stablestage3: Estimate Stable Stage Distribution In lefko3: Historical and Ahistorical Population Projection Matrix Analysis

Description

`stablestage3()` is a generic function that returns the stable stage distribution for a population projection matrix or set of matrices. This function is made to handle very large and sparse matrices supplied as `lefkoMat` objects or as individual matrices, and can be used with large historical matrices, IPMs, age x stage matrices, as well as ahistorical matrices.

Usage

 `1` ```stablestage3(mats, ...) ```

Arguments

 `mats` A lefkoMat object, or population projection matrix, for which the stable stage distribution is desired. `...` Other parameters.

Value

The value returned depends on the class of the `mats` argument. See related functions for details.

`stablestage3.lefkoMat()`
`stablestage3.matrix()`
 ``` 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88``` ```# Lathyrus deterministic example 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) lathsupp3 <- supplemental(stage3 = c("Sd", "Sd", "Sdl", "Sdl", "Sd", "Sdl", "mat"), stage2 = c("Sd", "Sd", "Sd", "Sd", "rep", "rep", "Sdl"), stage1 = c("Sd", "rep", "Sd", "rep", "npr", "npr", "Sd"), eststage3 = c(NA, NA, NA, NA, NA, NA, "mat"), eststage2 = c(NA, NA, NA, NA, NA, NA, "Sdl"), eststage1 = c(NA, NA, NA, NA, NA, NA, "NotAlive"), givenrate = c(0.345, 0.345, 0.054, 0.054, NA, NA, NA), multiplier = c(NA, NA, NA, NA, 0.345, 0.054, NA), type = c(1, 1, 1, 1, 3, 3, 1), type_t12 = c(1, 2, 1, 2, 1, 1, 1), stageframe = lathframe, historical = TRUE) ehrlen3 <- rlefko3(data = lathvert, stageframe = lathframe, year = "all", stages = c("stage3", "stage2", "stage1"), supplement = lathsupp3, yearcol = "year2", indivcol = "individ") ehrlen3mean <- lmean(ehrlen3) stablestage3(ehrlen3mean) # Cypripedium stochastic example rm(list=ls(all=TRUE)) 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) # Here we use supplemental() to provide overwrite and reproductive info 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") stablestage3(cypmatrix2r, stochastic = TRUE) ```