Compute Functional Entities composition based on a Species x Traits matrix
Source:R/sp_to_FE.R
sp.to.fe.RdCompute Functional Entities composition based on a Species x Traits matrix
Arguments
- sp_tr
a data frame containing species as rows and traits as columns.
- tr_cat
a data frame containing three columns for each trait (rows):
trait_name: names of all traits as in
sp_trdata frame;trait_type: category codes for each trait as followed: N for Nominal traits (factor variable), O for Ordinal traits (ordered variable), C for Circular traits (integer values), Q for Quantitative traits (numeric values) that is allowed only if there are at least 2 species with the same value, and F for fuzzy-coded traits (i.e. described with several 'sub-traits');
fuzzy_name name of fuzzy-coded trait to which 'sub-trait' belongs (if trait is not fuzzy, ignored so could be trait name or NA).
- fe_nm_type
a character string referring to the type of naming functional entities. Two possible values: "fe_rank" (FE are named after their decreasing rank in term of number of species i.e. fe_1 is the one gathering most species) and "tr_val" (FE are named after names of traits and of trait values for each FE, if possible, see details below). Default:
fe_nm_type = "fe_rank".- check_input
a logical value indicating whether key features the inputs are checked (e.g. class and/or mode of objects, names of rows and/or columns, missing values). If an error is detected, a detailed message is returned. Default:
check.input = TRUE.
Value
A list of objects containing:
fe_nm: a vector with names of all FE (following fe_nm_type). FE are ordered according to the decreasing number of species they gather.
sp_fe: a vector containing for each species the name of the FE it belongs to. FE order is done according to decreasing number of species.
fe_tr: a data frame containing traits values (variables in columns) for each FE (rows). FE order is done according to decreasing number of species.
fe_nb_sp: a vector with species number per FE. If all FE have only one species, a warning message is returned. FE are ordered according to the decreasing number of species they gather.
details_fe: a list containing: fe_codes a vector containing character referring to traits values (like a barcode) with names as in
fe_nm_typeand sorted according tofe_nb_sp; tr_uval a list containing for each trait a vector of its unique values or a data frame for fuzzy-coded traits; fuzzy_E a list with for each fuzzy-coded trait a data frame with names of entities (E) and names of species (sp); tr_nb_uval a vector with number of unique values per trait (or combinations for fuzzy-coded traits); max_nb_fe the maximum number of FE possible given number of unique values per trait.
Details
fe_nm_type = "tr_val" is allowed only if:
there are less than 7 traits;
none of them is fuzzy-coded (so that names are not too long)
all trait names and all trait values have different 2 first letters
If these 3 conditions are met, names of Functional Entities are made as a character string of up to 2 letters for trait name in upper case font then up to 2 letters for trait value in lower case font, separated by "_" between traits. Trait names are abbreviated to a single letter whenever possible. Examples: ("TAc2_TBxx_TCyy", "TAc3_TBff_TCyy") or ("A2_Bx_Cy", "A3_Bf_Cy")
Examples
# Load species traits data:
data("fruits_traits", package = "mFD")
# Transform species traits data:
# Only keep the first 4 traits to illustrate FEs:
fruits_traits <- fruits_traits[ , c(1:4)]
# Load trait types data:
data("fruits_traits_cat", package = "mFD")
# Transform the trait types data to only keep traits 1 - 4:
fruits_traits_cat <- fruits_traits_cat[c(1:4), ]
# Gather species into FEs:
## gathering species into FEs (FEs named according to the decreasing...
## ... number of species they gather):
sp_FEs <- mFD::sp.to.fe(
sp_tr = fruits_traits,
tr_cat = fruits_traits_cat,
fe_nm_type = "fe_rank")
## display FEs names:
sp_FEs$fe_nm
#> [1] "fe_1" "fe_2" "fe_3" "fe_4" "fe_5" "fe_6" "fe_7" "fe_8" "fe_9"
#> [10] "fe_10" "fe_11" "fe_12" "fe_13" "fe_14" "fe_15" "fe_16" "fe_17" "fe_18"
#> [19] "fe_19" "fe_20"
## display for each species the name of the FE it belongs to:
sp_FEs$sp_fe
#> apple apricot banana currant blackberry
#> "fe_1" "fe_2" "fe_6" "fe_7" "fe_3"
#> blueberry cherry grape grapefruit kiwifruit
#> "fe_8" "fe_9" "fe_10" "fe_11" "fe_12"
#> lemon lime litchi mango melon
#> "fe_4" "fe_13" "fe_14" "fe_15" "fe_5"
#> orange passion_fruit peach pear pineapple
#> "fe_4" "fe_16" "fe_17" "fe_1" "fe_18"
#> plum raspberry strawberry tangerine water_melon
#> "fe_2" "fe_3" "fe_19" "fe_20" "fe_5"
## display trait values for each FE:
sp_FEs$fe_tr
#> Size Plant Climate Seed
#> fe_1 5-10cm tree temperate pip
#> fe_2 3-5cm tree temperate pit
#> fe_3 1-3cm shrub temperate pip
#> fe_4 5-10cm tree subtropical pip
#> fe_5 10-20cm forb temperate pip
#> fe_6 10-20cm tree tropical none
#> fe_7 0-1cm shrub temperate pip
#> fe_8 0-1cm forb temperate pip
#> fe_9 1-3cm tree temperate pit
#> fe_10 1-3cm vine temperate pip
#> fe_11 10-20cm tree subtropical pip
#> fe_12 5-10cm vine temperate pip
#> fe_13 3-5cm tree tropical pip
#> fe_14 1-3cm tree tropical pit
#> fe_15 10-20cm tree tropical pit
#> fe_16 3-5cm vine tropical pip
#> fe_17 5-10cm tree temperate pit
#> fe_18 10-20cm forb tropical none
#> fe_19 1-3cm forb temperate pip
#> fe_20 3-5cm tree subtropical pip
## display the number of species per FEs:
sp_FEs$fe_nb_sp
#> fe_1 fe_2 fe_3 fe_4 fe_5 fe_6 fe_7 fe_8 fe_9 fe_10 fe_11 fe_12 fe_13
#> 2 2 2 2 2 1 1 1 1 1 1 1 1
#> fe_14 fe_15 fe_16 fe_17 fe_18 fe_19 fe_20
#> 1 1 1 1 1 1 1