diff_lM {lefko3}

Calculate Difference Matrices Between lefkoMat Objects of Equal Dimensions

Description

Function diff_lM() takes two lefkoMat objects with completely equal dimensions, including both the size and number of matrices, and gives the matrix differences between each corresponding set.

Usage

diff_lM(mpm1, mpm2)

Arguments

mpm1

The first lefkoMat object.

mpm2

The second lefkoMat object.

Value

An object of class lefkoDiff, which is a set of A, U, and F matrices corresponding to the differences between each set of matrices, followed by the hstages, ahstages, and labels elements from each input lefkoMat object. Elements labelled with a 1 at the end refer to mpm1, while those labelled 2 at the end refer to mpm2.

Notes

The exact difference is calculated as the respective matrix in mpm1 minus the corresponding matrix in mpm2.

This function first checks to see if the number of matrices is the same, and then whether the matrix dimensions are the same. If the two sets differ in at least one of these characteristics, then the function will yield a fatal error.

If the lengths and dimensions of the input lefkoMat objects are the same, then this will check if the labels element is essentially the same. If not, then the function will yield a warning, but will still operate.

Examples

sizevector <- c(0, 0, 0, 0, 0, 0, 1, 3, 6, 11, 19.5)
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, 1.5, 1.5, 3.5, 5)
comments <- c("Dormant seed", "1st yr protocorm", "2nd yr protocorm",
  "3rd yr protocorm", "Seedling", "Dormant adult",
  "Extra small adult (1 shoot)", "Small adult (2-4 shoots)",
  "Medium adult (5-7 shoots)", "Large adult (8-14 shoots)",
  "Extra large adult (>14 shoots)")
cypframe_raw <- sf_create(sizes = sizevector, stagenames = stagevector, 
  repstatus = repvector, obsstatus = obsvector, matstatus = matvector,
  propstatus = propvector, immstatus = immvector, indataset = indataset, 
  binhalfwidth = binvec, comments = comments)

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)

seeds_per_pod <- 5000

cypsupp2_raw <- supplemental(stage3 = c("SD", "P1", "P2", "P3", "SL", "SL", "D", 
    "XSm", "SD", "P1"),
  stage2 = c("SD", "SD", "P1", "P2", "P3", "SL", "SL", "SL", "rep", "rep"),
  eststage3 = c(NA, NA, NA, NA, NA, NA, "D", "XSm", NA, NA),
  eststage2 = c(NA, NA, NA, NA, NA, NA, "XSm", "XSm", NA, NA),
  givenrate = c(0.03, 0.15, 0.1, 0.1, 0.1, 0.05, NA, NA, NA, NA),
  multiplier = c(NA, NA, NA, NA, NA, NA, NA, NA, (0.5 * seeds_per_pod),
    (0.5 * seeds_per_pod)),
  type =c(1, 1, 1, 1, 1, 1, 1, 1, 3, 3),
  stageframe = cypframe_raw, historical = FALSE)
cypsupp3_raw <- supplemental(stage3 = c("SD", "SD", "P1", "P1", "P2", "P3",
    "SL", "SL", "SL", "D", "D", "SD", "P1"),
  stage2 = c("SD", "SD", "SD", "SD", "P1", "P2", "P3", "SL", "SL", "SL", "SL",
    "rep", "rep"),
  stage1 = c("SD", "rep", "SD", "rep", "SD", "P1", "P2", "P3", "SL", "P3",
    "SL", "mat", "mat"),
  eststage3 = c(NA, NA, NA, NA, NA, NA, NA, NA, NA, "XSm", "D", NA, NA),
  eststage2 = c(NA, NA, NA, NA, NA, NA, NA, NA, NA, "XSm", "XSm", NA, NA),
  eststage1 = c(NA, NA, NA, NA, NA, NA, NA, NA, NA, "XSm", "XSm", NA, NA),
  givenrate = c(0.01, 0.05, 0.10, 0.20, 0.1, 0.1, 0.05, 0.05, 0.05, NA, NA,
    NA, NA),
  multiplier = c(NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
    (0.5 * seeds_per_pod), (0.5 * seeds_per_pod)),
  type = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3),
  type_t12 = c(1, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1),
  stageframe = cypframe_raw, historical = TRUE)

cypmatrix2rp <- rlefko2(data = cypraw_v1, stageframe = cypframe_raw,
  year = "all", patch = "all", stages = c("stage3", "stage2"),
  size = c("size3added", "size2added"), supplement = cypsupp2_raw, 
  yearcol = "year2", patchcol = "patchid", indivcol = "individ")

cypmatrix2r <- rlefko2(data = cypraw_v1, stageframe = cypframe_raw,
  year = "all", stages = c("stage3", "stage2"),
  size = c("size3added", "size2added"), supplement = cypsupp2_raw, 
  yearcol = "year2", patchcol = "patchid", indivcol = "individ")

cypmatrix3rp <- rlefko3(data = cypraw_v1, stageframe = cypframe_raw,
  year = "all", patch = "all", stages = c("stage3", "stage2", "stage1"), 
  size = c("size3added", "size2added", "size1added"), supplement = cypsupp3_raw, 
  yearcol = "year2", patchcol = "patchid", indivcol = "individ")

cypmatrix3r <- rlefko3(data = cypraw_v1, stageframe = cypframe_raw,
  year = "all", stages = c("stage3", "stage2", "stage1"), 
  size = c("size3added", "size2added", "size1added"), supplement = cypsupp3_raw, 
  yearcol = "year2", patchcol = "patchid", indivcol = "individ")

cypmatrix2r_3 <- hist_null(cypmatrix2r)
cypmatrix2r_3 <- delete_lM(cypmatrix2r_3, year = 2004)
diff_r <- diff_lM(cypmatrix3r, cypmatrix2r_3)

cypmatrix2rp_3 <- hist_null(cypmatrix2rp)
cypmatrix2rp_3 <- delete_lM(cypmatrix2rp_3, year = 2004)
diff_rp <- diff_lM(cypmatrix3rp, cypmatrix2rp_3)