Usage
createGrowthObj(Formula=sizeNext~size, coeff=c(1,1), sd=1)
createSurvObj(Formula=surv~size, coeff=c(1,1))
createFecObj(Formula=list(fec1~size,fec2~size+size2),
coeff=list(c(1,1),c(1,1,1)),
Family = c("gaussian","binomial"),
Transform = c("log", "none"),
meanOffspringSize = NA, sdOffspringSize = NA,
offspringSplitter = data.frame(continuous = 1),
vitalRatesPerOffspringType = data.frame(NA),
fecByDiscrete = data.frame(NA),
offspringSizeExplanatoryVariables = "1",
fecConstants = data.frame(NA))Arguments
Formula
an object of class formula for createGrowthObj or createSurvObj, or a list of formulas for createFecObj
coeff
a numeric vector of length the number of coefficients
supplied by Formula, or a list for createFecObj
sd
a numeric vector of length 1, for createGrowthObj
fecConstants
for createFecObj, a list containing the value by which each of the fecundity rates will be multiplied in the order defined by the order in Formula. This data frame adjusts the probability of establishment of seeds or other stages in
Family
for createFecObj, a character vector containing the names of the families to be used for the glms, e.g., binomial, poisson, etc. Again, these must appear in the order defined by Formula
Transform
for createFecObj, a character vector containing the names of the
transforms to be used for the response variables, e.g., log, sqrt, -1, etc. Again, these must appear in the order defined by Formula
meanOffspringSize
for createFecObj, numeric vector, defining mean offspring size. Defaults to NA, in which case the function will use to data to assess the mean offspring size according to the relationship defined in offspringSizeExplanatoryVariables (which either simply f
sdOffspringSize
for createFecObj, numeric vector, defining standard deviation of offspring size. Defaults to NA, in which case the function will use the data to assess the standard deviation of offspring size; as described for meanOffspringSize
offspringSplitter
for createFecObj, dataframe with values defining the number of
offspring going into the indicated offspring category; will be re-scaled to
sum to 1 within the function. This argument needs to be entered as a data.frame, and the names in the data.f
vitalRatesPerOffspringType
for createFecObj, dataframe defining which fecundity rates (both functions and constants) apply to which offspring category. This only needs to be specified when some fecundity rates do not apply to all offspring categories. The offspring categories in th
fecByDiscrete
for createFecObj, data.frame defining number of offspring produced by each
discrete class ; defaults to 0. If specified, ALL discrete classes MUST appear in alphabetical order,
so NO "continuous". e.g. fecByDiscrete=data.frame(dormant=0,seedAge1=
offspringSizeExplanatoryVariables
for createFecObj, a character defining the relationship defining offspring size; the default is "1", indicating simply fitting a mean and a variance; alternatives would including defining offspring size as a function of maternal size (i.e., offspringSizeE