# Demographic Dataset of **Cypripedium candidum** Population, in Vertical Format 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. Same dataset as `cypdata`, but arranged in an ahistorical vertical format. data ## Format A data frame with 77 individuals, 322 rows, and 14 variables. Each row corresponds to a specific two-year transition for a specific individual. Variable codes are similar to those for `cypdata`, but use `.2` to identify occasion **t** and `.3` to identify occasion **t**+1. - **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. - **year2**: Year in occasion **t**. - **Inf2.2**: Number of double inflorescences in occasion **t**. - **Inf.2**: Number of inflorescences in occasion **t**. - **Veg.2**: Number of stems without inflorescences in occasion **t**. - **Pod.2**: Number of fruits in occasion **t**. - **Inf2.3**: Number of double inflorescences in occasion **t**+1. - **Inf.3**: Number of inflorescences in occasion **t**+1. - **Veg.3**: Number of stems without inflorescences in occasion **t**+1. - **Pod.3**: Number of fruits in occasion **t**+1. ## 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. ```r data(cypvert) ``` ## Examples ```r data(cypvert) 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_v2 <- historicalize3(data = cypvert, patchidcol = "patch", individcol = "plantid", year2col = "year2", sizea2col = "Inf2.2", sizea3col = "Inf2.3", sizeb2col = "Inf.2", sizeb3col = "Inf.3", sizec2col = "Veg.2", sizec3col = "Veg.3", repstra2col = "Inf2.2", repstra3col = "Inf2.3", repstrb2col = "Inf.2", repstrb3col = "Inf.3", feca2col = "Pod.2", feca3col = "Pod.3", repstrrel = 2, stageassign = cypframe_raw, stagesize = "sizeadded", censorcol = "censor", censor = FALSE, NAas0 = TRUE, NRasRep = TRUE, reduce = 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_v2, stageframe = cypframe_raw, year = "all", patch = "all", stages = c("stage3", "stage2"), size = c("size3added", "size2added"), supplement = cypsupp2r, yearcol = "year2", patchcol = "patchid", indivcol = "individ") lambda3(cypmatrix2r) ```

cypvert dataset