lefko3 (version 3.1.0)

sf_distrib: Test for overdispersion and zero inflation in size and fecundity

Description

Function sf_distrib takes a historically formatted vertical data as input and tests whether size and fecundity data are dispersed according to a Poisson distribution (where mean = variance), and whether the number of 0s exceeds expectations.

Usage

sf_distrib(data, size = NA, fec = NA, repst = NA)

Arguments

data

A historical vertical data file, which is a data frame of class hfvdata.

size

The name or column number of the variable corresponding to size.

fec

The name or column number of the variable corresponding to fecundity. Note that the name of the variable should correspond to the proper time, either time *t* or time *t*-1.

repst

The name or column number of the variable corresponding to reproductive status in time *t*. Required if fecundity distribution will be tested.

Value

Produces text describing the degree and significance of overdispersion and zero inflation. The tests are chi-squared score tests based on the expectations of mean = variance, and 0s as abundant as predicted by the value of lambda estimated from the dataset. See van der Broek (1995) for more details.

Examples

# NOT RUN {
data(lathyrus)

sizevector <- c(0, 4.6, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 1, 2, 3, 4, 5, 6, 7, 8, 9)
stagevector <- c("Sd", "Sdl", "Dorm", "Sz1nr", "Sz2nr", "Sz3nr", "Sz4nr", "Sz5nr",
                 "Sz6nr", "Sz7nr", "Sz8nr", "Sz9nr", "Sz1r", "Sz2r", "Sz3r", "Sz4r",
                 "Sz5r", "Sz6r", "Sz7r", "Sz8r", "Sz9r")
repvector <- c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1)
obsvector <- c(0, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1)
matvector <- c(0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1)
immvector <- c(1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0)
propvector <- c(1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0)
indataset <- c(0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1)
binvec <- c(0, 4.6, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 
            0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5)

lathframeln <- sf_create(sizes = sizevector, stagenames = stagevector, repstatus = repvector, 
                       obsstatus = obsvector, matstatus = matvector, immstatus = immvector, 
                       indataset = indataset, binhalfwidth = binvec, propstatus = propvector)

lathvertln <- verticalize3(lathyrus, noyears = 4, firstyear = 1988, patchidcol = "SUBPLOT",
                           individcol = "GENET", blocksize = 9, juvcol = "Seedling1988",
                           sizeacol = "lnVol88", repstracol = "Intactseed88",
                           fecacol = "Intactseed88", deadacol = "Dead1988",
                           nonobsacol = "Dormant1988", stageassign = lathframeln,
                           stagesize = "sizea", censorcol = "Missing1988",
                           censorkeep = NA, NAas0 = TRUE, censor = TRUE)

lathvertln$feca2 <- round(lathvertln$feca2)
lathvertln$feca1 <- round(lathvertln$feca1)
lathvertln$feca3 <- round(lathvertln$feca3)

sf_distrib(lathvertln, fec = "feca2", repst = "repstatus2")

# }