lefko3 (version 3.7.0)

cypdata: 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 27 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.

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.

Examples

# NOT RUN {
# Cypripedium example using blocksize
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")
                       
cypmatrix2r$A[[intersect(which(cypmatrix2r$labels$patch == "A"), 
  which(cypmatrix2r$labels$year2 == 2004))]]

lambda3(cypmatrix2r)

# Cypripedium example using partial repeat patterns with blocksize and part
# explicit variable name cast
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 = c("Inf.04", "Inf.05", "Inf.06", "Inf.07", "Inf.08", "Inf.09"),
  repstrbcol = c("Inf2.04", "Inf2.05", "Inf2.06", "Inf2.07", "Inf2.08", "Inf2.09"), 
  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")
                       
cypmatrix2r$A[[intersect(which(cypmatrix2r$labels$patch == "A"), 
  which(cypmatrix2r$labels$year2 == 2004))]]

lambda3(cypmatrix2r)
# }