stage_weight: Create a Vector of Stage Weights for Density Dependence...

In lefko3: Historical and Ahistorical Population Projection Matrix Analysis

Create a Vector of Stage Weights for Density Dependence Calculations

Description

Function stage_weight() creates a data frame summarizing the weighting of individuals of different stages, stage-stage combinations, ages, or age-stages relative to one another in terms of the total population size. Stage weights can be thought of as Lotka-Volterra coefficients applied to individuals of different stages within a single population.

Usage

stage_weight(mpm, stage2 = NA, stage1 = NA, age2 = NA, value = 1)

Arguments

mpm	The lefkoMat object to be used in projection. Can be an example MPM if function-based projection is planned.
stage2	A vector showing the name or number of a stage in occasion t that should be set to a positive number of individuals in the start vector. Abbreviations for groups of stages are also usable (see Notes). This input is required for all stage-based and age-by-stage MPMs. Defaults to NA.
stage1	A vector showing the name or number of a stage in occasion t-1 that should be set to a positive number of individuals in the start vector. Abbreviations for groups of stages are also usable (see Notes). This is only used for historical MPMs, since the rows of hMPMs correspond to stage-pairs in times t and t-1 together. Only required for historical MPMs, and will result in errors if otherwise used.
age2	A vector showing the age of each respective stage in occasion t that should be set to a positive number of individuals in the start vector. Only used for Leslie and age-by-stage MPMs. Defaults to NA.
value	A vector showing the values, in order, of the number of individuals set for the stage or stage-pair in question. Defaults to 1.

Value

A list of class lefkoEq, with four objects, which can be used as input in function projection3() and f_projection3(). The last three include the ahstages, hstages, and agestages objects from the lefkoMat object supplied in mpm. The first element in the list is a data frame with the following variables:

stage2	Stage at occasion t.
stage_id_2	The stage number associated with stage2.
stage1	Stage at occasion t-1, if historical. Otherwise NA.
stage_id_1	The stage number associated with stage1.
age2	The age of individuals in stage2 and, if applicable, stage1. Only used in age-by-stage MPMs.
row_num	A number indicating the respective starting vector element.
value	Number of individuals in corresponding stage or stage-pair.

Notes

Users should generally consider which stage to set as the reference, which should be designated with a value of 1.

In some life histories, certain stages may not count against population size with regards to the kind and value of density dependence decided on. An example might be the dormant seed stage in some plant species. These stage weight values should be set to 0.

Entries in stage2, and stage1 can include abbreviations for groups of stages. Use rep if all reproductive stages are to be used, nrep if all mature but non-reproductive stages are to be used, mat if all mature stages are to be used, immat if all immature stages are to be used, prop if all propagule stages are to be used, npr if all non-propagule stages are to be used, obs if all observable stages are to be used, nobs if all unobservable stages are to be used, and leave empty or use all if all stages in stageframe are to be used.

Examples

library(lefko3)
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)

cycaraw_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)

cycamatrix2r <- rlefko2(data = cycaraw_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")

cyca2_start <- start_input(cycamatrix2r, stage2 = c("SD", "P1", "P2"),
  value = c(500, 100, 200))

cyp2_dv <- density_input(cycamatrix2r, stage3 = c("SD", "P1"),
  stage2 = c("rep", "rep"), style = c(1, 1), alpha = c(0.5, 1.2),
  beta = c(1.0, 2.0), type = c(2, 1))

cyp_eq <- stage_weight(cycamatrix2r,
  stage2 = c("SD", "P1", "SL", "D", "XSm", "Sm", "Md", "Lg", "XLg"),
  value = c(0, 1, 1, 1, 1, 1, 1, 1, 1))

cyca_proj <- projection3(mpm = cycamatrix2r, start_frame = cyca2_start,
  density = cyp2_dv, stage_weights = cyp_eq, times = 10)
  
summary(cyca_proj)

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