Statistics and proportion for taxon traits — trait

Calculation of statistics and proportions of taxon traits for plot observations or groups of observations, considering data relationships, taxonomic ranks and the handling of not available values.

In trait_stats() you can use customized functions, which have to be defined as foo(x, w, ...), where 'x' is the (numeric) taxon trait and 'w' is the weight (e.g. the abundance).

With the arguments taxon_levels and merge_to the used taxonomic ranks can be defined, where the first one indicates which ranks have to be considered in the calculations and the second one determine the aggregation of taxa from a lower level to a parental one.

Usage

trait_stats(trait, object, ...)

# S4 method for class 'character,vegtable'
trait_stats(
  trait,
  object,
  FUN,
  head_var = "ReleveID",
  taxon_levels,
  merge_to,
  weight,
  suffix = "_stats",
  in_header = TRUE,
  ...
)

# S4 method for class 'formula,vegtable'
trait_stats(trait, object, ...)

trait_proportion(trait, object, ...)

# S4 method for class 'character,vegtable'
trait_proportion(
  trait,
  object,
  head_var = "ReleveID",
  trait_levels,
  taxon_levels,
  merge_to,
  include_nas = TRUE,
  weight,
  suffix = "_prop",
  in_header = TRUE,
  ...
)

# S4 method for class 'formula,vegtable'
trait_proportion(trait, object, ...)

Arguments

trait: Either a character value indicating the name of trait variable or a formula as 'trait ~ head_var'. Note that you can add multiple variables in the form trait_1 + ... + trait_n ~ head_var.
object: A vegtable object.
...: Further arguments passed among methods. In the case of the character method, they are passed to 'FUN'.
FUN: A function usually defined as foo(x) or as foo(x, w) for weighted statistics.
head_var: Character value, the name of the variable at slot header to be used as aggregation level for the calculation of statistics or proportions. If not provided, the function will use ReleveID by default.
taxon_levels: Character vector indicating the selected taxonomic ranks to be considered in the output.
merge_to: Character value indicating the taxonomic rank for aggregation of taxa. All ranks lower than the one indicated here will be assigned to the respective parents at the required taxonomic rank.
weight: Character value indicating the name of the variable at slot samples used as weight for the proportions. Usually the numeric abundance.
suffix: A suffix added to the name of the trait variable or to the levels of categorical trait variables. I is meant to avoid homonymous variables within the same object.
in_header: Logical value indicating whether the output should be inserted in the slot header or provided as data frame. In the case that 'head_var' (or the right term in the formula method) is different from ReleveID, the statistics and proportions will be inserted in the respective data frame at slot relations.
trait_levels: Character vector indicating a selection of levels from a trait, in the case that some levels should be ignored in the output. Trait levels that are skipped at output will be still used for the calculation of proportions. This argument gets only applied for the character method.
include_nas: Logical value indicating whether NAs should be considered for the calculation of proportions or not.

Value

A data frame with the proportions of traits levels or statistics for the trait variable, or an object of class vegtable including those results at the slot header.

Author

Miguel Alvarez kamapu78@gmail.com

Examples

veg <- cover_trans(Kenya_veg, to = "cover")
veg <- trait_proportion("lf_behn_2018", veg,
  trait_levels = "obligate_annual", weight = "cover", include_nas = FALSE
)
summary(veg$obligate_annual_prop)
#>    Min. 1st Qu.  Median    Mean 3rd Qu.    Max.    NA's 
#>  0.0077  0.2500  0.5000  0.4992  0.7143  1.0000    1039