markov_run {lefko3}

Creates Vector of Times Based on First-Order Markov Transition Matrix

Description

Creates a vector of randomly sampled years / times to be used in projection. Random sampling requires a 1st order Markovian transition matrix, showing the probability of transitioning to each time from each time. Note that this function is not required if the probability of transitioning to a particular time does not vary with time.

Usage

markov_run(main_times, mat, times = 10000L, start = NULL)

Arguments

main_times

An integer vector giving the years / times to use.

mat

A matrix giving the transition probabilities from each time to each time. Must have the same number of columns and rows as there are elements in vector times.

times

The number of times to project forward. Defaults to 10000.

start

The start time to use. Defaults to the first time in vector main_times.

Value

An integer vector giving the order of times / years to use in projection. This can be used as input in the year option in functions projection3() and f_projection3().

See Also

projection3()

f_projection3()

Examples

# Cypripedium example
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)

cypsupp3r <- supplemental(stage3 = c("SD", "SD", "P1", "P1", "P2", "P3", "SL",
    "D", "XSm", "Sm", "D", "XSm", "Sm", "mat", "mat", "mat", "SD", "P1"),
  stage2 = c("SD", "SD", "SD", "SD", "P1", "P2", "P3", "SL", "SL", "SL", "SL",
    "SL", "SL", "D", "XSm", "Sm", "rep", "rep"),
  stage1 = c("SD", "rep", "SD", "rep", "SD", "P1", "P2", "P3", "P3", "P3",
    "SL", "SL", "SL", "SL", "SL", "SL", "mat", "mat"),
  eststage3 = c(NA, NA, NA, NA, NA, NA, NA, "D", "XSm", "Sm", "D", "XSm", "Sm",
    "mat", "mat", "mat", NA, NA),
  eststage2 = c(NA, NA, NA, NA, NA, NA, NA, "XSm", "XSm", "XSm", "XSm", "XSm",
    "XSm", "D", "XSm", "Sm", NA, NA),
  eststage1 = c(NA, NA, NA, NA, NA, NA, NA, "XSm", "XSm", "XSm", "XSm", "XSm",
    "XSm", "XSm", "XSm", "XSm", NA, NA),
  givenrate = c(0.1, 0.1, 0.2, 0.2, 0.2, 0.2, 0.25, NA, NA, NA, NA, NA, NA,
    NA, NA, NA, NA, NA),
  multiplier = c(NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
    NA, 0.5, 0.5),
  type = c(1, 1, 1, 1, 1, 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, 1, 1, 1, 1, 1),
  stageframe = cypframe_raw, historical = TRUE)

cypmatrix3r <- rlefko3(data = cypraw_v1, stageframe = cypframe_raw, 
  year = "all", stages = c("stage3", "stage2", "stage1"),
  size = c("size3added", "size2added", "size1added"), 
  supplement = cypsupp3r, yearcol = "year2", indivcol = "individ")

used_years <-c(2005, 2006, 2007, 2008)

yr_tx_vec <- c(0.4, 0.2, 0.2, 0.2, 0.2, 0.4, 0.2, 0.2, 0.2, 0.2, 0.4, 0.2,
  0.2, 0.2, 0.2, 0.4)
yr_tx_mat <- matrix(yr_tx_vec, 4, 4)

set.seed(1)
cyp_markov_vec_1 <- markov_run(main_times = used_years, mat = yr_tx_mat,
  times = 100)

set.seed(2)
cyp_markov_vec_2 <- markov_run(main_times = used_years, mat = yr_tx_mat,
  times = 100)

set.seed(3)
cyp_markov_vec_3 <- markov_run(main_times = used_years, mat = yr_tx_mat,
  times = 100)

cypstoch_1 <- projection3(cypmatrix3r, nreps = 1, times = 100,
  year = cyp_markov_vec_1)
cypstoch_2 <- projection3(cypmatrix3r, nreps = 1, times = 100,
  year = cyp_markov_vec_2)
cypstoch_3 <- projection3(cypmatrix3r, nreps = 1, times = 100,
  year = cyp_markov_vec_3)