cypdata {lefko3} | 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)