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IPMpack (version 2.1)

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

35

Version

2.1

License

GPL

Maintainer

Sean McMahon

Last Published

March 17th, 2014

Functions in IPMpack (2.1)

Creates a Hossfeld function defining growth.

Combines growth and survival.

Functions to build survival objects

convertIncrement

Convert size increment according to time elapsed between censuses.

makeCompoundPmatrix

Builds a compound P matrix.

Calculates net reproductive rate (R0) from an IPM.

makeOffspringObj

Function to build offspring objects

growthCum-methods

~~ Methods for Function growthCum ~~

makegrowthObjHossfeld

Function to make a Hossfeld Growth Object

dataIPMpackHypericum

Hypericum Perennial Dataset

~~ Methods for Function growth ~~

Makes pictures of data with growth models

dataIPMpackSuccisa

Succisa pratensis Dataset

Estimates growth probabilities.

Models growth allowing for cumulative bin estimation.

growthObjIncr-class

Class "growthObjIncr"

growthModelComp

Compares growth and survival objects built from different covariate sets.

stochPassageTime

Estimates passage time in a discretely varying environment.

predictFutureDistribution

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

dataIPMpackSilwood

Silwood Monocarp Dataset

Estimates survivorship between two time censuses.

stochGrowthRateSampleList

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

makeIntegerFmatrix

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

IPMmatrix-class

Class "IPMmatrix"

growthObjHossfeld-class

Class "growthObjHossfeld"

dataIPMpackCryptantha

Cryptantha Perennial Dataset with Covariates

Defines passage time to a chosen continuous stage.

Estimates matrix element sensitivities and elasticities.

Makes pictures of survival.

coerceGrowthObj

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

plotGrowthModelComp

Plots compared models built with growthModelComp and survModelComp.

Builds F matrices.

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.

IPMpack-internal

Internal IPMpack objects.

dataIPMpackHypericumCov

Hypericum Perennial Dataset with covariates

addPdfGrowthPic

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

Function to build fecundity objects

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.

Estimates variation in passage time.

Estimates size/stage to age relationships

Calculates variation in life expectancy in a discretely stochastic environment.

makeCompoundFmatrix

Builds a compound F matrix.

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).

Calculates the mean life expectancy.

sampleVitalRateObj

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

Implements a logistic transform.

growthObj-class

Class "growthObj"

Function to build clonal reproduction objects

Builds P matrices.

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.

dataIPMpackSuccisa2

Succisa pratensis Dataset

growthObjLogIncr-class

Class "growthObjLogIncr"

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.

Builds C matrices.

growthObjNegBin-class

Class "growthObjNegBin"

Function to build growth objects

~~ Methods for Function surv ~~

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

makeCompoundCmatrix

Builds a compound C matrix.

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.

makeDiscreteTrans

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

growthObjLogIncrDeclineVar-class

Class "growthObjLogIncrDeclineVar"

growthObjIncrDeclineVar-class

Class "growthObjIncrDeclineVar"

Fitting Hossfeld growth function.

envMatrix-class

Class "envMatrix"

discreteTransInteger-class

Class "discreteTransInteger"

Builds environmental transition objects.

Generates random data in the form used by IPMpack.

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

Show a text file containing package news and updates.

fecObjInteger-class

Class "fecObjInteger"

diagnosticsPmatrix

Creates a series of diagnostic graphs for a P matrix.

growthObjPois-class

Class "growthObjPois"

makeFecObjInteger

Function to build fecundity objects

Builds IPM matrices.

survObjOverDisp-class

Class "survObjOverDisp"

simulateCarlina

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

Class "survObj"

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

discreteTrans-class

Class "discreteTrans"

growthObjDeclineVar-class

Class "growthObjDeclineVar"

growthObjTruncIncr-class

Class "growthObjTruncIncr"