Builds and analyses Integral Projection Models (IPMs).


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Documentation for package ‘IPMpack’ version 1.6

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A C D E F G H I L M P R S T V W

IPMpack-package Construction and analysis of integral projection models and associated measures of population growth, structure, perturbations (sensitivities and elasticities), overall population dynamics, age-specific metrics, etc.

-- A --

addPdfGrowthPic Adds probability density functions of density function of size or increment given current size and growth to plots.

-- C --

coerceGrowthObj Function to coerce growth or survival objects, i.e., impose user-defined parameters
coerceMatrixIPM Coerces a matrix population model to a IPMmatrix object.
coerceSurvObj Function to coerce growth or survival objects, i.e., impose user-defined parameters
contourPlot Produces a graph with the smooth kernel and associated value label.
convergeLambda Iterates until obtaining the number of bins required so that the difference in the chosen measure (lambda, R0, life expectancy of the first bin) falls below a chosen tolerance level
convergeLifeExpectancyFirstBin Iterates until obtaining the number of bins required so that the difference in the chosen measure (lambda, R0, life expectancy of the first bin) falls below a chosen tolerance level
convergeLifeExpectancyLastBin Iterates until obtaining the number of bins required so that the difference in the chosen measure (lambda, R0, life expectancy of the first bin) falls below a chosen tolerance level
convergeR0 Iterates until obtaining the number of bins required so that the difference in the chosen measure (lambda, R0, life expectancy of the first bin) falls below a chosen tolerance level
convertGrowthObjIncrTruncObj Convert an increment based growth object to a truncated increment based growth object.
convertIncrement Convert size increment according to time elapsed between censuses.
createCompoundCmatrix Builds a compound C matrix.
createCompoundFmatrix Builds a compound F matrix.
createCompoundPmatrix Builds a compound P matrix.
createFecObj Function to create growth or survival objects with user-defined parameters
createGrowthObj Function to create growth or survival objects with user-defined parameters
createIntegerFmatrix Builds P and F matrices built off regressions fitted to discrete variables (with probability mass functions rather than probability density functions).
createIntegerPmatrix Builds P and F matrices built off regressions fitted to discrete variables (with probability mass functions rather than probability density functions).
createIPMCmatrix Builds C matrices.
createIPMFmatrix Builds F matrices.
createIPMPmatrix Builds P matrices.
createMPMFmatrix Builds discrete F matrices from the types of data structures used in IPMpack.
createMPMPmatrix Builds a discrete P matrix from the types of data structures used in IPMpack.
createSurvObj Function to create growth or survival objects with user-defined parameters
cryptaDataCovSubset Cryptantha Perennial Dataset with Covariates

-- D --

diagnosticsPmatrix Creates a series of diagnostic graphs for a P matrix.
discreteTrans-class Class '"discreteTrans"'
discreteTransInteger-class Class '"discreteTransInteger"'

-- E --

elas Estimates matrix element sensitivities and elasticities.
envMatrix-class Class "envMatrix"

-- F --

fecObj-class Class "fecObj"
fecObjInteger-class Class "fecObjInteger"

-- G --

generateData Generates random data in the form used by IPMpack.
generateDataDiscrete Generates data including discrete stages (e.g. seedbank).
generateDataStoch Generates data with stochastic covariates.
getIPMoutput Gets IPM output from a list of P matrices (only survival and size information) or full IPMs (P matrices + F matrices; the latter include sexual reproduction information).
getIPMoutputDirect Gets IPM output from a list of survival, growth, and (facultatively) fecundity objects.
getListRegObjects Calculates growth objects reflecting distribution of parameters from lm or glm.
getListRegObjectsFec Calculates growth objects reflecting distribution of parameters from lm or glm.
growSurv Combines growth and survival.
growth Estimates growth probabilities.
growth-method ~~ Methods for Function 'growth' ~~
growth-methods ~~ Methods for Function 'growth' ~~
growthCum Models growth allowing for cumulative bin estimation.
growthCum-method ~~ Methods for Function 'growthCum' ~~
growthCum-methods ~~ Methods for Function 'growthCum' ~~
growthModelComp Compares growth and survival objects built from different covariate sets.
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 Class "growthObjPois"
growthObjTruncIncr-class Class '"growthObjTruncIncr"'

-- H --

Hossfeld Creates a Hossfeld function defining growth.
hyperDataCovSubset Hypericum Perennial Dataset with covariates
hyperDataSubset Hypericum Perennial Dataset

-- I --

IPMmatrix-class Class '"IPMmatrix"'
IPMpack Construction and analysis of integral projection models and associated measures of population growth, structure, perturbations (sensitivities and elasticities), overall population dynamics, age-specific metrics, etc.

