stablestage3.matrix: Estimate Stable Stage Distribution of a Single Population...

In lefko3: Historical and Ahistorical Population Projection Matrix Analysis

Estimate Stable Stage Distribution of a Single Population Projection Matrix

Description

stablestage3.matrix() returns the stable stage distribution for a population projection matrix. This function can handle large and sparse matrices, and so can be used with large historical matrices, IPMs, age x stage matrices, as well as smaller ahistorical matrices.

Usage

## S3 method for class 'matrix'
stablestage3(mats, force_sparse = "auto", ...)

Arguments

mats	A population projection matrix of class matrix.
force_sparse	A text string indicating whether to use sparse matrix encoding ("yes") when supplied with standard matrices. Defaults to "auto", in which case sparse matrix encoding is used with square matrices with at least 50 rows and no more than 50% of elements with values greater than zero.
...	Other parameters.

Value

This function returns the stable stage distribution corresponding to the input matrix.

Notes

Speed can sometimes be increased by shifting from automatic sparse matrix determination to forced dense or sparse matrix projection. This will most likely occur when matrices have between 30 and 300 rows and columns. Defaults work best when matrices are very small and dense, or very large and sparse.

See Also

stablestage3()

stablestage3.lefkoMat()

stablestage3.list()

stablestage3.dgCMatrix()

Examples

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", "mat"),
  stage2 = c("Sd", "Sd", "Sd", "Sd", "rep", "rep", "Sdl"),
  stage1 = c("Sd", "rep", "Sd", "rep", "npr", "npr", "Sd"),
  eststage3 = c(NA, NA, NA, NA, NA, NA, "mat"),
  eststage2 = c(NA, NA, NA, NA, NA, NA, "Sdl"),
  eststage1 = c(NA, NA, NA, NA, NA, NA, "NotAlive"),
  givenrate = c(0.345, 0.345, 0.054, 0.054, NA, NA, NA),
  multiplier = c(NA, NA, NA, NA, 0.345, 0.054, NA),
  type = c(1, 1, 1, 1, 3, 3, 1), type_t12 = c(1, 2, 1, 2, 1, 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")

ehrlen3mean <- lmean(ehrlen3)
stablestage3(ehrlen3mean$A[[1]])

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