cond_hmpm: Extract Conditional Ahistorical Matrices from Historical MPM

In lefko3: Historical and Ahistorical Population Projection Matrix Analysis

Extract Conditional Ahistorical Matrices from Historical MPM

Description

Function cond_hmpm() takes historical MPMs and decomposes them into ahistorical matrices conditional upon stage in time t-1. In effect, the function takes each historical matrix within a lefkoMat object, and forms one ahistorical matrix for each stage in time t-1.

Usage

cond_hmpm(hmpm, matchoice = NULL, err_check = NULL)

Arguments

hmpm	A historical matrix projection model of class lefkoMat.
matchoice	A character denoting whether to use A, U, or F matrices. Defaults to A matrices.
err_check	A logical value denoting whether to include a data frame of element equivalence from the conditional matrices to the original matrices. Used only for debugging purposes. Defaults to FALSE.

Value

A lefkoCondMat object, with the following elements:

Mcond	A multi-level list holding the conditional A matrices derived from the input lefkoMat object. The top level of the list corresponds to each historical matrix in turn, and the lower level corresponds to each stage in time t-1, with individual conditional matrices named for the latter.
hstages	A data frame matrix showing the pairing of ahistorical stages used to create historical stage pairs.
ahstages	A data frame detailing the characteristics of associated ahistorical stages.
labels	A data frame showing the patch and year of each input full A matrix in order.
err_check	An optional data frame showing the order of used element indices to create conditional matrices.

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)

cypsupp3r <- supplemental(stage3 = c("SD", "SD", "P1", "P1", "P2", "P3", "SL",
    "D", "XSm", "Sm", "D", "XSm", "Sm", "mat", "mat", "mat", "SD", "P1"),
  stage2 = c("SD", "SD", "SD", "SD", "P1", "P2", "P3", "SL", "SL", "SL", "SL",
    "SL", "SL", "D", "XSm", "Sm", "rep", "rep"),
  stage1 = c("SD", "rep", "SD", "rep", "SD", "P1", "P2", "P3", "P3", "P3",
    "SL", "SL", "SL", "SL", "SL", "SL", "mat", "mat"),
  eststage3 = c(NA, NA, NA, NA, NA, NA, NA, "D", "XSm", "Sm", "D", "XSm", "Sm",
    "mat", "mat", "mat", NA, NA),
  eststage2 = c(NA, NA, NA, NA, NA, NA, NA, "XSm", "XSm", "XSm", "XSm", "XSm",
    "XSm", "D", "XSm", "Sm", NA, NA),
  eststage1 = c(NA, NA, NA, NA, NA, NA, NA, "XSm", "XSm", "XSm", "XSm", "XSm",
    "XSm", "XSm", "XSm", "XSm", NA, NA),
  givenrate = c(0.1, 0.1, 0.2, 0.2, 0.2, 0.2, 0.25, NA, NA, NA, NA, NA, NA,
    NA, NA, NA, NA, NA),
  multiplier = c(NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
    NA, 0.5, 0.5),
  type = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3),
  type_t12 = c(1, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1),
  stageframe = cypframe_raw, historical = TRUE)

cypmatrix3r <- rlefko3(data = cypraw_v1, stageframe = cypframe_raw,
  year = "all", patch = "all", stages = c("stage3", "stage2", "stage1"),
  size = c("size3added", "size2added", "size1added"),
  supplement = cypsupp3r, yearcol = "year2", patchcol = "patchid",
  indivcol = "individ")

cypcondmats <- cond_hmpm(cypmatrix3r)
summary(cypcondmats)

lefko3 documentation built on June 8, 2025, 10:04 a.m.