npe_summary {neonPlantEcology}

Get plant biodiversity information for NEON plots

Description

npe_summary calculates various biodiversity and cover indexes at the plot or subplot scale at each timestep for each plot. Outputs a data frame with number of species, percent cover, relative percent cover (relative to the cover of the other plants), and shannon diversity, for natives, exotics and all species. Also calculates all of these metrics for the families and/or species of your choice.

Usage

npe_summary(
  neon_div_object,
  scale = "plot",
  trace_cover = 0.5,
  timescale = "annual",
  betadiversity = FALSE,
  families = NA
)

Arguments

neon_div_object

the raw vegan::diversity data downloaded using neonPlantEcology::download_plant_div() or #' the function neonUtilities::loadByProduct() with the dpID arguement set to "DP1.10058.001".

scale

what level of aggregation? This can be "1m", "10m", "100m", "plot" or "site". "plot" is the default.

trace_cover

cover value for subplots where only occupancy was recorded

timescale

by default npe_summary groups everything by year. The user may set this argument to "all" to have the function aggregate the years together and then calculate diversity and cover indexes, or "subannual" for bout-level.

betadiversity

If evaluating at the plot or site level, should beta diversity (turnover and nestedness) be calculated. If scale = plot, it will calculate betadiversity within each plot, using the combined species presences within the 1 and 10 m subplots, and so it's calcuated from 8 subplots before 2020, 6 after. if scale = site, it calculates the betadiversity between plots.

families

Which specific families should the metrics be calculated for? This can be a concatenated vector if the user want more than one family.

Value

a data frame of higher-level summary information. Number of species, Shannon-Weaver alpha diversity, cover, relative cover, for all species together and grouped by nativeStatusCode.

Examples

data("D14")
plot_level <- neonPlantEcology::npe_summary(neon_div_object = D14, scale = "plot")