Function to coerce growth or survival objects, i.e., impose user-defined parameters

Description

Supplied with a growth and survival object, over-writes coefficients, and for growth, the sd of growth

Usage

coerceGrowthObj(growthObj, coeff, sd)
coerceSurvObj(survObj,coeff)

Arguments

Details

These functions can be used to impose coefficients and sd on growth and survival objects where direct fitting is not desired

Value

an object of class growthObj / survObj

Author(s)

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

See Also

makeSurvObj, makeGrowthObj

Examples

dff<-generateData()

#for growth
gr1 <- makeGrowthObj(dataf=dff,
Formula=sizeNext~size,regType="constantVar")

#halve the slope
gr2 <- coerceGrowthObj(gr1,coeff=c(gr1@fit$coefficients[1],
    gr1@fit$coefficients[2]*0.5),
    sd=gr1@sd)

par(mfrow=c(1,2),pty="s")
picGrow(dff,gr1)
picGrow(dff,gr2)

#for survival
sv1 <- makeSurvObj(dataf=dff,
Formula=surv~size)

#halve the slope
sv2 <- coerceSurvObj(sv1,coeff=c(sv1@fit$coefficients[1],
    sv1@fit$coefficients[2]*0.5))

par(mfrow=c(1,2),pty="s")
picSurv(dff,sv1)
picSurv(dff,sv2)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(IPMpack)
Loading required package: Matrix
Loading required package: MASS
Loading required package: nlme
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/IPMpack/coerceGrowthObj.Rd_%03d_medium.png", width=480, height=480)
> ### Name: coerceGrowthObj
> ### Title: Function to coerce growth or survival objects, i.e., impose
> ###   user-defined parameters
> ### Aliases: coerceGrowthObj coerceSurvObj
> 
> ### ** Examples
> 
> dff<-generateData()
> 
> #for growth
> gr1 <- makeGrowthObj(dataf=dff,
+ Formula=sizeNext~size,regType="constantVar")
> 
> #halve the slope
> gr2 <- coerceGrowthObj(gr1,coeff=c(gr1@fit$coefficients[1],
+     gr1@fit$coefficients[2]*0.5),
+     sd=gr1@sd)
> 
> par(mfrow=c(1,2),pty="s")
> picGrow(dff,gr1)
> picGrow(dff,gr2)
> 
> #for survival
> sv1 <- makeSurvObj(dataf=dff,
+ Formula=surv~size)
> 
> #halve the slope
> sv2 <- coerceSurvObj(sv1,coeff=c(sv1@fit$coefficients[1],
+     sv1@fit$coefficients[2]*0.5))
> 
> par(mfrow=c(1,2),pty="s")
> picSurv(dff,sv1)
> picSurv(dff,sv2)
> 
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>