image3.list: Create Matrix Images for Matrices in a List

In lefko3: Historical and Ahistorical Population Projection Matrix Analysis

Create Matrix Images for Matrices in a List

Description

Function image3.list plots matrix images for matrices contained in a list of matrices.

Usage

## S3 method for class 'list'
image3(mats, used = "all", ...)

Arguments

mats	A list class object.
used	A numeric vector of projection matrices within mats to represent as matrix images. Can also take the text value "all", which will produce images of all matrices. Defaults to "all".
...	Other parameters.

Value

Plots a matrix image, or series of matrix images, denoting non-zero elements as red space and zero elements as white space.

Examples

# Lathyrus example
data(lathyrus)

sizevector <- c(0, 100, 13, 127, 3730, 3800, 0)
stagevector <- c("Sd", "Sdl", "VSm", "Sm", "VLa", "Flo", "Dorm")
repvector <- c(0, 0, 0, 0, 0, 1, 0)
obsvector <- c(0, 1, 1, 1, 1, 1, 0)
matvector <- c(0, 0, 1, 1, 1, 1, 1)
immvector <- c(1, 1, 0, 0, 0, 0, 0)
propvector <- c(1, 0, 0, 0, 0, 0, 0)
indataset <- c(0, 1, 1, 1, 1, 1, 1)
binvec <- c(0, 100, 11, 103, 3500, 3800, 0.5)

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

lathvert <- verticalize3(lathyrus, noyears = 4, firstyear = 1988,
  patchidcol = "SUBPLOT", individcol = "GENET", blocksize = 9,
  juvcol = "Seedling1988", sizeacol = "Volume88", repstracol = "FCODE88",
  fecacol = "Intactseed88", deadacol = "Dead1988",
  nonobsacol = "Dormant1988", stageassign = lathframe, stagesize = "sizea",
  censorcol = "Missing1988", censorkeep = NA, censor = TRUE)

lathsupp3 <- supplemental(stage3 = c("Sd", "Sd", "Sdl", "Sdl", "Sd", "Sdl"), 
  stage2 = c("Sd", "Sd", "Sd", "Sd", "rep", "rep"),
  stage1 = c("Sd", "rep", "Sd", "rep", "all", "all"), 
  givenrate = c(0.345, 0.345, 0.054, 0.054, NA, NA),
  multiplier = c(NA, NA, NA, NA, 0.345, 0.054),
  type = c(1, 1, 1, 1, 3, 3), type_t12 = c(1, 2, 1, 2, 1, 1),
  stageframe = lathframe, historical = TRUE)

ehrlen3 <- rlefko3(data = lathvert, stageframe = lathframe, year = "all", 
  stages = c("stage3", "stage2", "stage1"), supplement = lathsupp3,
  yearcol = "year2", indivcol = "individ")

image3(ehrlen3$A, used = 1)

lefko3 documentation built on Oct. 14, 2023, 1:07 a.m.