Builds and analyses Integral Projection Models (IPMs).

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Documentation for package ‘IPMpack’ version 2.1

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

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
coerceSurvObj Function to coerce growth or survival objects, i.e., impose user-defined parameters
convergeIPM Iterates until obtaining the number of bins required so that the difference in the chosen measure (lambda, R0, life expectancy of a chosenBin) falls below a chosen tolerance level
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.
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.

-- D --

dataIPMpackCryptantha Cryptantha Perennial Dataset with Covariates
dataIPMpackHypericum Hypericum Perennial Dataset
dataIPMpackHypericumCov Hypericum Perennial Dataset with covariates
dataIPMpackSilwood Silwood Monocarp Dataset
dataIPMpackSuccisa Succisa pratensis Dataset
dataIPMpackSuccisa2 Succisa pratensis Dataset
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.
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.

-- I --

invLogit Implements a logistic transform.
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.
IPMpackNews Show a text file containing package news and updates.

-- 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.

-- M --

makeClonalObj Function to build clonal reproduction objects
makeClonalObjInteger Function to build fecundity 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. 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 Function to build growth objects
makegrowthObjHossfeld Function to make a Hossfeld Growth Object
makeIntegerFmatrix Builds P and F matrices built off regressions fitted to discrete variables (with probability mass functions rather than probability density functions).
makeIntegerPmatrix Builds P and F matrices built off regressions fitted to discrete variables (with probability mass functions rather than probability density functions).
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.

-- 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'.
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.

-- S --

sampleIPM Builds list of IPMs or P matrices from list growth, survival, fecundity and discreteTrans objects. It is helpful when building multiple IPMs for study of parameter uncertainty or stochastic dynamics.
sampleIPMOutput 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).
sampleSequentialIPMs Makes a list of IPMs where there is a discrete covariate.
sampleVitalRateObj Calculates growth objects reflecting distribution of parameters from lm or glm.
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.
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. Alternatively, tracks population structure in a stochastic environment if trackStruct is TRUE.
stochGrowthRateSampleList Estimating the stochastic population growth rate (lambda_s) or invasion rat.
stochPassageTime Estimates passage time in a discretely varying environment.
stochPassageTime-method Class "envMatrix"
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.

-- V --

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

-- W --

wrapHossfeld Fitting Hossfeld growth function.

-- misc --

.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 P matrices (only survival and size information) or full IPMs (P matrices + F matrices; the latter include sexual reproduction information).
.getListRegObjects Calculates growth objects reflecting distribution of parameters from lm or glm.
.getListRegObjectsFec Calculates growth objects reflecting distribution of parameters from lm or glm.
.makeListIPMs Makes a list of IPMs where there is a discrete covariate.
.makeListPmatrix Builds list of IPMs or P matrices from list growth, survival, fecundity and discreteTrans objects. It is helpful when building multiple IPMs for study of parameter uncertainty or stochastic dynamics.