lefko3 (version 3.3.2)

elasticity3.list: Estimate Elasticity of Population Growth Rate of a List of Matrices

Description

elasticity3.list() returns the elasticities of lambda to elements of a single 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 list
elasticity3(mats, stochastic = FALSE, steps = 10000, time_weights = NA, ...)

Arguments

mats

A list of objects of class matrix.

stochastic

A logical value determining whether to conduct a deterministic (FALSE) or stochastic (TRUE) elasticity analysis. Defaults to FALSE.

steps

The number of times to project forward in stochastic simulation. Defaults to 10,000.

time_weights

Numeric vector denoting the probabilistic weightings of annual matrices. Defaults to equal weighting among times.

...

Other parameters.

Value

This function returns an object of class lefkoElas, which is a list with 7 elements. The first, h_elasmats, is a list of historical elasticity matrices, though in the standard list case it returns a NULL value. The second, ah_elasmats, is a list of either ahistorical elasticity matrices. Since the list used as input contains no stage information, all matrices are assumed to be ahistorical and elasticities are provided via this element. The third element, h_stages, and the fourth element, ah_stages, are NULL. The last 3 elements are the original A matrices in element A, followed by NULL values for the U and F elements.

Notes

Deterministic elasticities are estimated as eqn. 9.72 in Caswell (2001, Matrix Population Models). Stochastic elasticities are estimated as eqn. 14.99 in Caswell (2001). Note that stochastic elasticities are of stochastic \(\lambda\), while stochastic sensitivities are with regard to the log of the stochastic \(\lambda\).

See Also

elasticity3()

elasticity3.lefkoMat()

elasticity3.matrix()

Examples

# NOT RUN {
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)

lathrepm <- matrix(0, 7, 7)
lathrepm[1, 6] <- 0.345
lathrepm[2, 6] <- 0.054

lathover3 <- overwrite(stage3 = c("Sd", "Sd", "Sdl"),
  stage2 = c("Sd", "Sd", "Sd"), stage1 = c("Sd", "rep", "rep"),
  givenrate = c(0.345, 0.345, 0.054))

ehrlen3 <- rlefko3(data = lathvert, stageframe = lathframe,
  year = c(1989, 1990), stages = c("stage3", "stage2", "stage1"),
  repmatrix = lathrepm, overwrite = lathover3, yearcol = "year2",
  indivcol = "individ")

elasticity3(ehrlen3$A, stochastic = TRUE)

# }