lmean  R Documentation 
Function lmean()
estimates mean projection matrices as elementwise
arithmetic means. It produces lefkoMat
objects if provided with them,
or single matrices in a simple oneelement list if provided a list of
matrices.
lmean(mats, matsout = NULL, force_sparse = FALSE)
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. 
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 survivaltransition 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 nonzero 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 
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)
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