# elasticity3.matrix: Estimate Elasticity of Population Growth Rate of a Single... In lefko3: Historical and Ahistorical Population Projection Matrix Analysis

## Description

`elasticity3.matrix()` returns the elasticities of lambda to elements of a single matrix. Because this handles only one matrix, the elasticities are inherently deterministic and based on the dominant eigen value as the best metric of the population growth rate. 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

 ```1 2``` ```## S3 method for class 'matrix' elasticity3(mats, sparse = "auto", ...) ```

## Arguments

 `mats` An object of class `matrix`. `sparse` A text string indicating whether to use sparse matrix encoding (`"yes"`) or dense matrix encoding (`"no"`). Defaults to `"auto"`. `...` Other parameters.

## Value

This function returns a single elasticity matrix.

`elasticity3()`

`elasticity3.lefkoMat()`

`elasticity3.list()`

## Examples

 ``` 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``` ```# Lathyrus 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) elasticity3(ehrlen3mean\$A[[1]]) # Cypripedium 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) cypsupp2r <- supplemental(stage3 = c("SD", "P1", "P2", "P3", "SL", "SL", "D", "XSm", "Sm", "SD", "P1"), stage2 = c("SD", "SD", "P1", "P2", "P3", "SL", "SL", "SL", "SL", "rep", "rep"), eststage3 = c(NA, NA, NA, NA, NA, NA, "D", "XSm", "Sm", NA, NA), eststage2 = c(NA, NA, NA, NA, NA, NA, "XSm", "XSm", "XSm", NA, NA), givenrate = c(0.10, 0.20, 0.20, 0.20, 0.25, 0.40, NA, NA, NA, NA, NA), multiplier = c(NA, NA, NA, NA, NA, NA, NA, NA, NA, 0.5, 0.5), type =c(1, 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") elasticity3(cypmatrix2r\$A[[1]]) ```

lefko3 documentation built on July 22, 2021, 9:10 a.m.