Rarefy BioTIME data to an equal number of samples per year

Takes the output of gridding and applies sample-based rarefaction to standardise the number of samples per year within each cell-level time series (i.e. assemblageID).

Usage

resampling(
  x,
  measure,
  resamps = 1L,
  conservative = FALSE,
  summarise = TRUE,
  verbose = TRUE
)

Arguments

x

(data.frame) BioTIME gridded data to be resampled (in the format of the output of the gridding function).

measure

(character) currency to be retained during the sample-based rarefaction. Can be either defined by a single column name or a vector of two or more column names.

resamps

(integer) number of repetitions. Default is 1.

conservative

(logical). FALSE by default. If TRUE, whenever a NA is found in the measure field(s), the whole sample is removed instead of the missing observations only.

summarise

(logical). TRUE by default. If FALSE, the function returns abundance and/or biomass summed at the SAMPLE_DESC level git pull(i.e., per sample), rather than per species per year.

verbose

(logical). TRUE by default. If FALSE, warnings when NA values or one-year-long time series are found in x and excluded are hidden.

Value

Returns a single long form data.frame containing the total currency or currencies of interest (sum) for each species in each year within each rarefied time series (i.e. assemblageID). An extra integer column called resamp indicates the specific iteration.

Details

Sample-based rarefaction prevents temporal variation in sampling effort from affecting diversity estimates (see Gotelli N.J., Colwell R.K. 2001 Quantifying biodiversity: procedures and pitfalls in the measurement and comparison of species richness. Ecology Letters 4(4), 379-391) by selecting an equal number of samples across all years in a time series. resampling counts the number of unique samples taken in each year (sampling effort), identifies the minimum number of samples across all years, and then uses this minimum to randomly resample each year down to that number. Thus, standardising the sampling effort between years, standard biodiversity metrics can be calculated based on an equal number of samples (e.g. using getAlphaMetrics, getAlphaMetrics). measure is a character input specifying the chosen currency to be used during the sample-based rarefaction. It can be a single column name or a vector of two or more column names - e.g. for BioTIME, measure="ABUNDANCE", measure="BIOMASS" or measure = c("ABUNDANCE", "BIOMASS").

By default, any observations with NA within the currency field(s) are removed. You can choose to remove the full sample where such observations are present by setting conservative to TRUE. resamps can be used to define multiple iterations, effectively creating multiple alternative datasets as in each iteration different samples will be randomly selected for the years where number of samples > minimum. Note that the function always returns a single data frame, i.e. if resamps > 1, the returned data frame is the result of individual data frames concatenated together, one from each iteration identified by a numerical unique identifier 1:resamps.

Examples

if (FALSE) { # \dontrun{
  set.seed(42)
  x <- gridding(BTsubset_meta, BTsubset_data)
  resampling(x, measure = "BIOMASS", summarise = TRUE)
  resampling(x, measure = "ABUNDANCE", verbose = FALSE)
  resampling(x, measure = c("ABUNDANCE","BIOMASS"))
  # Without summarising the species abundances are summed at the SAMPLE_DESC level
  resampling(x, measure = "BIOMASS", summarise = FALSE, conservative = FALSE)
} # }