Description Usage Arguments Value Examples

`sf_create()`

returns a data frame describing each ahistorical life
history stage in the life history model. This data frame can be used as
input into MPM creation functions such as `flefko3()`

, where it
determines how each stage is treated during matrix estimation.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 |

`sizes` |
A numeric vector of the typical or representative size of each life history stage. |

`stagenames` |
An optional vector of stage names, in the same order as
elements in sizes. If an IPM or function-based matrix with many stages is
desired, then two stages that occur within the dataset and represent the
lower and upper size limits of the IPM must be marked as |

`repstatus` |
A vector denoting the binomial reproductive status of each life history stage. Defaults to 1. |

`obsstatus` |
A vector denoting the binomial observation status of each life history stage. Defaults to 1, but may be changed for unobservable stages. |

`propstatus` |
A vector denoting whether each life history stage is a propagule. Such stages are generally only used in fecundity estimation. Defaults to NA. |

`immstatus` |
A vector denoting whether each stage is immature. Must be composed of binomial values if given. Defaults to NA. |

`matstatus` |
A vector denoting whether each stage is mature. Must be
composed of binomial values if given. Defaults to 1 for all stages defined
in |

`minage` |
An optional vector denoting the minimum age at which a stage can occur. Only used in age x stage matrix development. Defaults to NA. |

`maxage` |
An optional vector denoting the maximum age at which a stage should occur. Only used in age x stage matrix development. Defaults to NA. |

`indataset` |
A vector designating which stages are found within the
dataset. While |

`binhalfwidth` |
A numeric vector giving the half-width of size bins. Required to classify individuals appropriately within size classes. Defaults to 0.5 for all sizes. |

`comments` |
An optional vector of text entries holding useful text descriptions of all stages. |

`ipmbins` |
If an IPM is desired, then this parameter sets the number of stages to create for that IPM. This number is in addition to any stages that are not size-classified. Defaults to 100, and numbers greater than this yield a warning about the loss of statistical power and increasing chance of matrix over-parameterization resulting from increasing numbers of stages. |

`roundsize` |
This parameter sets the precision of size classification, and equals the number of digits used in rounding sizes. Defaults to 5. |

A data frame of class `stageframe`

, which includes information
on the stage name, size, reproductive status, observation status, propagule
status, immaturity status, maturity status, presence within the core dataset,
counts of similarly sized stages, raw bin half-width, and the minimum,
center, and maximum of each size bin, as well as its width. If minimum and
maximum ages were specified, then these are also included. Also includes an
empty string variable that can be used to describe stages meaningfully. This
object can be used as the `stageframe`

input for `flefko3()`

`flefko2()`

, `rlefko3()`

, and `rlefko2()`

.

Variables in this data frame include the following:

`stage` |
The unique names of the stages to be analyzed. |

`size` |
The typical or representative size at which each stage occurs. |

`repstatus` |
A binomial variable showing whether each stage is reproductive. |

`obsstatus` |
A binomial variable showing whether each stage is observable. |

`propstatus` |
A binomial variable showing whether each stage is a propagule. |

`immstatus` |
A binomial variable showing whether each stage can occur as immature. |

`matstatus` |
A binomial variable showing whether each stage occurs in maturity. |

`indataset` |
A binomial variable describing whether each stage occurs in the input dataset. |

`binhalfwidth_raw` |
The half-width of the size bin, as input. |

`min_age` |
The minimum age at which the stage may occur. |

`max_age` |
The maximum age at which the stage may occur. |

`sizebin_min` |
The minimum size at which the stage may occur. |

`sizebin_max` |
The maximum size at which the stage may occur. |

`sizebin_center` |
The centroid of the size bin at which the stage may occur. |

`sizebin_width` |
The width of the size bin corresponding to the stage. |

`comments` |
A text field for stage descriptions. |

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 | ```
# Lathyrus example
data(lathyrus)
sizevector <- c(0, 100, 13, 127, 3730, 3800, 0)
stagevector <- c("Sd", "Sdl", "VSm", "Sm", "VLa", "Flo", "Dorm")
repvector <- c(0, 0, 0, 0, 0, 1, 0)
obsvector <- c(0, 1, 1, 1, 1, 1, 0)
matvector <- c(0, 0, 1, 1, 1, 1, 1)
immvector <- c(1, 1, 0, 0, 0, 0, 0)
propvector <- c(1, 0, 0, 0, 0, 0, 0)
indataset <- c(0, 1, 1, 1, 1, 1, 1)
binvec <- c(0, 100, 11, 103, 3500, 3800, 0.5)
lathframe <- sf_create(sizes = sizevector, stagenames = stagevector,
repstatus = repvector, obsstatus = obsvector, matstatus = matvector,
immstatus = immvector, indataset = indataset, binhalfwidth = binvec,
propstatus = propvector)
lathvert <- verticalize3(lathyrus, noyears = 4, firstyear = 1988,
patchidcol = "SUBPLOT", individcol = "GENET", blocksize = 9,
juvcol = "Seedling1988", sizeacol = "Volume88", repstracol = "FCODE88",
fecacol = "Intactseed88", deadacol = "Dead1988",
nonobsacol = "Dormant1988", stageassign = lathframe, stagesize = "sizea",
censorcol = "Missing1988", censorkeep = NA, censor = TRUE)
lathsupp3 <- supplemental(stage3 = c("Sd", "Sd", "Sdl", "Sdl", "Sd", "Sdl", "mat"),
stage2 = c("Sd", "Sd", "Sd", "Sd", "rep", "rep", "Sdl"),
stage1 = c("Sd", "rep", "Sd", "rep", "npr", "npr", "Sd"),
eststage3 = c(NA, NA, NA, NA, NA, NA, "mat"),
eststage2 = c(NA, NA, NA, NA, NA, NA, "Sdl"),
eststage1 = c(NA, NA, NA, NA, NA, NA, "NotAlive"),
givenrate = c(0.345, 0.345, 0.054, 0.054, NA, NA, NA),
multiplier = c(NA, NA, NA, NA, 0.345, 0.054, NA),
type = c(1, 1, 1, 1, 3, 3, 1), type_t12 = c(1, 2, 1, 2, 1, 1, 1),
stageframe = lathframe, historical = TRUE)
ehrlen3 <- rlefko3(data = lathvert, stageframe = lathframe, year = "all",
stages = c("stage3", "stage2", "stage1"), supplement = lathsupp3,
yearcol = "year2", indivcol = "individ")
ehrlen3mean <- lmean(ehrlen3)
ehrlen3mean$A[[1]]
# Cypripedium example
rm(list=ls(all=TRUE))
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", "SL", "D",
"XSm", "Sm", "SD", "P1"),
stage2 = c("SD", "SD", "P1", "P2", "P3", "SL", "SL", "SL", "SL", "rep",
"rep"),
eststage3 = c(NA, NA, NA, NA, NA, NA, "D", "XSm", "Sm", NA, NA),
eststage2 = c(NA, NA, NA, NA, NA, NA, "XSm", "XSm", "XSm", NA, NA),
givenrate = c(0.10, 0.20, 0.20, 0.20, 0.25, 0.40, NA, NA, NA, NA, NA),
multiplier = c(NA, NA, NA, NA, NA, NA, NA, NA, NA, 0.5, 0.5),
type =c(1, 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")
cyp2mean <- lmean(cypmatrix2r)
cyp2mean
``` |

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