makeGrowthObj: Function to build growth objects

In wpetry/IPMpack2: Builds and analyses Integral Projection Models (IPMs).

Function to build growth objects

Description

A function that fits regressions that define growth (following next size, size increment, or log size increment) and from these build growth objects for which methods to build an IPM object are defined; alternatively, the function creates growth objects following a specified formula with specified coefficients and sd.

Usage

makeGrowthObj(dataf=NULL, Formula = sizeNext ~ size, 
	regType = "constantVar", Family = "gaussian", link = NULL, coeff=NULL,sd=NULL)

Arguments

dataf	a dataframe with columns ‘size’ and ‘sizeNext’(‘size’ is size at t, ‘sizeNext’ is size at t+1); facultatively, dataf may include ‘covariate’ and ‘covariatel’ for a single discrete covariate, indicating values at t, and at t+1, respectively; these must take values of sequential integers, starting at ‘1’. For models fitting growth increment, 'incr' or 'logincr' may be directly provided as a column in the dataframe, otherwise they are calculated as dataf$sizeNext - dataf$size or log(dataf$sizeNext - dataf$size), respectively.
Formula	a formula describing the desired explanatory variables (interactions, etc) according to the R notation for formula. style, i.e. separated by ‘+’, ‘*’, ‘:’ and response variable. Possible covariates include ‘size’, 'size2' (size^2), ‘size3’ (size^3),‘logsize’ (log(size)), ‘logsize2’ (log(size)^2), and ‘covariate’ (if this name is used, the assumption is made that this is a discrete covariate from which compound matrices may be constructed); or any other covariate available in dataf.
regType	possible values include ‘constantVar’ or ‘changingVar’
Family	possible values include ‘gaussian’, ‘poisson’, ‘negbin’
link	defaults to NULL, currently only relevant with Family="negbin", and only "log" and "identity" are permitted
coeff	numeric vector of required coefficients to be imposed if dataf is NULL; must be compatible with Formula
sd	numeric of required sd to be imposed if dataf is NULL

Value

An object of class growthObj, or growthObjPois, growthObjIncr, or growthObjLogIncr; or growthObjDeclineVar, or growthObjIncrDeclineVar, or growthObjLogIncrDeclineVar. These are S4 objects which contain the slots:

fit	an object of class lm or glm or gls that can be used with predict in the growth methods

Slots can be listed by using slotNames(growthObj)

Note

See manual for details on building case-specific growth objects. Note that DeclineVar objects cannot currently be constructed without a data-frame.

Author(s)

C. Jessica E. Metcalf, Sean M. McMahon, Roberto Salguero-Gomez & Eelke Jongejans

See Also

makeSurvObj, makeFecObj

Examples

#generate data
dff <- generateData()
#make simple linear regression growth object relating size to size at t+1
(gr1 <- makeGrowthObj(dataf = dff, Formula = sizeNext~size))
#same but relating size to incr
(gr1 <- makeGrowthObj(dataf = dff, Formula = incr ~ size))

#assess fit 
picGrow(dff,gr1)

#same but relating size to incr and discrete covariate
(gr1 <- makeGrowthObj(dataf = dff, Formula = incr ~ size + covariate, 
	regType = "changingVar"))
#with declining increment
(gr1 <- makeGrowthObj(dataf = dff, Formula = incr ~ size + covariate, 
	regType = "changingVar"))

#now specifying parameters and supplying no data
gr1 <- makeGrowthObj(Formula = incr ~ size + covariate,coeff=c(1,1,1),sd=1)

wpetry/IPMpack2 documentation built on Sept. 29, 2022, 9:41 a.m.