IPMpack (version 1.6)

getListRegObjects: Calculates growth objects reflecting distribution of parameters from lm or glm.

Description

Function generates pdfs corresponding to estimated parameters and the variance covariance matrix that defines them using a multivariate normal distribution and then defines the corresponding growth or survival objects.

Usage

getListRegObjects(Obj,nsamp=1000)
getListRegObjectsFec(Obj,nsamp=1000)

Arguments

Obj

a growth or survival object with a slot named "fit" for getListRegObjects containing an lm or glm, etc or a fertility object with a slot named "fitFec" for getListRegObjectsFec, likewise.

nsamp

desired number of samples from the posterior multivariate normal

Value

• list of growth or survival objects containing an lm or glm; or fertility objects likewise

See Also

makeGrowthObj,makeSurvObj,getIPMoutputDirect

Examples

# Data with size and sizeNext
dff <- generateData()
gr1 <- makeGrowthObj(dff)
sv1 <- makeSurvObj(dff)
fv1 <- makeFecObj(dff,Transform="log")

#higher nsamp are advisable for a detailed analysis
grList <- getListRegObjects(gr1, nsamp=10)
svList <- getListRegObjects(sv1, nsamp=10)
fvList <- getListRegObjectsFec(fv1, nsamp=10)


res <- getIPMoutputDirect(survObjList = svList,
                               growObjList = grList,
                               fecObjList = fvList,
                               targetSize = 6,
                               nBigMatrix = 100,
                               minSize = 1.1*min(dff$size,na.rm=TRUE),
                               maxSize = 1.1*max(dff$size,na.rm=TRUE),
                               integrateType="midpoint",correction="constant", 
                               storePar=FALSE)


  
     # Plot out with different colours for different rows:
     par(mfrow = c(2,2), bty = "l", pty = "s")
     plot(res$meshpoints, res$LE[1, ], xlab = "Continuous (e.g. size) stage", 
     	ylab = "Life expectancy", type= "l", ylim = range(res$LE, na.rm=TRUE))
     for (j in 1:nrow(res$LE)) points(res$meshpoints,res$LE[j, ],col=j, type = "l")

     plot(res$meshpoints, res$pTime[1, ], xlab="Continuous (e.g. Size) stage", 
     	ylab = "Passage time", type = "l", ylim = range(res$pTime, na.rm=TRUE))
     for (j in 1:nrow(res$pTime)) points(res$meshpoints,res$pTime[j, ],col=j,  type = "l")
     
     plot(res$meshpoints, Re(res$stableStage[1, ]), xlab="Continuous (e.g. Size) stage", 
     	ylab = "Stable distribution", type = "l", ylim = range(Re(res$stableStage), na.rm=TRUE))
     for (j in 1:nrow(res$stableStage)) points(res$meshpoints,Re(res$stableStage[j, ]),
     	col=j,  type = "l")
     	
     hist(res$lambda,col="grey", xlab=expression(lambda), main="")