lefko3 (version 3.1.0)

summary.lefkoMod: Summary of Class "lefkoMod"

Description

A function to sumarize the viewable output for an R object of class lefkoMod. This function shows the best-fit models, summarizes the numbers of models in the model tables, shows the criterion used to determine the best-fit models, and provides some basic quality control information.

Usage

# S3 method for lefkoMod
summary(object, ...)

Arguments

object

An R object of class lefkoMod resulting from modelsearch().

...

Other parameters.

Value

A summary of the object, showing the best-fit models for all vital rates, with constants of 0 or 1 used for unestimated models. This is followed by a summary of the number of models tested per vital rate, and a table showing the names of the parameters used to model vital rates and represent tested factors. At the end is a section describing the number of individuals and individual transitions used to estimate each vital rate best-fit model.

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)

lathmodelsln2 <- modelsearch(lathvertln, historical = FALSE, approach = "lme4", suite = "main",
                             vitalrates = c("surv", "obs", "size", "repst", "fec"), 
                             juvestimate = "Sdl", bestfit = "AICc&k", sizedist = "gaussian", 
                             fecdist = "poisson", indiv = "individ", patch = "patchid", 
                             year = "year2", year.as.random = TRUE, patch.as.random = TRUE,
                             show.model.tables = TRUE, quiet = TRUE)

summary(lathmodelsln2)
# }
# NOT RUN {
# }