append_lP: Append Projections Into New lefkoProj Object

In lefko3: Historical and Ahistorical Population Projection Matrix Analysis

Append Projections Into New lefkoProj Object

Description

Function append_lP() combines two population projections. It takes two lefkoProj objects and appends them into a new lefkoPrpoj object.

Usage

append_lP(proj1 = NULL, proj2 = NULL)

Arguments

proj1	A lefkoProj object.
proj2	A second lefkoProj object, based on the same stageframe as proj1.

Value

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

projection	A list of lists of matrices showing the total number of individuals per stage per occasion. The first list corresponds to each pop-patch followed by each population (this top-level list is a single element in f_projection3()). The inner list corresponds to replicates within each pop-patch or population.
stage_dist	A list of lists of the actual stage distribution in each occasion in each replicate in each pop-patch or population.
rep_value	A list of lists of the actual reproductive value in each occasion in each replicate in each pop-patch or population.
pop_size	A list of matrices showing the total population size in each occasion per replicate (row within data frame) per pop-patch or population (list element). NA values will result if projections with different numbers of time steps are appended.
labels	A data frame showing the order of populations and patches in item projection.
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.
labels	A short data frame indicating the population (always 1), and patch (either the numeric index of the single chosen patch, or 1 in all other cases). Any pop-patches having the same designation across the two input projections will be appended together.
control	A data frame showing the number of replicates and time steps corresponding to each set of projections, where each set corresponds to a pop-patch within the labels object of each input projection.
density	The data frame input under the density option. Only provided if input by the user for at least one of the two projections. Output as a nested list corresponding to each pop-patch - replicate.
density_vr	The data frame input under the density_vr option. Only provided if input by the user for at least one of the two projections. Output as a nested list corresponding to each pop-patch - replicate.

Notes

lefkoProj objects resulting from previous appends can also be appended.

See Also

projection3()

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)

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(0.1, 0.2, 0.2, 0.2, 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_AB <- rlefko2(data = cypraw_v1, stageframe = cypframe_raw, 
  year = "all", patch = c("A", "B"), stages = c("stage3", "stage2"),
  size = c("size3added", "size2added"), supplement = cypsupp2r,
  yearcol = "year2",  patchcol = "patchid", indivcol = "individ")

cypmatrix2r_AC <- rlefko2(data = cypraw_v1, stageframe = cypframe_raw, 
  year = "all", patch = c("A", "C"), stages = c("stage3", "stage2"),
  size = c("size3added", "size2added"), supplement = cypsupp2r,
  yearcol = "year2",  patchcol = "patchid", indivcol = "individ")

cypproj1 <- projection3(cypmatrix2r_AB, nreps = 5, times = 15,
  stochastic = TRUE)
cypproj2 <- projection3(cypmatrix2r_AC, nreps = 10, times = 20,
  stochastic = TRUE)
cypproj3 <- append_lP(cypproj1, cypproj2)

lefko3 documentation built on Sept. 11, 2024, 9:35 p.m.