Running examples in 'lefko3-Ex.R' failed
The error most likely occurred in:

> ### Name: cypdata
> ### Title: Demographic Dataset of _Cypripedium candidum_ Population, in
> ###   Horizontal Format
> ### Aliases: cypdata
> ### Keywords: datasets
> 
> ### ** 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, size1col = "Inf2.04", size2col = "Inf.04",
+                           size3col = "Veg.04", repstr1col = "Inf.04",
+                           repstr2col = "Inf2.04", fec1col = "Pod.04",
+                           stageassign = cypframe_raw, stagesize = "sizeadded",
+                           NAas0 = TRUE, NRasRep = TRUE)
> 
> rep_cyp_raw <- matrix(0, 11, 11)
> rep_cyp_raw[1:2,7:11] <- 0.5
> 
> cypover2r <- overwrite(stage3 = c("SD", "P1", "P2", "P3", "D", "XSm", "Sm", "SL", "SL"),
+                        stage2 = c("SD", "SD", "P1", "P2", "P3", "P3", "P3", "P3", "SL"),
+                        eststage3 = c(NA, NA, NA, NA, "D", "XSm", "Sm", NA, NA),
+                        eststage2 = c(NA, NA, NA, NA, "D", "D", "D", NA, NA),
+                        givenrate = c(0.1, 0.2, 0.2, 0.2, NA, NA, NA, 0.25, 0.4),
+                        type = c("S", "S", "S", "S", "S", "S", "S", "S", "S"))
> 
> cypmatrix2r <- rlefko2(data = cypraw_v1, stageframe = cypframe_raw, year = "all",
+                        patch = "all", stages = c("stage3", "stage2", "stage1"),
+                        size = c("size3added", "size2added"),
+                        repmatrix = rep_cyp_raw, overwrite = cypover2r,
+                        yearcol = "year2", patchcol = "patchid",
+                        indivcol = "individ")
Warning in `[<-.factor`(`*tmp*`, ri, value = "Dead") :
  invalid factor level, NA generated
Warning in `[<-.factor`(`*tmp*`, which(data$usedstage3 == "NotAlive"), value = "Dead") :
  invalid factor level, NA generated
Error in rlefko2(data = cypraw_v1, stageframe = cypframe_raw, year = "all",  : 
  Some stages in dataset do not match those detailed in the input stageframe.FALSE
Execution halted