summary_hfv: Summary of Classes "hfvdata" and "hfvlist

In lefko3: Historical and Ahistorical Population Projection Matrix Analysis

Summary of Classes "hfvdata" and "hfvlist

Description

A function to simplify the viewing of basic information describing demographic data in historical vertical format (data frames of class hfvdata, or bootstrapped data frames in lists of class hfvlist).

Usage

summary_hfv(
  object,
  popid = "popid",
  patchid = "patchid",
  individ = "individ",
  year2id = "year2",
  full = FALSE,
  err_check = TRUE,
  ...
)

Arguments

object	An object of either class hfvdata or class hfvlist.
popid	A string denoting the name of the variable denoting population identity.
patchid	A string denoting the name of the variable denoting patch identity.
individ	A string denoting the name of the variable denoting individual identity.
year2id	A string denoting the name of the variable denoting the year in time t.
full	A logical value indicating whether to include basic data frame summary information in addition to hfvdata-specific summary information. Defaults to FALSE.
err_check	A logical value indicating whether to check for errors in stage assignment.
...	Other parameters.

Value

A summary of the object. If an object of class hfvdata is entered, then the first line of output shows the numbers of populations, patches, individuals, and time steps. If full = TRUE, then this is followed by a standard data frame summary of the hfv dataset. If err_check = TRUE, then a subset of the original data frame input as object is exported with only rows showing stage assignment issues.

If an object of class hfvlist in entered, then the first line of output shows the number of bootstrapped datasets. This is followed by lines showing the mean number of rows and variables per data frame, as well as the mean numbers of populations, patches, individuals, and years per data frame. This is followed by lines showing the total number of unique populations, patches, individuals, and years sampled across the bootstrapped data frames. If full = TRUE, then this is followed by standard data frame summaries of all bootstrapped data frames. If err_check = TRUE, then a data frame is output with all of the problem rows across all bootstrapped data frames, starting with a new variable giving the bootstrap number of origin.

Notes

Stage assignment issue identified by option err_check fall under two categories. First, all rows showing NoMatch as the identified stage for stage1, stage2, or stage3 are identified. Second, all rows showing stage1 = "NotAlive" and alive1 = 1, stage2 = "NotAlive" and alive2 = 1, or stage3 = "NotAlive" and alive3 = 1 are identified.

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)

summary_hfv(cypraw_v1)

cypraw_v1_boot <- bootstrap3(cypraw_v1, reps = 3)

summary_hfv(cypraw_v1_boot)

lefko3 documentation built on Nov. 5, 2025, 7:20 p.m.