rlefko2: Create Raw Ahistorical Matrix Projection Model
In lefko3: Historical and Ahistorical Population Projection Matrix Analysis

rlefko2

R Documentation

Create Raw Ahistorical Matrix Projection Model

Description

Function rlefko2() returns raw ahistorical MPMs, including the associated component transition and fecundity matrices, a data frame describing the ahistorical stages used, and a data frame describing the population, patch, and occasion time associated with each matrix.

Usage

rlefko2(
  data,
  stageframe,
  year = "all",
  pop = NULL,
  patch = NULL,
  censor = FALSE,
  stages = NULL,
  alive = c("alive3", "alive2"),
  obsst = NULL,
  size = c("sizea3", "sizea2"),
  sizeb = NULL,
  sizec = NULL,
  repst = c("repstatus3", "repstatus2"),
  matst = c("matstatus3", "matstatus2"),
  fec = c("feca3", "feca2"),
  supplement = NULL,
  repmatrix = NULL,
  overwrite = NULL,
  yearcol = NULL,
  popcol = NULL,
  patchcol = NULL,
  indivcol = NULL,
  censorcol = NULL,
  censorkeep = 0,
  NRasRep = FALSE,
  reduce = FALSE,
  simple = FALSE,
  err_check = FALSE,
  sparse_output = FALSE
)

Arguments

`data`	A vertical demographic data frame, with variables corresponding to the naming conventions in functions `verticalize3()` and `historicalize3()`. Alternatively, a list of bootstrapped data of class `hfv_list`.
`stageframe`	A stageframe object that includes information on the size, observation status, propagule status, reproduction status, immaturity status, and maturity status of each ahistorical stage.
`year`	A variable corresponding to observation occasion, or a set of such values, given in values associated with the `year` term used in vital rate model development. Can also equal `"all"`, in which case matrices will be estimated for all occasion times. Defaults to `"all"`.
`pop`	A variable designating which populations will have matrices estimated. Should be set to specific population names, or to `"all"` if all populations should have matrices estimated.
`patch`	A variable designating which patches or subpopulations will have matrices estimated. Should be set to specific patch names, or to `"all"` if matrices should be estimated for all patches. Defaults to `NA`, in which case patch designations are ignored..
`censor`	If `TRUE`, then data will be removed according to the variable set in `censorcol`, such that only data with censor values equal to `censorkeep` will remain. Defaults to `FALSE`.
`stages`	An optional vector denoting the names of the variables within the main vertical dataset coding for the stages of each individual in occasions t+1 and t. The names of stages in these variables should match those used in the `stageframe` exactly. If left blank, then `rlefko2()` will attempt to infer stages by matching values of `alive`, `size`, `repst`, and `matst` to characteristics noted in the associated `stageframe`.
`alive`	A vector of names of binomial variables corresponding to status as alive (`1`) or dead (`0`) in occasions t+1 and t, respectively.
`obsst`	A vector of names of binomial variables corresponding to observation status in occasions t+1, t, and t-1, respectively. Defaults to `NULL`, in which case observation status is not used.
`size`	A vector of names of variables coding the primary size variable in occasions t+1 and t, respectively. Defaults to `c("sizea3", "sizea2")`.
`sizeb`	A vector of names of variables coding the secondary size variable in occasions t+1 and t, respectively. Defaults to `NULL`, in which case this variable is not used.
`sizec`	A vector of names of variables coding the tertiary size variable in occasions t+1 and t, respectively. Defaults to `NULL`, in which case this variable is not used.
`repst`	A vector of names of variables coding reproductive status in occasions t+1 and t, respectively. Defaults to `c("repstatus3", "repstatus2")`. Must be supplied if `stages` is not provided.
`matst`	A vector of names of variables coding maturity status in occasions t+1 and t, respectively. Defaults to `c("matstatus3", "matstatus2")`. Must be supplied if `stages` is not provided.
`fec`	A vector of names of variables coding fecundity in occasions t+1 and t, respectively. Defaults to `c("feca3", "feca2")`.
`supplement`	An optional data frame of class `lefkoSD` that provides supplemental data that should be incorporated into the MPM. Three kinds of data may be integrated this way: transitions to be estimated via the use of proxy transitions, transition overwrites from the literature or supplemental studies, and transition multipliers for fecundity. This data frame should be produced using the `supplemental()` function. Should be used in place of or in addition to an overwrite table (see `overwrite` below) and a reproduction matrix (see `repmatrix` below).
`repmatrix`	An optional reproduction matrix. This matrix is composed mostly of 0s, with non-zero entries acting as element identifiers and multipliers for fecundity (with 1 equaling full fecundity). If left blank, and no `supplement` is provided, then `rlefko2()` will assume that all stages marked as reproductive produce offspring at 1x that of estimated fecundity, and that offspring production will yield the first stage noted as propagule or immature. To prevent this behavior, input just `0`, which will result in fecundity being estimated only for transitions noted in `supplement` above. Must be the dimensions of an ahistorical matrix.
`overwrite`	An optional data frame developed with the `overwrite()` function describing transitions to be overwritten either with given values or with other estimated transitions. Note that this function supplements overwrite data provided in `supplement`.
`yearcol`	The variable name or column number corresponding to occasion t in the dataset.
`popcol`	The variable name or column number corresponding to the identity of the population.
`patchcol`	The variable name or column number corresponding to patch in the dataset.
`indivcol`	The variable name or column number coding individual identity.
`censorcol`	The variable name or column number denoting the censor status. Only needed if `censor = TRUE`.
`censorkeep`	The value of the censor variable denoting data elements to keep. Defaults to `0`.
`NRasRep`	If `data` does not include stage assignments, then this option determines whether non-reproductive and reproductive individuals should be lumped into the same stages. Defaults to `FALSE`.
`reduce`	A logical value denoting whether to remove ahistorical stages associated with only zero transitions. These are removed only if the respective row and column sums in ALL matrices estimated equal 0. Defaults to `FALSE`.
`simple`	A logical value indicating whether to produce `A`, `U`, and `F` matrices, or only the latter two. Defaults to `FALSE`, in which case all three are output.
`err_check`	A logical value indicating whether to append extra information used in matrix calculation within the output list. Defaults to `FALSE`.
`sparse_output`	A logical value indicating whether to output matrices in sparse format. Defaults to `FALSE`, in which case all matrices are output in standard matrix format.

