lefko3 (version 3.1.0)

summary.lefkoMat: Summary of Class "lefkoMat"

Description

A function to simplify the viewing of basic information describing the matrices produced through functions flefko3(), flefko2(), rlefko3(), and rlefko2().

Usage

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

Arguments

object

An object of class lefkoMat.

...

Other parameters.

Value

A summary of the object, showing the number of each type of matrix, the number of annual matrices, the number of estimated (non-zero) elements across all matrices and per matrix, the number of unique transitions in the dataset, and the number of individuals.

Examples

# NOT RUN {
data(cypdata)

sizevector <- c(0, 0, 0, 0, 0, 0, 1, 2.5, 4.5, 8, 17.5)
stagevector <- c("SD", "P1", "P2", "P3", "SL", "D", "XSm", 
                 "Sm", "Md", "Lg", "XLg")
repvector <- c(0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1)
obsvector <- c(0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1)
matvector <- c(0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1)
immvector <- c(0, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0)
propvector <- c(1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0)
indataset <- c(0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1)
binvec <- c(0, 0, 0, 0, 0, 0.5, 0.5, 1, 1, 2.5, 7)

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

cypraw_v1 <- verticalize3(data = cypdata, noyears = 6, firstyear = 2004,
                          patchidcol = "patch", individcol = "plantid",
                          blocksize = 4, sizeacol = "Inf2.04", sizebcol = "Inf.04",
                          sizeccol = "Veg.04", repstracol = "Inf.04",
                          repstrbcol = "Inf2.04", fecacol = "Pod.04",
                          stageassign = cypframe_raw, stagesize = "sizeadded",
                          NAas0 = TRUE, NRasRep = TRUE)

rep_cyp_raw <- matrix(0, 11, 11)
rep_cyp_raw[1:2,7:11] <- 0.5

cypover2r <- overwrite(stage3 = c("SD", "P1", "P2", "P3", "SL", "SL", "D", 
                       "XSm", "Sm"), stage2 = c("SD", "SD", "P1", "P2", "P3", 
                       "SL", "SL", "SL", "SL"), eststage3 = c(NA, NA, NA, NA, 
                       NA, NA, "D", "XSm", "Sm"), eststage2 = c(NA, NA, NA, NA, 
                       NA, NA, "XSm", "XSm", "XSm"), givenrate = c(0.1, 0.2, 
                       0.2, 0.2, 0.25, 0.4, NA, NA, NA), type = c("S", "S", "S",
                       "S", "S", "S", "S", "S", "S"))

cypmatrix2r <- rlefko2(data = cypraw_v1, stageframe = cypframe_raw, year = "all",
                       patch = "all", stages = c("stage3", "stage2", "stage1"),
                       size = c("size3added", "size2added"),
                       repmatrix = rep_cyp_raw, overwrite = cypover2r,
                       yearcol = "year2", patchcol = "patchid",
                       indivcol = "individ")
                       
summary(cypmatrix2r)

# }