summary.lefkoMatList: Summary of Class "lefkoMatList"

In lefko3: Historical and Ahistorical Population Projection Matrix Analysis

Summary of Class "lefkoMatList"

Description

A function to simplify the viewing of basic information describing the bootstrapped matrices produced through functions flefko3(), flefko2(), rlefko3(), rlefko2(), aflefko2(), rleslie(), and fleslie() when using bootstrapped data input in format hfvlist.

Usage

## S3 method for class 'lefkoMatList'
summary(
  object,
  elem_summaries = FALSE,
  colsums = TRUE,
  check_cycle = TRUE,
  ...
)

Arguments

object	An object of class lefkoMatList.
elem_summaries	A logical value indicating whether to include summaries of all lefkoMat elements within the input lefkoMatList object. Defaults to FALSE.
colsums	If elem_summaries = TRUE, then this is a logical value indicating whether column sums should be shown for U matrices, allowing users to check stage survival probabilities. Defaults to TRUE.
check_cycle	If elem_summaries = TRUE, then this is a logical value indicating whether to test matrices for stage discontinuities in the life cycle. Defaults to TRUE.
...	Other parameters.

Value

A general summary of the lefkoMatList object, showing the number and type of lefkoMat objects included, the mean number of annual matrices per lefkoMat element, the mean size of each matrix, the mean number of estimated (non-zero) elements across all matrices and per matrix, the mean number of unique transitions in the bootstrapped datasets, the mean number of individuals, and summaries of the column sums of the survival-transition matrices across all lefkoMat objects.

if elem_summaries = TRUE, then summary.lefkoMat{} output is also shown for each lefkoMat object per entered lefkoMatList object.

Stage discontinuities may also be also checked across all lefkoMat objects with function cycle_check. This function will also yield warnings if any survival-transition matrices include elements outside of the interval [0,1], if any fecundity matrices contain negative elements, and if any matrices include NA values.

Notes

Under the Gaussian and gamma size distributions, the number of estimated parameters may differ between the two ipm_method settings. Because the midpoint method has a tendency to incorporate upward bias in the estimation of size transition probabilities, it is more likely to yield non- zero values when the true probability is extremely close to 0. This will result in the summary.lefkoMat function yielding higher numbers of estimated parameters than the ipm_method = "CDF" yields in some cases.

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)

cypraw_v1_boot <- bootstrap3(cypraw_v1, reps = 3)

# Here we use supplemental() to provide overwrite and reproductive info
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_boot <- rlefko2(data = cypraw_v1_boot, stageframe = cypframe_raw, 
  year = "all", patch = "all", stages = c("stage3", "stage2", "stage1"),
  size = c("size3added", "size2added"), supplement = cypsupp2r,
  yearcol = "year2", patchcol = "patchid", indivcol = "individ")

summary(cypmatrix2r_boot)

lefko3 documentation built on Nov. 5, 2025, 7:20 p.m.