-method Man page Man page
surv,numeric,data.frame,survObjOverDisp-method Man page
surv,numeric,numeric,survObjOverDisp-method Man page
surv-methods Man page
survModelComp Man page Source code
survObj-class Man page
survObjOverDisp-class Man page
survivorship Man page Source code
timeToSize Man page Source code
varLifeExpect Man page Source code
varPassageTime Man page Source code
wrapHossfeld Man page Source code

Files

DESCRIPTION
IPMpack.Rproj
NAMESPACE
R
R/IPMpack-Analyses.r
R/IPMpack-Classes_and_Methods.R
R/IPMpack-Hidden.r
R/IPMpack-Matrices.R
R/IPMpack-Util.r
R/IPMpack-Vital_Rate_Obj.r
TODO.txt
build
build/vignette.rds
data
data/dataIPMpackCryptantha.csv.gz
data/dataIPMpackHypericum.csv.gz
data/dataIPMpackHypericumCov.csv.gz
data/dataIPMpackSilwood.csv.gz
data/dataIPMpackSuccisa.csv.gz
data/dataIPMpackSuccisa2.csv.gz
inst
inst/doc
inst/doc/IPMpack_Vignette.R
inst/doc/IPMpack_Vignette.Rnw
inst/doc/IPMpack_Vignette.pdf
man
man/Hossfeld.Rd
man/IPMmatrix-class.Rd
man/IPMpack-internal.Rd
man/IPMpack-package.Rd
man/IPMpackNews.Rd
man/R0Calc.Rd
man/addPdfGrowthPic.Rd
man/coerceGrowthObj.Rd
man/convergeIPM.Rd
man/convertIncrement.Rd
man/dataIPMpackCryptantha.csv.Rd
man/dataIPMpackHypericum.csv.Rd
man/dataIPMpackHypericumCov.csv.Rd
man/dataIPMpackSilwood.csv.Rd
man/dataIPMpackSuccisa.csv.Rd
man/dataIPMpackSuccisa2.csv.Rd
man/diagnosticsPmatrix.Rd
man/discreteTrans-class.Rd
man/discreteTransInteger-class.Rd
man/elas.Rd
man/envMatrix-class.Rd
man/fecObj-class.Rd
man/fecObjInteger-class.Rd
man/generateData.Rd
man/growSurv.Rd
man/growth-methods.Rd
man/growth.Rd
man/growthCum-methods.Rd
man/growthCum.Rd
man/growthModelComp.Rd
man/growthObj-class.Rd
man/growthObjDeclineVar-class.Rd
man/growthObjHossfeld-class.Rd
man/growthObjIncr-class.Rd
man/growthObjIncrDeclineVar-class.Rd
man/growthObjLogIncr-class.Rd
man/growthObjLogIncrDeclineVar-class.Rd
man/growthObjNegBin-class.Rd
man/growthObjPois.Rd
man/growthObjTruncIncr-class.Rd
man/largeMatrixCalc.Rd
man/logit.Rd
man/makeClonalObj.Rd
man/makeCompoundCmatrix.Rd
man/makeCompoundFmatrix.Rd
man/makeCompoundPmatrix.Rd
man/makeDiscreteTrans.Rd
man/makeDiscreteTransInteger.Rd
man/makeEnvObj.Rd
man/makeFecObj.Rd
man/makeFecObjInteger.Rd
man/makeGrowthObj.Rd
man/makeGrowthObjHossfeld.Rd
man/makeIPMCmatrix.Rd
man/makeIPMFmatrix.Rd
man/makeIPMPmatrix.Rd
man/makeIPMmatrix.Rd
man/makeIntegerFmatrix.Rd
man/makeOffspringObj.Rd
man/makeSurvObj.Rd
man/meanLifeExpect.Rd
man/passageTime.Rd
man/picGrow.Rd
man/picSurv.Rd
man/plotGrowthModelComp.Rd
man/predictFutureDistribution.Rd
man/sampleIPM.Rd
man/sampleIPMOutput.Rd
man/sampleSequentialIPMs.Rd
man/sampleVitalRateObj.Rd
man/sensParams.Rd
man/simulateCarlina.Rd
man/sizeToAge.Rd
man/stochGrowthRateManyCov.Rd
man/stochGrowthRateSampleList.Rd
man/stochPassageTime.Rd
man/surv-methods.Rd
man/surv.Rd
man/survObj-class.Rd
man/survObjOverDisp-class.Rd
man/survivorship.Rd
man/timeToSize.Rd
man/varLifeExpect.Rd
man/varPassageTime.Rd
man/wrapHossfeld.Rd
vignettes
vignettes/IPMpack_Vignette-fig7.pdf
vignettes/IPMpack_Vignette.Rnw
vignettes/Rd.sty
vignettes/Sweave.sty
IPMpack documentation built on May 21, 2017, 12:57 a.m.