cypvert {lefko3}

Demographic Dataset of Cypripedium candidum Population, in Vertical Format

Description

A dataset containing the states and fates of Cypripedium candidum (white lady's slipper orchids), family Orchidaceae, from a population in Illinois, USA, resulting from monitoring that occurred annually between 2004 and 2009. Same dataset as cypdata, but arranged in an ahistorical vertical format.

Usage

data(cypvert)

Format

A data frame with 77 individuals, 322 rows, and 14 variables. Each row corresponds to a specific two-year transition for a specific individual. Variable codes are similar to those for cypdata, but use .2 to identify occasion t and .3 to identify occasion t+1.

plantid

A numeric variable giving a unique number to each individual.

patch

A variable refering to patch within the population.

X

An X coordinate for the plant within the population.

Y

A Y coordinate for the plant within the population.

censor

A variable coding for whether the data point is valid. An entry of 1 means that it is so.

year2

Year in occasion t.

Inf2.2

Number of double inflorescences in occasion t.

Inf.2

Number of inflorescences in occasion t.

Veg.2

Number of stems without inflorescences in occasion t.

Pod.2

Number of fruits in occasion t.

Inf2.3

Number of double inflorescences in occasion t+1.

Inf.3

Number of inflorescences in occasion t+1.

Veg.3

Number of stems without inflorescences in occasion t+1.

Pod.3

Number of fruits in occasion t+1.

Source

Shefferson, R.P., R. Mizuta, and M.J. Hutchings. 2017. Predicting evolution in response to climate change: the example of sprouting probability in three dormancy-prone orchid species. Royal Society Open Science 4(1):160647.

Examples

data(cypvert)

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_v2 <- historicalize3(data = cypvert, patchidcol = "patch", 
  individcol = "plantid", year2col = "year2", sizea2col = "Inf2.2", 
  sizea3col = "Inf2.3", sizeb2col = "Inf.2", sizeb3col = "Inf.3", 
  sizec2col = "Veg.2", sizec3col = "Veg.3", repstra2col = "Inf2.2", 
  repstra3col = "Inf2.3", repstrb2col = "Inf.2", repstrb3col = "Inf.3", 
  feca2col = "Pod.2", feca3col = "Pod.3", repstrrel = 2, 
  stageassign = cypframe_raw, stagesize = "sizeadded", censorcol = "censor",
  censor = FALSE, NAas0 = TRUE, NRasRep = TRUE, reduce = TRUE)
  
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_v2, stageframe = cypframe_raw, 
  year = "all", patch = "all", stages = c("stage3", "stage2"),
  size = c("size3added", "size2added"), supplement = cypsupp2r,
  yearcol = "year2", patchcol = "patchid", indivcol = "individ")
  
lambda3(cypmatrix2r)