lefko3 (version 3.1.0)

lmean: Estimate Mean Projection Matrices

Description

lmean() estimates mean projection matrices as element-wise arithmetic means.

Usage

lmean(mats, matsout = "all")

Arguments

mats

A lefkoMat object.

matsout

A string identifying which means to estimate. Option "pop" indicates population-level only, "patch" indicates patch-level only, and "all" indicates that both patch- and population-level means should be estimated.

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 and F matrices. All matrices output in the matrix class.

U

A list of mean survival-transition matrices sorted as in A. All matrices output in the matrix class.

F

A list of mean fecundity matrices sorted as in A. All matrices output in the matrix class.

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 pop, patch, or year2 are NA in the original labels set, then these will be re-labeled as A, 1, or 1, respectively.

matrixqc

A short vector describing the number of non-zero elements in U and F mean matrices, and the number of annual matrices.

modelqc

The qc portion of the modelsuite input, if provided.

dataqc

A vector showing the numbers of individuals and rows in the vertical dataset used as input.

Examples

# NOT RUN {
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

lathover3 <- overwrite(stage3 = c("Sd", "Sd", "Sdl"), stage2 = c("Sd", "Sd", "Sd"), 
                       stage1 = c("Sd", "rep", "rep"), givenrate = c(0.345, 0.054))

ehrlen3 <- rlefko3(data = lathvert, stageframe = lathframe, year = c(1989, 1990), 
                   stages = c("stage3", "stage2", "stage1"), repmatrix = lathrepm, 
                   overwrite = lathover3, yearcol = "year2", 
                   indivcol = "individ")

ehrlen3mean <- lmean(ehrlen3)
ehrlen3mean$A[[1]]

# }