lmean {lefko3} | R Documentation |
Estimate Mean Projection Matrices
Description
Function lmean()
estimates mean projection matrices as element-wise
arithmetic means. It produces lefkoMat
objects if provided with them,
or single matrices in a simple one-element list if provided a list of
matrices.
Usage
lmean(mats, matsout = NULL, force_sparse = FALSE)
Arguments
mats |
A |
matsout |
A string identifying which means to estimate. Option
|
force_sparse |
A logical value identifying whether to output the mean matrices in sparse format, if input as standard matrices. |
Value
Yields a lefkoMat
object with the following characteristics:
A |
A list of full mean projection matrices in order of sorted
populations, patches, and years. These are typically estimated as the sums
of the associated mean |
U |
A list of mean survival-transition matrices sorted as in |
F |
A list of mean fecundity matrices sorted as in |
hstages |
A data frame showing the pairing of ahistorical stages used to create historical stage pairs. Given if the MPM is historical. |
ahstages |
A data frame detailing the characteristics of associated ahistorical stages. |
labels |
A data frame detailing the order of population, patch, and
year of each mean matrix. If |
matrixqc |
A short vector describing the number of non-zero elements in
|
modelqc |
This is the |
dataqc |
A vector showing the numbers of individuals and rows in the
vertical dataset used as input. Only output from |
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(0.10, 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")
cyp2mean <- lmean(cypmatrix2r)