adapt3 (version 2.0.0)

cypa_data: Demographic Dataset of Cypripedium parviflorum Population, in Horizontal Format

Description

A dataset containing the states and fates of a population of the terrestrial orchid species Cypripedium parviflorum (small yellow lady's slipper orchids) in Illinois, USA. The dataset resulted from annual monitoring from 1994 and 2011.

Usage

data(cypa_data)

Format

A data frame with 1119 individuals and 37 variables. Each row corresponds to an unique individual, and each variable from Inf.94 on refers to the state of the individual in a particular year.

plant_id

A numeric variable giving a unique number to each individual.

Inf.94

Number of inflorescences in 1994.

Veg.94

Number of stems without inflorescences in 1994.

Inf.95

Number of inflorescences in 1995.

Veg.95

Number of stems without inflorescences in 1995.

Inf.96

Number of inflorescences in 1996.

Veg.96

Number of stems without inflorescences in 1996.

Inf.97

Number of inflorescences in 1997.

Veg.97

Number of stems without inflorescences in 1997.

Inf.98

Number of inflorescences in 1998.

Veg.98

Number of stems without inflorescences in 1998.

Inf.99

Number of inflorescences in 1999.

Veg.99

Number of stems without inflorescences in 1999.

Inf.00

Number of inflorescences in 2000.

Veg.00

Number of stems without inflorescences in 2000.

Inf.01

Number of inflorescences in 2001.

Veg.01

Number of stems without inflorescences in 2001.

Inf.02

Number of inflorescences in 2002.

Veg.02

Number of stems without inflorescences in 2002.

Inf.03

Number of inflorescences in 2003.

Veg.03

Number of stems without inflorescences in 2003.

Inf.04

Number of inflorescences in 2004.

Veg.04

Number of stems without inflorescences in 2004.

Inf.05

Number of inflorescences in 2005.

Veg.05

Number of stems without inflorescences in 2005.

Inf.06

Number of inflorescences in 2006.

Veg.06

Number of stems without inflorescences in 2006.

Inf.07

Number of inflorescences in 2007.

Veg.07

Number of stems without inflorescences in 2007.

Inf.08

Number of inflorescences in 2008.

Veg.08

Number of stems without inflorescences in 2008.

Inf.09

Number of inflorescences in 2009.

Veg.09

Number of stems without inflorescences in 2009.

Inf.10

Number of inflorescences in 2010.

Veg.10

Number of stems without inflorescences in 2010.

Inf.11

Number of inflorescences in 2011.

Veg.11

Number of stems without inflorescences in 2011.

Examples

library(lefko3)

data(cypa_data)

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 = cypa_data, noyears = 18, firstyear = 1994,
  individcol = "plant_id", blocksize = 2, sizeacol = "Inf.94",
  sizebcol = "Veg.94", repstracol = "Inf.94", fecacol = "Inf.94",
  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", stages = c("stage3", "stage2", "stage1"),
  size = c("size3added", "size2added"), supplement = cypsupp2r,
  yearcol = "year2", indivcol = "individ")
                       
lambda3(cypmatrix2r)