cypvert: Demographic Dataset of _Cypripedium candidum_ Population, in...

Description Usage Format Source Examples

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

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Format

A data frame with 77 individuals, 331 rows, and 12 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 time t and .3 to identify time t+1.

plantid

A numeric variable giving a unique number to each individual.

patch

A variable refering to patch 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 time t.

Inf2.2

Number of double inflorescences in time t.

Inf.2

Number of inflorescences in time t.

Veg.2

Number of stems without inflorescences in time t.

Pod.2

Number of fruits in time t.

Inf2.3

Number of double inflorescences in time t+1.

Inf.3

Number of inflorescences in time t+1.

Veg.3

Number of stems without inflorescences in time t+1.

Pod.3

Number of fruits in time 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

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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)

cypframe_raw

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", "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_v2, stageframe = cypframe_raw, 
  year = "all", patch = "all", stages = c("stage3", "stage2"),
  size = c("size3added", "size2added"), supplement = cypsupp2r,
  yearcol = "year2", patchcol = "patchid", indivcol = "individ")
  
cypmatrix2r$A[[intersect(which(cypmatrix2r$labels$patch == "A"), 
  which(cypmatrix2r$labels$year2 == 2004))]]

lambda3(cypmatrix2r)

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