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.

Files in this package

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

All documentation is copyright its authors; we didn't write any of that.