lefko3 (version 3.1.0)

stablestage3.lefkoMat: Estimate Stable Stage Distribution for a lefkoMat Object

Description

stablestage3.lefkoMat() returns the stable stage distributions of all $A matrices in an object of class lefkoMat. 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 lefkoMat
stablestage3(mats)

Arguments

mats

An object of class lefkoMat.

Value

This function returns the stable stage distributions corresponding to the matrices in a lefkoMat object. For square matrices with fewer than 400 rows, the stable stage distribution is given as the right eigenvector associated with largest real part of all eigenvalues estimated via the eig_gen() function in the C++ Armadillo library divided by the sum of the associated right eigenvector. For larger matrices, the function assumes that the matrix is sparse and conducts a similar calculation but using the eigs_gen() for sparse matrix eigen analysis.

The output depends on whether the lefkoMat object used as input is ahistorical or historical. If the former, then a single data frame is output, which includes the number of the matrix within the $A element of the input lefkoMat object, followed by the stage id (numeric and assigned through sf_create()), the stage name, and the estimated proportion of the stable stage distribution (ss_prop).

If a historical matrix is used as input, then two data frames are output into a list object. The $hist element contains a data frame where the stable stage distribution is given in terms of across-year stage pairs. The structure includes the matrix number, the numeric stage designations for stages in times t and t-1, respectively, followed by the respective stage names, and ending with the estimated proportion of the stable stage distribution for that stage within its matrix (ss_prop). The $ahist element contains the stable stage distribution in stages as given in the original stageframe. It includes a data frame with the matrix of origin, the numeric stage designation, stage name, and the stable stage distribution estimated as the sum of distribution elements from $hist corresponding to the equivalent stage in time t, irrespective of stage in time t-1.

See Also

stablestage3()

stablestage3.matrix()

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)
stablestage3(ehrlen3mean)

# }