cypa_data {adapt3} | R Documentation |
Demographic Dataset of Cypripedium parviflorum Population, in Horizontal Format
Description
A dataset containing the states and fates of Cypripedium parviflorum (small yellow lady's slipper orchids), family Orchidaceae, from a population in Illinois, USA, resulting from monitoring that occurred annually between 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.
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
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)