cycle_check: Check Continuity of Life Cycle through Matrices in lefkoMat...

In lefko3: Historical and Ahistorical Population Projection Matrix Analysis

Check Continuity of Life Cycle through Matrices in lefkoMat Objects

Description

Function cycle_check() tests whether stages, stage-pairs, or age-stages connect in matrices within lefkoMat objects.

Usage

cycle_check(mpm, quiet = NULL)

Arguments

mpm	An object of class lefkoMat, a matrix, or a list of matrices.
quiet	A logical variable indicating whether to suppress diagnostic messages. Defaults to FALSE.

Value

Returns a list with two elements, both of which are also lists. The first list, no_in, contains as many elements as matrices, with each element containing an integer vector showing the identification numbers of stages, stage-pairs, or age-stages, in each matrix that do not show any transitions leading to them. The second list, no_out, is structured similarly to the first, but shows stages, stage-pairs, or age-stages from which there are no transitions leading out.

Notes

This function tests whether stages, stage-pairs, and age-stages are connected to others in matrices used for projection. Whether stages, stage-pairs, or age-stages are shown depends on whether the MPM is ahistorical / age-based, historical stage-based, or age-by-stage, respectively. Checks are performed by testing whether each column in a matrix includes non-zero transitions to other columns, and by testing whether any columns have no transitions to them from other columns. If any such columns are found, then function cycle_check will export an integer vector giving the column numbers with problems. These column numbers may then be checked against the stage_id column of the associated stageframe in the case of a ahistorical or age-based MPM, against the row number of the associated hstages data frame in the case of a historical MPM, or against the row number of the associated agestages data frame in the case of an age-by-stage MPM.

Examples

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)

cypsupp2r <- supplemental(stage3 = c("SD", "P1", "P2", "P3", "SL", "D", 
    "XSm", "Sm", "SD", "P1"),
  stage2 = c("SD", "SD", "P1", "P2", "P3", "SL", "SL", "SL", "rep",
    "rep"),
  eststage3 = c(NA, NA, NA, NA, NA, "D", "XSm", "Sm", NA, NA),
  eststage2 = c(NA, NA, NA, NA, NA, "XSm", "XSm", "XSm", NA, NA),
  givenrate = c(0.10, 0.20, 0.20, 0.20, 0.25, NA, NA, NA, NA, NA),
  multiplier = c(NA, NA, NA, NA, NA, NA, NA, NA, 0.5, 0.5),
  type =c(1, 1, 1, 1, 1, 1, 1, 1, 3, 3),
  stageframe = cypframe_raw, historical = FALSE)

cypmatrix2r <- rlefko2(data = cypraw_v1, stageframe = cypframe_raw, 
  year = "all", patch = "all", stages = c("stage3", "stage2", "stage1"),
  size = c("size3added", "size2added"), supplement = cypsupp2r,
  yearcol = "year2", patchcol = "patchid", indivcol = "individ")

cycle_check(cypmatrix2r)

lefko3 documentation built on April 4, 2025, 2:53 a.m.