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IPMpack (version 2.0)

Builds and analyses Integral Projection Models (IPMs).

Description

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).

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Version

Install

install.packages('IPMpack')

Monthly Downloads

50

Version

2.0

License

GPL

Maintainer

Sean McMahon

Last Published

July 26th, 2013

Functions in IPMpack (2.0)

fecObjInteger-class

Class "fecObjInteger"

IPMpack-internal

Internal IPMpack objects.

Class "survObj"

~~ Methods for Function surv ~~

addPdfGrowthPic

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

makegrowthObjHossfeld

Function to make a Hossfeld Growth Object

growthObjLogIncr-class

Class "growthObjLogIncr"

discreteTransInteger-class

Class "discreteTransInteger"

dataIPMpackSilwood

Silwood Monocarp Dataset

growthObjTruncIncr-class

Class "growthObjTruncIncr"

dataIPMpackHypericum

Hypericum Perennial Dataset

makeIntegerFmatrix

Builds P and F matrices built off regressions fitted to discrete variables (with probability mass functions rather than probability density functions).

dataIPMpackSuccisa2

Succisa pratensis Dataset

Combines growth and survival.

growthObjPois-class

Class "growthObjPois"

~~ Methods for Function growth ~~

makeCompoundFmatrix

Builds a compound F matrix.

dataIPMpackCryptantha

Cryptantha Perennial Dataset with Covariates

IPMmatrix-class

Class "IPMmatrix"

Builds P matrices.

Makes pictures of survival.

simulateCarlina

Generates random data in the form used by IPMpack based on the population dynamics of Carlina vulgaris

Creates a Hossfeld function defining growth.

makeOffspringObj

Function to build offspring objects

Projects how long it takes to get from a starting distribution to a target continuous stage value.

Estimates survivorship between two time censuses.

stochGrowthRateSampleList

Estimating the stochastic population growth rate (lambda_s) or invasion rat.

growthObjLogIncrDeclineVar-class

Class "growthObjLogIncrDeclineVar"

Implements a logistic transform.

Defines passage time to a chosen continuous stage.

convertIncrement

Convert size increment according to time elapsed between censuses.

Estimates sensitivity and elasticity of lambda (or R0, or Life expectancy of a chosen bin) to parameters underlying an IPM.

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.

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.

Estimates matrix element sensitivities and elasticities.

growthObjIncrDeclineVar-class

Class "growthObjIncrDeclineVar"

envMatrix-class

Class "envMatrix"

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).

dataIPMpackHypericumCov

Hypericum Perennial Dataset with covariates

growthObj-class

Class "growthObj"

Builds F matrices.

sampleVitalRateObj

Calculates growth objects reflecting distribution of parameters from lm or glm.

Calculates net reproductive rate (R0) from an IPM.

stochPassageTime

Estimates passage time in a discretely varying environment.

Builds IPM matrices.

Fitting Hossfeld growth function.

coerceGrowthObj

Function to coerce growth or survival objects, i.e., impose user-defined parameters

Generates random data in the form used by IPMpack.

makeCompoundCmatrix

Builds a compound C matrix.

plotGrowthModelComp

Plots compared models built with growthModelComp and survModelComp.

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.

Builds environmental transition objects.

Estimates variation in passage time.

Estimates size/stage to age relationships

diagnosticsPmatrix

Creates a series of diagnostic graphs for a P matrix.

Models growth allowing for cumulative bin estimation.

growthObjDeclineVar-class

Class "growthObjDeclineVar"

growthObjIncr-class

Class "growthObjIncr"

growthObjNegBin-class

Class "growthObjNegBin"

makeFecObjInteger

Function to build fecundity objects

Function to build clonal reproduction objects

growthCum-methods

~~ Methods for Function growthCum ~~

sampleSequentialIPMs

Makes a list of IPMs where there is a discrete covariate.

Function to build fecundity objects

makeCompoundPmatrix

Builds a compound P matrix.

predictFutureDistribution

Predicts continuous (e.g. size) stage distribution in the future giving current population's stage distribution.

Calculates variation in life expectancy in a discretely stochastic environment.

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).

Estimates growth probabilities.

discreteTrans-class

Class "discreteTrans"

growthObjHossfeld-class

Class "growthObjHossfeld"

growthModelComp

Compares growth and survival objects built from different covariate sets.

survObjOverDisp-class

Class "survObjOverDisp"

makeDiscreteTrans

Builds matrix for transitions between discrete (e.g. seedbank, dormant) and continuous (e.g. size) stages.

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.

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

dataIPMpackSuccisa

Succisa pratensis Dataset

Functions to build survival objects

Calculates the mean life expectancy.

Function to build growth objects

Builds C matrices.

Makes pictures of data with growth models

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