abundance_byyr: Create tables of abundance and basal area by year.

In fgeo.analyze: Analyze ForestGEO Data

Description

• abundance_byyr() first picks the main stem of each tree (see ?fgeo.tool::pick_main_stem()). Then, for each species and each round-mean-year of measurement, it counts the number of trees. The result includes main stems within a given dbh range.

• basal_area_byyr() first sums the basal basal area of all stems of each tree. Then, for each species and each round-mean-year of measurement, it sums the basal area of all trees. The result includes all stems within a given dbh range (notice the difference with abundance_byyr()).

Usage

abundance_byyr(vft, ...)

basal_area_byyr(vft, ...)

Arguments

vft	A ForestGEO-like dataframe; particularly a ViewFullTable. As such, it should contain columns PlotName, CensusID, TreeID, StemID, Status, DBH, Genus, SpeciesName, ExactDate, PlotCensusNumber, Family, Tag, and HOM. ExactDate should contain dates from 1980-01-01 to the present day in the format yyyy-mm-dd.
...	Expressions to pick main stems of a specific dbh range (e.g. DBH >= 10 or DBH >= 10, DBH < 20, or DBH >= 10 & DBH < 20).

Details

You don't need to pick stems by status before feeding data to these functions. Doing so may make your code more readable but it should not affect the result. This is because the expressions passed to ... pick data by dbh and exclude the missing dbh values associated to non-alive stems, including dead, missing, and gone stems.

Value

A dataframe.

See Also

fgeo.tool::pick_main_stem().

Other functions for abundance and basal area: abundance()

Examples

library(fgeo.tool)

# Example data
vft <- tibble(
  PlotName = c("luq", "luq", "luq", "luq", "luq", "luq", "luq", "luq"),
  CensusID = c(1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L),
  TreeID = c(1L, 1L, 2L, 2L, 1L, 1L, 2L, 2L),
  StemID = c(1.1, 1.2, 2.1, 2.2, 1.1, 1.2, 2.1, 2.2),
  Status = c(
    "alive", "dead", "alive", "alive", "alive", "gone",
    "dead", "dead"
  ),
  DBH = c(10L, NA, 20L, 30L, 20L, NA, NA, NA),
  Genus = c("Gn", "Gn", "Gn", "Gn", "Gn", "Gn", "Gn", "Gn"),
  SpeciesName = c("spp", "spp", "spp", "spp", "spp", "spp", "spp", "spp"),
  ExactDate = c(
    "2001-01-01", "2001-01-01", "2001-01-01", "2001-01-01",
    "2002-01-01", "2002-01-01", "2002-01-01",
    "2002-01-01"
  ),
  PlotCensusNumber = c(1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L),
  Family = c("f", "f", "f", "f", "f", "f", "f", "f"),
  Tag = c(1L, 1L, 2L, 2L, 1L, 1L, 2L, 2L),
  HOM = c(130L, 130L, 130L, 130L, 130L, 130L, 130L, 130L)
)

vft

abundance_byyr(vft, DBH >= 10, DBH < 20)

abundance_byyr(vft, DBH >= 10)

basal <- basal_area_byyr(vft, DBH >= 10)
basal

# Skip R CMD check for speed

measurements_is_installed <- requireNamespace("measurements", quietly = TRUE)
if (measurements_is_installed) {
  # Convert units
  years <- c("yr_2001", "yr_2002")
  basal_he <- basal %>%
    purrr::modify_at(
      years,
      ~ measurements::conv_unit(.x, from = "mm2", to = "hectare")
    )
  basal_he

  # Standardize
  number_of_hectares <- 50
  basal_he %>%
    purrr::map_at(years, ~ .x / number_of_hectares)
}

fgeo.analyze documentation built on Dec. 5, 2020, 9:06 a.m.