npe_longform {neonPlantEcology}

Convert raw NEON diversity object to longform plant cover data frame

Description

The diversity data from NEON comes as a list containing 2 data frames of data that need to be combined, among other things. Here, we take those two data frames and combine them into a longform data frame that can then be further modified for analysis. Most of the unneccessary information from the raw data has been removed. Column names that remain are plotID, subplotID, year, taxonID, cover, scientificName, nativeStatusCode, family, and site.

Usage

npe_longform(
  neon_div_object,
  trace_cover = 0.5,
  pc_na_value = 0.5,
  scale = "plot",
  verbose = FALSE,
  timescale = "annual"
)

Arguments

neon_div_object

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

trace_cover

cover value for subplots where only occupancy was recorded

pc_na_value

sometimes the raw data from neon will have NA's in the percent cover cells. This is assumed to be a data entry error and is set to 0.5 by default.

scale

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

verbose

if true, prints details of which eventID errors were fixed into the console

timescale

what level of temporal aggregation? can be "subannual", which is only important for sites with multiple sampling bouts per year, "annual" or "all" for the full time series.

Value

a data frame with each row a single observation of species cover at the spatial and temporal scale chosen by the user.

Examples

data("D14")
lf <- npe_longform(D14)