-- L --

largeMatrixCalc Calculates population growth rate (lambda) and stable stage distribution in a computationally efficient way when the number of bins in the IPM is large.
logit Implements a logistic transform.

-- M --

makeClonalObj Function to build clonal reproduction objects
makeClonalObjInteger Function to build fecundity objects
makeDiscreteTrans Builds matrix for transitions between discrete (e.g. seedbank, dormant) and continuous (e.g. size) stages.
makeDiscreteTransInteger Builds matrix for transitions between discrete (e.g. seedbank, dormant) and continuous (e.g. size) stages, for situation where continuous variable is an integer (e.g. number of leaves).
makeEnvObj Builds environmental transition objects.
makeFecObj Function to build fecundity objects
makeFecObjInteger Function to build fecundity objects
makeGrowthObj Functions to build growth objects for constant environments, or discretely varying environments
makegrowthObjHossfeld Function to make a Hossfeld Growth Object
makeListFmatrix Builds list of F (sexual reproduction) matrices from lists of growth, survival and fecundity objects.
makeListIPMs MakeS list IPMs where there is a discrete covariate.
makeListPmatrix Builds list of P matrices from list growth and survival objects.
makePostFecObjs Make list of fecundity objects corresponding to posterior of Bayes fit
makePostGrowthObjs Make list of growth objects corresponding to posterior of Bayes fit
makePostSurvivalObjs Make list of survival objects corresponding to posterior of Bayes fit
makeSurvObj Functions to build survival objects
meanLifeExpect Calculates the mean life expectancy.

-- P --

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 'survModelComp'.
plotResultsStochStruct Tracks population structure in a stochastic environment.
plotSurvModelComp Plots compared models built with 'growthModelComp' and 'survModelComp'.
predictFutureDistribution Predicts continuous (e.g. size) stage distribution in the future giving current population's stage distribution.

-- R --

R0Calc Calculates net reproductive rate (R0) from an IPM.
runSimpleModel Runs a simple model using default survival and growth functions.

-- S --

sens Estimates matrix element sensitivities and elasticities.
sensParams Estimates sensitivity and elasticity of lambda (or R0, or Life expectancy of a chosen bin) to parameters underlying an IPM.
sensParamsLifeExpect Estimates sensitivity and elasticity of lambda (or R0, or Life expectancy of a chosen bin) to parameters underlying an IPM.
sensParamsR0 Estimates sensitivity and elasticity of lambda (or R0, or Life expectancy of a chosen bin) to parameters underlying an IPM.
SilwoodDataClean Silwood Monocarp Dataset
simulateCarlina Generates random data in the form used by IPMpack based on the population dynamics of Carlina vulgaris
sizeToAge Estimates size/stage to age relationships
stochGrowthRateManyCov Estimates stochastic population growth rates (lambda_s) or invasion rate with many varying covariates.
stochGrowthRateSampleList Estimating the stochastic population growth rate (lambda_s).
stochGrowthRateSampleListDD Estimating the stochastic invasion rate.
stochPassageTime Estimates passage time in a discretely varying environment.
stochPassageTime-method Class "envMatrix"
succisaDataSubset Succisa pratensis Dataset
surv Survival
surv-method ~~ Methods for Function surv ~~
surv-method Class '"survObjOverDisp"'
surv-methods ~~ Methods for Function surv ~~
survivorship Estimates survivorship between two time censuses.
survModelComp Compares growth and survival objects built from different covariate sets.
survObj-class Class "survObj"
survObjOverDisp-class Class '"survObjOverDisp"'

-- T --

timeToSize Projects how long it takes to get from a starting distribution to a target continuous stage value.
trackPopStructManyCov Tracks population structure in a stochastic environment.

-- V --

varLifeExpect Calculates variation in life expectancy in a discretely stochastic environment.
varPassageTime Estimates variation in passage time.

-- W --

wrapHossfeld Fitting Hossfeld growth function.