Value

If the user inputs a standard hfv_data object in argument data, then this function will return an object of class lefkoMat. If the user inputs an object of class hfv_list in argument data, then the output will be an object of class lefkoMatList, in which each element is an object of class lefkoMat.

A lefkoMat object is a list that holds one full matrix projection model and all of its metadata. The structure has the following elements:

`A`	A list of full projection matrices in order of sorted populations, patches, and occasions. All matrices output in the `matrix` class, or in the `dgCMatrix` class from the `Matrix` package if sparse.
`U`	A list of survival transition matrices sorted as in `A`. All matrices output in the `matrix` class, or in the `dgCMatrix` class from the `Matrix` package if sparse.
`F`	A list of fecundity matrices sorted as in `A`. All matrices output in the `matrix` class, or in the `dgCMatrix` class from the `Matrix` package if sparse.
`hstages`	A data frame matrix showing the pairing of ahistorical stages used to create historical stage pairs. Set to NA for ahistorical matrices.
`agestages`	A data frame showing age-stage pairs. In this function, it is set to NA. Only used in output to function `aflefko2`().
`ahstages`	A data frame detailing the characteristics of associated ahistorical stages, in the form of a modified stageframe that includes status as an entry stage through reproduction.
`labels`	A data frame giving the population, patch, and year of each matrix in order.
`dataqc`	A vector showing the numbers of individuals and rows in the vertical dataset used as input.
`matrixqc`	A short vector describing the number of non-zero elements in `U` and `F` matrices, and the number of annual matrices.
`modelqc`	This is the `qc` portion of the `modelsuite` input in function-based MPMs. Empty in this function.

Notes

The default behavior of this function is to estimate fecundity with regards to transitions specified via associated fecundity multipliers in the supplement. If this field is left empty, then fecundity will be estimated at full for all transitions leading from reproductive stages to immature and propagule stages.

Users may at times wish to estimate MPMs using a dataset incorporating multiple patches or subpopulations. Should the aim of analysis be a general MPM that does not distinguish these patches or subpopulations, the patchcol variable should be left to NA, which is the default. Otherwise the variable identifying patch needs to be named.

Input options including multiple variable names must be entered in the order of variables in occasion t+1 and t. Rearranging the order WILL lead to erroneous calculations, and may lead to fatal errors.

Although this function is capable of assigning stages given an input stageframe, it lacks the power of verticalize3() and historicalize3() in this regard. Users are strongly encouraged to use the latter two functions for stage assignment.

Examples

# Lathyrus example
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)

lathsupp2 <- supplemental(stage3 = c("Sd", "Sdl", "Sd", "Sdl"), 
  stage2 = c("Sd", "Sd", "rep", "rep"),
  givenrate = c(0.345, 0.054, NA, NA),
  multiplier = c(NA, NA, 0.345, 0.054),
  type = c(1, 1, 3, 3), stageframe = lathframe, historical = FALSE)

ehrlen2 <- rlefko2(data = lathvert, stageframe = lathframe, year = "all", 
  stages = c("stage3", "stage2"), supplement = lathsupp2, yearcol = "year2",
  indivcol = "individ")

# Cypripedium example
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)

# 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 <- 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")

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