# Builds and analyses Integral Projection Models (IPMs).

## Documentation for package ‘IPMpack’ version 2.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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.