IPMpack (version 2.1)

makeSurvObj: Functions to build survival objects

Description

A function to fit logistic regressions defining survival following user defined formulas (e.g., size+size^2, etc) to build survival objects for which methods to build an IPM object are defined.

Usage

makeSurvObj(dataf,Formula=surv~size+size2, coeff=NULL)

Arguments

dataf

a dataframe with columns `size' and `surv'(`size' is size at t, `surv' is 0 for death of the individual and 1 for survival); 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'.

Formula

a formula describing the desired explanatory variables (interactions, etc) in classical R style, i.e. separated by `+', `*', `:'. Possible covariates include `size', 'size2' (size^2), `size3' (size^3),`logsize' (log(size)), `logsize2' (log(size)^2), and `covariate'. Response should be 'surv' to match dataf

coeff

numeric vector of required coefficients to be imposed if dataf is NULL; must be compatible with Formula

Value

An object of class survObj which is a S4 object which contains the slots:

fit

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

Slots can be listed by using slotNames(survObj)

See Also

picSurv

Examples

#generate data
dff <- generateData()
#make simple logistic regression survival object relating survival to size at t
sv1 <- makeSurvObj(dff, Formula=surv~size)
#assess fit for model with discrete environmental classes fitted
sv1 <- makeSurvObj(dff, Formula=surv~size+covariate)

#now specifying parameters and supplying no data
sv1 <- makeSurvObj(Formula = surv ~ size + covariate,coeff=c(1,1,1))