makeSurvObj: Functions to build survival objects

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

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)

Note

See manual for details on building case-specific survival objects.

Author(s)

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

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))

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