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||2014-03-17 03:08:17|
|Maintainer||Sean McMahon <firstname.lastname@example.org>|
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.
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.