elasticity3.matrix: Estimate Elasticity of Population Growth Rate of a Single...

In lefko3: Historical and Ahistorical Population Projection Matrix Analysis

Estimate Elasticity of Population Growth Rate of a Single Matrix

Description

elasticity3.matrix() returns the elasticities of lambda to elements of a single matrix. Because this handles only one matrix, the elasticities are inherently deterministic and based on the dominant eigen value as the best metric of the population growth rate. 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'
elasticity3(mats, force_sparse = "auto", ...)

Arguments

mats	An object of class matrix.
force_sparse	A text string indicating whether to use sparse matrix encoding ("yes") or not ("no") with standard matrix input. 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 a single elasticity 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

elasticity3()

elasticity3.lefkoMat()

elasticity3.list()

elasticity3.dgCMatrix()

summary.lefkoElas()

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", "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)
elasticity3(ehrlen3mean$A[[1]])

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