IPMpack (version 2.0)

makeOffspringObj: Function to build offspring objects

Description

A function that fits regressions that define offspring size and from these build growth objects for which methods to build an IPM object are defined; alternatively, the function creates offspring objects following a specified formula with specified coefficients and sd. Note that if an "offspringNext" column is available in the data, the data will be subsetted based on whether offspringType="sexual" or "clonal" (the default is "sexual"); - otherwise, appropriate data must be supplied.

Usage

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

Arguments

dataf

a dataframe with columns `size' and `sizeNext'(`size' is size of parent at t, and may not be known, `sizeNext' is offspring size at t+1); facultatively, dataf may include `covariate' and `covariatel' for a single discrete covariate, indicating

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), `s

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

reproductionType

whether the relationship should be fitted for sexual or clonal offspring; the default is "sexual"; this will only be relevant if data is provided and has a column "offspringNext"

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

See Also

makeGrowthObj, makeSurvObj, makeFecObj

Examples

#generate data
dff <- generateData()

#make simple linear regression growth object relating size to size at t+1
off1 <- makeOffspringObj(dataf = dff, Formula = sizeNext~1)

#now specifying parameters and supplying no data
off1 <- makeOffspringObj(Formula = incr ~ size + covariate,coeff=c(1,1,1),sd=1)

##make an Fmatrix with this
dff<-generateData()
dff$fec[dff$fec==0] <- NA

off1 <- makeOffspringObj(dataf = dff, Formula = sizeNext~1)
fv1 <- makeFecObj(dff, Formula = fec~size, Transform = "log", 
    doOffspring=FALSE)
Fmatrix1 <- makeIPMFmatrix(fecObj = fv1, nBigMatrix = 20, 
	minSize = min(dff$size, na.rm = TRUE), maxSize = max(dff$size,
na.rm = TRUE), correction="constant", offspringObj=off1)

#compare with the other approach (where offspring object is not separate)
fv2 <- makeFecObj(dff, Formula = fec~size, Transform = "log",
	offspringSizeExplanatoryVariables = "1", doOffspring=TRUE)
Fmatrix2 <- makeIPMFmatrix(fecObj = fv2, nBigMatrix = 20, 
	minSize = min(dff$size, na.rm = TRUE), maxSize = max(dff$size,
na.rm = TRUE), correction="constant", offspringObj=NULL)

par(mfrow=c(1,2))
image(Fmatrix1); image(Fmatrix2)