functional_identity: Calculates functional identity

In asgersvenning/bachelor: Bachelor Data And Functions

Calculates functional identity

Description

Calculates functional identity from a species-trait matrix and possibly an abundance vector. Functional identity is simply a fancy way of saying (community-weighted) mean traits.

Usage

functional_identity(x, a = rep(1, nrow(x)))

Arguments

x	numeric matrix. Species-trait matrix.
a	optional numeric vector. Species-abundances (matrix), can be missing.

Value

A table of community functional identity (community weighted mean traits). In case 'a' is missing, simply the mean a table with one row, containing the mean traits.

Details

Names of functional traits are derived from x if present, otherwise they are formatted as "X"+"column number" to be aligned with FD::dbFD.

In case of some of or all of the traits are factors, the trait levels must be converted to dummy columns. This can be done using the 'gower_traits' function in this package.

References

\insertRef

Villeger2008asgerbachelor

Examples

## Not run: 
# An example using the data also supplied in the package. 
# Note that the first part of the example, 
# just shows how to create species-abundance and species-trait tables from the data, 
# as well as subsetting species in the intersection of both data sources.
library(hash)
FIA_dict <- hash(PLANTS_meta$plants_code, PLANTS_meta$fia_code)
PLANTS_dict <- invert(FIA_dict)

tSP <- FIA %>% 
  filter(INVYR>2000) %>% 
  group_by(ID,SPCD) %>% 
  summarise(
    dens = mean(individuals/samples, na.rm = T),
    .groups = "drop"
  ) %>% 
  filter(SPCD %in% values(FIA_dict,PLANTS_tG$traits$plants.code)) %>% 
  pivot_wider(ID,SPCD,values_from=dens,names_prefix = "SP",values_fill = 0)

PLANTS_tG <- PLANTS_traits %>% 
  filter(plants_code %in% values(PLANTS_dict, str_remove(names(tSP)[-1],"^SP"))) %>% 
  gower_traits(T)

tFI <- functional_identity(PLANTS_tG$traits[,-1],rep(1,372))

## End(Not run)

asgersvenning/bachelor documentation built on May 2, 2023, 7:06 a.m.