Usage
makeFecObj(dataf, fecConstants=data.frame(NA),
Formula=list(fec~size),Family="gaussian",
Transform="none",meanOffspringSize=NA,
sdOffspringSize=NA,offspringSplitter=data.frame(continuous=1),
vitalRatesPerOffspringType=data.frame(NA),fecByDiscrete=data.frame(NA),
offspringSizeExplanatoryVariables="1", coeff=NULL,doOffspring=TRUE,
reproductionType="sexual")
Arguments
dataf
a dataframe with columns "size", "sizeNext", "stage", "stageNext", and any additional columns with fecundity data. UIf fecundity data is transformed via log, etc, this MUST BE MADE CLEAR in the argument Transform since the fecundity object produced must generate total reproductive output.)
fecConstants
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 sexual reproduction that are not explicitly incorporated for each parent (e.g., 25% of seeds across all individuals germinate). The default is NA if no constants are used (equivalent to multiplying by 1).
Formula
a formulas describing the desired explanatory variables (interactions, etc) in classical R style, i.e. separated by `+', `*', `:' and the response variables of choice. Possible covariates include `size', 'size2' (size^2), `size3' (size^3),`logsize' (log(size)), and `covariate' (if this name is used, the assumption is made that this is a discrete covariate from which compound matrices may be constructed), and any other covariates available in dataf. Again, these must appear in the order defined by the Formula argument. See formula in base for more details. Family
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
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
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 fits a mean, or may fit more complex relationships linking maternal size to offspring size).
sdOffspringSize
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
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.frame need to precisely match the used stage names in the data file.
vitalRatesPerOffspringType
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 the column names of this dataframe should match those in the offspringSplitter exactly. The row names of the dataframe should match the fecundity column names in the data file and the supplied fecundity constants, in that order. In the dataframe, a '1' indicates that a fecundity rate applies to an offspring category, while a '0' indicates an omission. For instance, establishment and seedling survival rates may be applicable to seedlings, but not to seeds that go into a seedbank (depending on the life cycle and definition of vital rates).
fecByDiscrete
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=4.2,seedOld=0)
offspringSizeExplanatoryVariables
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., offspringSizeExplanatoryVariables="size") or more complex polynomials of size (i.e., offspringSizeExplanatoryVariables="size+size2"). The corresponding relationship is fitted to the data contained in dataf, taking as the response variable the column "sizeNext" in dataf for rows where the column "offspringNext" is equal to "sexual" and the column "stageNext" is equal to "continuous".
coeff
list of numeric vector of required coefficients to be imposed if dataf is NULL for each element of the Formula list in order; must be compatible with Formula
doOffspring
argument defining whether you wish to fit an offspring regression as part of this function (TRUE), or do it separately (see makeOffspringObj); if this is FALSE, other argument relating to the offspring distribution will be ignored
reproductionType
argument specifying if "sexual" or "clonal" offspring should be considered; default is "sexual".