lefko3 (version 3.1.0)

repvalue3.matrix: Estimate Reproductive Value for a Population Projection Matrix

Description

repvalue3.matrix() returns the reproductive values for stages in a population projection matrix. The function makes no assumptions about whether the matrix is ahistorical and simply provides standard reproductive values corresponding to each row, meaning that the overall reproductive values of basic life history stages in a historical matrix are not provided (the repvalue3.lefkoMat() function estimates these on the basis of stage description information provided in the lefkoMat object used as input in that function). This function can handle large and sparse matrices, and so can be used with large historical matrices, IPMs, age x stage matrices, as well as smaller ahistorical matrices.

Usage

# S3 method for matrix
repvalue3(mats)

Arguments

mats

A population projection matrix.

Value

This function returns a vector data frame characterizing the reproductive values for stages of a population projection matrix. This is given as the left eigenvector associated with largest real part of the dominant eigenvalue, divided by the first non-zero element of the left eigenvector. Eigen analysis is handled by the eig_gen() function in the C++ Armadillo library for square matrices with fewer than 400 rows, and using the eigs_gen() function for larger matrices.

See Also

repvalue3()

repvalue3.lefkoMat()

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", reduce = TRUE)

ehrlen3mean <- lmean(ehrlen3)
repvalue3(ehrlen3mean$A[[1]])

# }