cypdata: Demographic Dataset of _Cypripedium candidum_ Population, in...
In lefko3: Historical and Ahistorical Population Projection Matrix Analysis

cypdata

R Documentation

Demographic Dataset of Cypripedium candidum Population, in Horizontal 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.

Usage

data(cypdata)

Format

A data frame with 77 individuals and 29 variables. Each row corresponds to an unique individual, and each variable from size.04 on refers to the state of the individual in a particular year.

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.
Inf2.04: Number of double inflorescences in 2004.
Inf.04: Number of inflorescences in 2004.
Veg.04: Number of stems without inflorescences in 2004.
Pod.04: Number of fruits in 2004.
Inf2.05: Number of double inflorescences in 2005.
Inf.05: Number of inflorescences in 2005.
Veg.05: Number of stems without inflorescences in 2005.
Pod.05: Number of fruits in 2005.
Inf2.06: Number of double inflorescences in 2006.
Inf.06: Number of inflorescences in 2006.
Veg.06: Number of stems without inflorescences in 2006.
Pod.06: Number of fruits in 2006.
Inf2.07: Number of double inflorescences in 2007.
Inf.07: Number of inflorescences in 2007.
Veg.07: Number of stems without inflorescences in 2007.
Pod.07: Number of fruits in 2007.
Inf2.08: Number of double inflorescences in 2008.
Inf.08: Number of inflorescences in 2008.
Veg.08: Number of stems without inflorescences in 2008.
Pod.08: Number of fruits in 2008.
Inf2.09: Number of double inflorescences in 2009.
Inf.09: Number of inflorescences in 2009.
Veg.09: Number of stems without inflorescences in 2009.
Pod.09: Number of fruits in 2009.

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(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", "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_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")
                       
lambda3(cypmatrix2r)

lefko3 documentation built on Sept. 11, 2024, 9:35 p.m.