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

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).

AuthorCJE Metcalf, SM McMahon, R Salguero-Gomez, E Jongejans, C Merow
Date of publication2014-03-17 03:08:17
MaintainerSean McMahon <ipmpack@gmail.com>
LicenseGPL
Version2.1

View on CRAN

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 a 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

addPdfGrowthPic Man page
coerceGrowthObj Man page
coerceSurvObj Man page
convergeIPM Man page
convertIncrement Man page
createCompoundCmatrix Man page
createCompoundFmatrix Man page
createCompoundPmatrix Man page
createIntegerFmatrix Man page
createIntegerPmatrix Man page
createIPMCmatrix Man page
createIPMFmatrix Man page
createIPMPmatrix Man page
dataIPMpackCryptantha Man page
dataIPMpackHypericum Man page
dataIPMpackHypericumCov Man page
dataIPMpackSilwood Man page
dataIPMpackSuccisa Man page
dataIPMpackSuccisa2 Man page
diagnosticsPmatrix Man page
discreteTrans-class Man page
discreteTransInteger-class Man page
elas Man page
envMatrix-class Man page
fecObj-class Man page
fecObjInteger-class Man page
generateData Man page
.getIPMoutput Man page
.getIPMoutputDirect Man page
.getListRegObjects Man page
.getListRegObjectsFec Man page
growSurv Man page
growth Man page
growthCum Man page
growthCum-methods 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,growthObjIncrDeclineVar-met Man page
growthCum,numeric,numeric,data.frame,growthObjIncr-method Man page
growthCum,numeric,numeric,data.frame,growthObjLogIncrDeclineVar- Man page
growthCum,numeric,numeric,data.frame,growthObjLogIncr-method Man page
growthCum,numeric,numeric,data.frame,growthObj-method 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
growthIntegrate,numeric,numeric,numeric,numeric,growthObjHossfel Man page
growth-methods Man page
growthModelComp 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,growthObjIncrDeclineVar-method Man page
growth,numeric,numeric,data.frame,growthObjIncr-method Man page
growth,numeric,numeric,data.frame,growthObjLogIncrDeclineVar-met Man page
growth,numeric,numeric,data.frame,growthObjLogIncr-method Man page
growth,numeric,numeric,data.frame,growthObj-method 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,growthObjIncrDeclineVar-method Man page
growth,numeric,numeric,numeric,growthObjIncr-method Man page
growth,numeric,numeric,numeric,growthObjLogIncr-method Man page
growth,numeric,numeric,numeric,growthObjTruncIncr-method Man page
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
Hossfeld Man page
invLogit Man page
IPMmatrix-class Man page
IPMpack Man page
IPMpackNews Man page
IPMpack-package Man page
largeMatrixCalc Man page
makeClonalObj Man page
makeClonalObjInteger Man page
makeCompoundCmatrix Man page
makeCompoundFmatrix Man page
makeCompoundPmatrix Man page
makeDiscreteTrans Man page
makeDiscreteTransInteger Man page
makeEnvObj Man page
makeFecObj Man page
makeFecObjInteger Man page
makeGrowthObj Man page
makegrowthObjHossfeld Man page
makeIntegerFmatrix Man page
makeIntegerPmatrix Man page
makeIPMCmatrix Man page
makeIPMFmatrix Man page
makeIPMmatrix Man page
makeIPMPmatrix Man page
.makeListIPMs Man page
.makeListPmatrix Man page
makeOffspringObj Man page
makeSurvObj Man page
meanLifeExpect Man page
passageTime Man page
picGrow Man page
picSurv Man page
plotGrowthModelComp Man page
plotSurvModelComp Man page
predictFutureDistribution Man page
R0Calc Man page
.requireCachedGenerics Man page
sampleIPM Man page
sampleIPMOutput Man page
sampleSequentialIPMs Man page
sampleVitalRateObj Man page
sens Man page
sensParams Man page
simulateCarlina Man page
sizeToAge Man page
stochGrowthRateManyCov Man page
stochGrowthRateSampleList Man page
stochPassageTime Man page
stochPassageTime,numeric,IPMmatrix,envMatrix-method Man page
surv Man page
survivorship Man page
surv-methods Man page
survModelComp Man page
surv,numeric,data.frame,survObj-method Man page
surv,numeric,data.frame,survObj-method Man page
surv,numeric,data.frame,survObjOverDisp-method Man page
surv,numeric,numeric,survObjOverDisp-method Man page
survObj-class Man page
survObjOverDisp-class Man page
timeToSize Man page
varLifeExpect Man page
varPassageTime Man page
wrapHossfeld Man page

