projection3: Conduct Population Projection Simulations

Description Usage Arguments Value Notes Examples

View source: R/RcppExports.R

Description

Function projection3() runs projection simulations. It projects the population forward in time by a user-defined number of occasions, and can perform these projections as replicates. Projections may be deterministic or stochastic. If deterministic, then projections will be cyclical if matrices exist covering multiple occasions for each population or patch. If stochastic, then annual matrices will be shuffled within patches and populations. There is no limit to the number of replicates.

Usage

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projection3(
  mpm,
  nreps = 1L,
  times = 10000L,
  stochastic = FALSE,
  standardize = FALSE,
  growthonly = TRUE,
  integeronly = FALSE,
  start_vec = NULL,
  tweights = NULL
)

Arguments

mpm

A matrix projection model of class lefkoMat, or a list of full matrix projection matrices.

nreps

The number of replicate projections.

times

Number of occasions to iterate per replicate. Defaults to 10,000.

stochastic

A logical value denoting whether to conduct a stochastic projection or a deterministic / cyclical projection.

standardize

A logical value denoting whether to re-standardize the population size to 1.0 at each occasion. Defaults to FALSE.

growthonly

A logical value indicating whether to produce only the projected population size at each occasion, or a vector showing the stage distribution followed by the reproductive value vector followed by the full population size at each occasion. Defaults to TRUE.

integeronly

A logical value indicating whether to round the number of individuals projected in each stage at each occasion to the nearest integer. Defaults to FALSE.

start_vec

An optional numeric vector denoting the starting stage distribution for the projection. Defaults to a single individual of each stage.

tweights

An optional numeric vector denoting the probabilistic weightings of annual matrices. Defaults to equal weighting among occasions.

Value

A list of class lefkoProj, which always includes the first three elements of the following, and also includes the remaiing elements below when a lefkoMat object is used as input:

projection

A list of matrices showing the total number of individuals per stage per occasion, or showing the former with the projected stage distribution and reproductive value per stage per occasion followed by the total population size per occasion (all row-bound in order). Each matrix corresponds to a different patch or population. If more than 1 replicate is projected, then the results from these replicates will be stacked within the same data frame.

labels

A data frame showing the order of populations and patches in item projection.

control

A short vector indicating the number of replicates and the number of occasions projected per replicate.

ahstages

The original stageframe used in the study.

hstages

A data frame showing the order of historical stage pairs.

agestages

A data frame showing the order of age-stage pairs.

Notes

Projections are run both at the patch level and at the population level. Population level estimates will be noted at the end of the data frame with 0 entries for patch designation.

Weightings given in tweights do not need to sum to 1. Final weightings used will be based on the proportion per element of the sum of elements in the user-supplied vector.

The resulting data frames in element projection are separated by pop-patch according to the order provided in element labels, but the matrices for each element of projection have the result of each replicate stacked in order on top of one another without any break or indication. Results for each replicate must be separated using the information provided in elements control and the 3 stage descriptor elements.

Examples

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# 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)

lathrepm <- matrix(0, 7, 7)
lathrepm[1, 6] <- 0.345
lathrepm[2, 6] <- 0.054

lathsupp3 <- supplemental(stage3 = c("Sd", "Sd", "Sdl", "Sdl", "Sd", "Sdl"), 
  stage2 = c("Sd", "Sd", "Sd", "Sd", "rep", "rep"),
  stage1 = c("Sd", "rep", "Sd", "rep", "all", "all"), 
  givenrate = c(0.345, 0.345, 0.054, 0.054, NA, NA),
  multiplier = c(NA, NA, NA, NA, 0.345, 0.054),
  type = c(1, 1, 1, 1, 3, 3), type_t12 = c(1, 2, 1, 2, 1, 1),
  stageframe = lathframe, historical = TRUE)

ehrlen3 <- rlefko3(data = lathvert, stageframe = lathframe,
  year = c(1989, 1990), stages = c("stage3", "stage2", "stage1"),
  repmatrix = lathrepm, supplement = lathsupp3, yearcol = "year2",
  indivcol = "individ")

lathproj <- projection3(ehrlen3, nreps = 5, stochastic = TRUE)

# Cypripedium example
rm(list = ls(all=TRUE))
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", "SD", "P1"),
  stage2 = c("SD", "SD", "SD", "SD", "P1", "P2", "P3", "SL", "SL", "SL", "SL",
    "SL", "SL", "rep", "rep"),
  stage1 = c("SD", "rep", "SD", "rep", "SD", "P1", "P2", "P3", "P3", "P3",
    "SL", "SL", "SL", "mat", "mat"),
  eststage3 = c(NA, NA, NA, NA, NA, NA, NA, "D", "XSm", "Sm", "D", "XSm", "Sm",
    NA, NA),
  eststage2 = c(NA, NA, NA, NA, NA, NA, NA, "XSm", "XSm", "XSm", "XSm", "XSm",
    "XSm", NA, NA),
  eststage1 = c(NA, NA, NA, NA, NA, NA, NA, "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),
  multiplier = c(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, 3, 3),
  type_t12 = c(1, 2, 1, 2, 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")

cypstoch <- projection3(cypmatrix3r, nreps = 5, stochastic = TRUE)

lefko3 documentation built on Sept. 8, 2021, 9:07 a.m.