R: Calculates basal area for each species in a quadrat

getBasalAreas {plantTracker}

R Documentation

Calculates basal area for each species in a quadrat

Description

This function calculates the total basal area for each species present in a quadrat for each year of data collection. Both the absolute basal area (in the same units of area as the input data.frame) is returned, as well as the percentage of the total occupied basal area in the quadrat that is occupied by a given species ("percent total basal area"). If you'd like to ultimately calculate the population growth rate (lambda) for each species, you can use the getLambda function directly, which takes raw species occurrence data (like in 'dat' here) and returns lambda values for each species and quadrat for each transition in the dataset. This function should only be used if the individuals in 'dat' were mapped as polygons that are representative of their actual basal area, i.e. were not mapped as points.

Usage

getBasalAreas(
  dat,
  inv,
  species = "Species",
  quad = "Quad",
  site = "Site",
  year = "Year",
  geometry = "geometry",
  ...
)

Arguments

`dat`	An sf data.frame in which each row represents a unique polygon (either a genet or a ramet) in a unique site/quadrat/year combination. A data.frame returned by `trackSpp` can be put directly into this function. However, it is not necessary for 'dat' to have demographic data or unique identifiers (i.e. 'trackIDs') assigned. 'dat' must have columns that contain... a unique identification for each research site in character format with no NAs (the default column name is "Site") species name in character format with no NAs (the default column name is "Species") unique quadrat identifier in character format with no NAs (the default column name is "Quad") year of data collection in integer format with no NAs (the default column name is "Year") an s.f 'geometry' column that contains a polygon or multipolygon data type for each individual observation (the default column name is "geometry") This function should only be used if the individuals in 'dat' were mapped as polygons that are representative of their actual basal area, i.e. were not mapped as points.
`inv`	The name of each element of the list is a quadrat name in 'dat', and the contents of that list element is a numeric vector of all of the years in which that quadrat (or other unique spatial area) was sampled. Make sure this is the years the quadrat was actually sampled, not just the years that have data in the 'dat' argument! This argument allows the function to differentiate between years when the quadrat wasn't sampled and years when there just weren't any individuals of a species present in that quadrat.
`species`	An optional character string argument. Indicates the name of the column in 'dat' that contains species name data. It is unnecessary to include a value for this argument if the column name is "Species" (default value is 'Species').
`quad`	An optional character string argument. Indicates the name of the column in 'dat' that contains quadrat name data. It is unnecessary to include a value for this argument if the column name is "Quad" (default is 'Quad').
`site`	An optional character string argument. Indicates the name of the column in 'dat' that contains site name data. It is unnecessary to include a value for this argument if the column name is "Site" (default value is 'Site').
`year`	An optional character string argument. Indicates the name of the column in 'dat' that contains data for year of sampling. It is unnecessary to include a value for this argument if the column name is "Year" (default is 'Year').
`geometry`	An optional character string argument. Indicates the name of the column in 'dat' that contains sf geometry data. It is unnecessary to include a value for this argument if the column name is "geometry" (default is 'geometry').
`...`	Other arguments passed on to methods. Not currently used.

Value

getBasalAreas() returns a data.frame with the columns "Site", "Quad", "Year" and "Species". No two rows will have the same values for all four of these columns. The column "absolute_basalArea" has the area of the quadrat that is occupied by a species in a given unique site/quadrat/year combination. This is in the same units as the area in 'dat'. "quad_basalArea" gives the combined basal area of all organisms in a given site/quadrat/year. "percent_basalArea" gives the percentage of occupied basal area within a quadrat that is occupied by each species in a given site/quadrat/year. For example, species A has a basal area of 22 cm^2 in quadrat 1 in 2005 ("absolute_basalArea = 22). In 2005, there are 50 cm^2 of quadrat 1 that are occupied by organisms ("quad_basalArea" = 55). 44% of the occupied basal area in quadrat 1 in 2005 is occupied by species A ("percent_basalArea" = 44). There may be an 'NA' in the "percent_basalArea" column if the "quad_basalArea" for that species and year is 0.

Examples

dat <- grasslandData[grasslandData$Site == "AZ" &
 grasslandData$Year %in% c(1922:1925),]
names(dat)[1] <- "speciesName"
inv <- grasslandInventory[unique(dat$Quad)]
outDat <- trackSpp(dat = dat,
 inv = inv,
 dorm = 1,
 buff = .05,
 buffGenet = 0.005,
 clonal = data.frame("Species" = unique(dat$speciesName),
 "clonal" = c(TRUE,FALSE)),
 species = "speciesName",
 aggByGenet = TRUE
 )
getBasalAreas(dat = outDat, inv = inv,
species = "speciesName")