Files

IPMpack
IPMpack/inst
IPMpack/inst/doc
IPMpack/inst/doc/IPMpack_Vignette.pdf
IPMpack/inst/doc/IPMpack_Vignette.R
IPMpack/inst/doc/IPMpack_Vignette.Rnw
IPMpack/NAMESPACE
IPMpack/data
IPMpack/data/dataIPMpackSilwood.csv.gz
IPMpack/data/dataIPMpackSuccisa.csv.gz
IPMpack/data/dataIPMpackCryptantha.csv.gz
IPMpack/data/dataIPMpackSuccisa2.csv.gz
IPMpack/data/dataIPMpackHypericumCov.csv.gz
IPMpack/data/dataIPMpackHypericum.csv.gz
IPMpack/R
IPMpack/R/IPMpack-Util.r
IPMpack/R/IPMpack-Classes_and_Methods.R IPMpack/R/IPMpack-Matrices.R
IPMpack/R/IPMpack-Hidden.r
IPMpack/R/IPMpack-Analyses.r
IPMpack/R/IPMpack-Vital_Rate_Obj.r
IPMpack/vignettes
IPMpack/vignettes/IPMpack_Vignette.Rnw
IPMpack/vignettes/IPMpack_Vignette-fig7.pdf
IPMpack/MD5
IPMpack/build
IPMpack/build/vignette.rds
IPMpack/DESCRIPTION
IPMpack/man
IPMpack/man/makeCompoundFmatrix.Rd IPMpack/man/wrapHossfeld.Rd IPMpack/man/Hossfeld.Rd IPMpack/man/varPassageTime.Rd IPMpack/man/convergeIPM.Rd IPMpack/man/sampleSequentialIPMs.Rd IPMpack/man/discreteTransInteger-class.Rd IPMpack/man/growthObjTruncIncr-class.Rd IPMpack/man/IPMpackNews.Rd IPMpack/man/survivorship.Rd IPMpack/man/IPMpack-package.Rd IPMpack/man/picGrow.Rd IPMpack/man/predictFutureDistribution.Rd IPMpack/man/varLifeExpect.Rd IPMpack/man/makeIPMFmatrix.Rd IPMpack/man/dataIPMpackSuccisa.csv.Rd IPMpack/man/elas.Rd IPMpack/man/growthObjIncr-class.Rd IPMpack/man/survObj-class.Rd IPMpack/man/makeEnvObj.Rd IPMpack/man/growthObj-class.Rd IPMpack/man/simulateCarlina.Rd IPMpack/man/passageTime.Rd IPMpack/man/dataIPMpackHypericumCov.csv.Rd IPMpack/man/growSurv.Rd IPMpack/man/fecObjInteger-class.Rd IPMpack/man/makeDiscreteTrans.Rd IPMpack/man/dataIPMpackCryptantha.csv.Rd IPMpack/man/IPMpack-internal.Rd IPMpack/man/surv-methods.Rd IPMpack/man/sampleVitalRateObj.Rd IPMpack/man/picSurv.Rd IPMpack/man/coerceGrowthObj.Rd IPMpack/man/stochPassageTime.Rd IPMpack/man/largeMatrixCalc.Rd IPMpack/man/growth-methods.Rd IPMpack/man/growthObjIncrDeclineVar-class.Rd IPMpack/man/survObjOverDisp-class.Rd IPMpack/man/surv.Rd IPMpack/man/dataIPMpackSilwood.csv.Rd IPMpack/man/diagnosticsPmatrix.Rd IPMpack/man/R0Calc.Rd IPMpack/man/growthObjLogIncr-class.Rd IPMpack/man/makeIPMmatrix.Rd IPMpack/man/dataIPMpackSuccisa2.csv.Rd IPMpack/man/dataIPMpackHypericum.csv.Rd IPMpack/man/sensParams.Rd IPMpack/man/makeClonalObj.Rd IPMpack/man/logit.Rd IPMpack/man/growthModelComp.Rd IPMpack/man/addPdfGrowthPic.Rd IPMpack/man/convertIncrement.Rd IPMpack/man/IPMmatrix-class.Rd IPMpack/man/growthCum-methods.Rd IPMpack/man/makeIPMCmatrix.Rd IPMpack/man/growth.Rd IPMpack/man/sampleIPM.Rd IPMpack/man/growthObjNegBin-class.Rd IPMpack/man/growthObjLogIncrDeclineVar-class.Rd IPMpack/man/stochGrowthRateManyCov.Rd IPMpack/man/generateData.Rd IPMpack/man/discreteTrans-class.Rd IPMpack/man/makeFecObjInteger.Rd IPMpack/man/makeFecObj.Rd IPMpack/man/makeCompoundCmatrix.Rd IPMpack/man/sampleIPMOutput.Rd IPMpack/man/envMatrix-class.Rd IPMpack/man/growthObjDeclineVar-class.Rd IPMpack/man/makeGrowthObjHossfeld.Rd IPMpack/man/makeGrowthObj.Rd IPMpack/man/makeDiscreteTransInteger.Rd IPMpack/man/stochGrowthRateSampleList.Rd IPMpack/man/timeToSize.Rd IPMpack/man/meanLifeExpect.Rd IPMpack/man/growthCum.Rd IPMpack/man/fecObj-class.Rd IPMpack/man/plotGrowthModelComp.Rd IPMpack/man/growthObjPois.Rd IPMpack/man/sizeToAge.Rd IPMpack/man/growthObjHossfeld-class.Rd IPMpack/man/makeSurvObj.Rd IPMpack/man/makeIPMPmatrix.Rd IPMpack/man/makeCompoundPmatrix.Rd IPMpack/man/makeIntegerFmatrix.Rd IPMpack/man/makeOffspringObj.Rd

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