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IPMpack (version 1.6)

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

49

Version

1.6

License

GPL

Maintainer

Sean McMahon

Last Published

December 30th, 2012

Functions in IPMpack (1.6)

growthObjPois-class

Class "growthObjPois"

discreteTrans-class

Class "discreteTrans"

makePostSurvivalObjs

Make list of survival objects corresponding to posterior of Bayes fit

IPMmatrix-class

Class "IPMmatrix"

createIPMFmatrix

Builds F matrices.

diagnosticsPmatrix

Creates a series of diagnostic graphs for a P matrix.

growthObjHossfeld-class

Class "growthObjHossfeld"

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

createCompoundFmatrix

Builds a compound F matrix.

createMPMFmatrix

Builds discrete F matrices from the types of data structures used in IPMpack.

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

Estimates matrix element sensitivities and elasticities.

stochGrowthRateSampleList

Estimating the stochastic population growth rate (lambda_s).

Creates a Hossfeld function defining growth.

Produces a graph with the smooth kernel and associated value label.

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).

createIPMPmatrix

Builds P matrices.

growthObj-class

Class "growthObj"

growthCum-methods

~~ Methods for Function growthCum ~~

Calculates net reproductive rate (R0) from an IPM.

stochGrowthRateManyCov

Estimates stochastic population growth rates (lambda_s) or invasion rate with many varying covariates.

growthObjIncrDeclineVar-class

Class "growthObjIncrDeclineVar"

makeListPmatrix

Builds list of P matrices from list growth and survival objects.

~~ Methods for Function surv ~~

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).

Builds environmental transition objects.

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

convertIncrement

Convert size increment according to time elapsed between censuses.

getIPMoutputDirect

Gets IPM output from a list of survival, growth, and (facultatively) fecundity objects.

hyperDataSubset

Hypericum Perennial Dataset

makePostGrowthObjs

Make list of growth objects corresponding to posterior of Bayes fit

createMPMPmatrix

Builds a discrete P matrix from the types of data structures used in IPMpack.

~~ Methods for Function growth ~~

stochGrowthRateSampleListDD

Estimating the stochastic invasion rate.

addPdfGrowthPic

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

Runs a simple model using default survival and growth functions.

Calculates variation in life expectancy in a discretely stochastic environment.

Combines growth and survival.

predictFutureDistribution

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

Fitting Hossfeld growth function.

generateDataDiscrete

Generates data including discrete stages (e.g. seedbank).

Models growth allowing for cumulative bin estimation.

growthObjIncr-class

Class "growthObjIncr"

Functions to build growth objects for constant environments, or discretely varying environments

Function to build fecundity objects

stochPassageTime

Estimates passage time in a discretely varying environment.

Class "survObj"

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.

Calculates the mean life expectancy.

makeDiscreteTrans

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

Estimates survivorship between two time censuses.

makeListFmatrix

Builds list of F (sexual reproduction) matrices from lists of growth, survival and fecundity objects.

Generates random data in the form used by IPMpack.

Estimates variation in passage time.

getListRegObjects

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

envMatrix-class

Class "envMatrix"

growthObjLogIncrDeclineVar-class

Class "growthObjLogIncrDeclineVar"

Function to build clonal reproduction objects

growthObjNegBin-class

Class "growthObjNegBin"

coerceGrowthObj

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

Makes pictures of data with growth models

cryptaDataCovSubset

Cryptantha Perennial Dataset with Covariates

hyperDataCovSubset

Hypericum Perennial Dataset with covariates

Implements a logistic transform.

MakeS list IPMs where there is a discrete covariate.

Defines passage time to a chosen continuous stage.

Functions to build survival objects

convertGrowthObjIncrTruncObj

Convert an increment based growth object to a truncated increment based growth object.

makegrowthObjHossfeld

Function to make a Hossfeld Growth Object

SilwoodDataClean

Silwood Monocarp Dataset

coerceMatrixIPM

Coerces a matrix population model to a IPMmatrix object.

Estimates size/stage to age relationships

createGrowthObj

Function to create growth or survival objects with user-defined parameters

IPMpack-internal

Internal IPMpack objects.

createIntegerFmatrix

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

Estimates growth probabilities.

trackPopStructManyCov

Tracks population structure in a stochastic environment.

simulateCarlina

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

fecObjInteger-class

Class "fecObjInteger"

generateDataStoch

Generates data with stochastic covariates.

growthModelComp

Compares growth and survival objects built from different covariate sets.

growthObjLogIncr-class

Class "growthObjLogIncr"

growthObjTruncIncr-class

Class "growthObjTruncIncr"

growthObjDeclineVar-class

Class "growthObjDeclineVar"

Makes pictures of survival.

createCompoundCmatrix

Builds a compound C matrix.

createIPMCmatrix

Builds C matrices.

plotGrowthModelComp

Plots compared models built with growthModelComp and survModelComp.

survObjOverDisp-class

Class "survObjOverDisp"

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.

createCompoundPmatrix

Builds a compound P matrix.

discreteTransInteger-class

Class "discreteTransInteger"

makeFecObjInteger

Function to build fecundity objects

makePostFecObjs

Make list of fecundity objects corresponding to posterior of Bayes fit

succisaDataSubset

Succisa pratensis Dataset