Extract species x traits information from long format data — fb_format_species

Convert a flat data.frame with traits values for different species into a proper data.frame object that can then be used by other functions. The final output contains species in rows and traits in columns.

Usage

fb_format_species_traits(data, species, traits)

Arguments

data: a data.frame in a long format (see example).
species: a character of length 1. Name of the column with species names.
traits: a character of length >= 1. Name(s) of trait column(s).

Value

A data.frame with species in rows and traits in columns, with the first column names "species" containing the species names.

Examples

library("funbiogeo")

filename <- system.file("extdata", "raw_mammals_data.csv", 
                        package = "funbiogeo")
all_data <- read.csv(filename)

head(all_data)
#>   species           order    site longitude latitude count adult_body_mass
#> 1  sp_001 Cetartiodactyla  fb_103  7.271821 59.09736     1        461900.8
#> 2  sp_001 Cetartiodactyla fb_1001 20.771821 52.59736     1        461900.8
#> 3  sp_001 Cetartiodactyla  fb_102  6.771821 59.09736     1        461900.8
#> 4  sp_001 Cetartiodactyla  fb_104  7.771821 59.09736     1        461900.8
#> 5  sp_001 Cetartiodactyla  fb_101  6.271821 59.09736     1        461900.8
#> 6  sp_001 Cetartiodactyla fb_1000 20.271821 52.59736     1        461900.8
#>   gestation_length litter_size max_longevity sexual_maturity_age diet_breadth
#> 1              235        1.25           324               668.2            1
#> 2              235        1.25           324               668.2            1
#> 3              235        1.25           324               668.2            1
#> 4              235        1.25           324               668.2            1
#> 5              235        1.25           324               668.2            1
#> 6              235        1.25           324               668.2            1

traits <- c("adult_body_mass", "gestation_length", "litter_size", 
            "max_longevity", "sexual_maturity_age", "diet_breadth")

species_traits <- fb_format_species_traits(all_data, "species", traits)
head(species_traits)
#>   species adult_body_mass gestation_length litter_size max_longevity
#> 1  sp_001       461900.76           235.00        1.25         324.0
#> 2  sp_002           21.11            19.89        5.64          48.0
#> 3  sp_005           31.60            24.50        4.94          48.0
#> 4  sp_006           21.90            23.68        5.16          52.8
#> 5  sp_010            8.31               NA        1.73         252.0
#> 6  sp_013        31756.51            63.50        4.98         354.0
#>   sexual_maturity_age diet_breadth
#> 1              668.20            1
#> 2               76.04           NA
#> 3               43.27           NA
#> 4               57.93            4
#> 5                  NA            1
#> 6              679.37            1