npe_community_matrix {neonPlantEcology}

Create a species abundance or occurrence matrix

Description

npe_community_matrix creates a wide matrix of species cover or binary (presence/absence) values with the plot/subplot/year as rownames. This is useful for the vegan package, hence the name.

Usage

npe_community_matrix(
  x,
  scale = "plot",
  trace_cover = 0.5,
  timescale = "annual",
  input = "neon_div_object",
  binary = FALSE
)

Arguments

x

Input object. See input argument help for more details.

scale

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

trace_cover

cover value for subplots where only occupancy was recorded

timescale

what temporal resolution? can be "subannual", which is really only applicable at sites where there are multiple bouts per year, "annual" or "all", which dissolves together the entire time series.

input

by default, longform dataframe is calculated from the diversity object and then converted to a community matrix, set this option to "lf" to use a longform data frame that was created separately (and perhaps modified). Another option is input = "divStack", which is using the output from the divStack function in the neonPlants package. Using a premade longform data frame or a divStack output will use the spatial and temporal scale of that input data separately

binary

should the matrix be converted from percent cover to binary?

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".

Value

a data frame with each row a site aggregated at the spatial and temporal scales chosen by the user. Each column is a single species, and cell values can be either cover (a value between 0 and 100) or occurrence (1 or 0)

Examples

data("D14")
comm <- npe_community_matrix(D14)