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Extract species x traits information from long format data
Source:R/fb_format_species_traits.R
fb_format_species_traits.Rd
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.
Value
A data.frame
with species in rows and traits in columns, with the
first column names "species"
containing the species names.
Examples
filename <- system.file(
"extdata", "woodiv_raw_data.csv", package = "funbiogeo"
)
all_data <- read.csv(filename)
head(all_data)
#> site country longitude latitude species count family genus
#> 1 26351755 Portugal 2635000 1755000 JPHO 1 Cupressaceae Juniperus
#> 2 26351755 Portugal 2635000 1755000 PPIR 1 Pinaceae Pinus
#> 3 26351765 Portugal 2635000 1765000 JPHO 1 Cupressaceae Juniperus
#> 4 26351955 Portugal 2635000 1955000 JPHO 1 Cupressaceae Juniperus
#> 5 26351955 Portugal 2635000 1955000 PPIR 1 Pinaceae Pinus
#> 6 26351965 Portugal 2635000 1965000 JPHO 1 Cupressaceae Juniperus
#> binomial endemism cultivated plant_height seed_mass sla
#> 1 Juniperus phoenicea 0 0 4.88150 79.86000 4.365246
#> 2 Pinus pinaster 0 0 19.75384 55.83434 3.357539
#> 3 Juniperus phoenicea 0 0 4.88150 79.86000 4.365246
#> 4 Juniperus phoenicea 0 0 4.88150 79.86000 4.365246
#> 5 Pinus pinaster 0 0 19.75384 55.83434 3.357539
#> 6 Juniperus phoenicea 0 0 4.88150 79.86000 4.365246
#> wood_density
#> 1 0.6487500
#> 2 0.4430277
#> 3 0.6487500
#> 4 0.6487500
#> 5 0.4430277
#> 6 0.6487500
traits <- c("plant_height", "seed_mass", "sla", "wood_density")
species_traits <- fb_format_species_traits(all_data, "species", traits)
head(species_traits)
#> species plant_height seed_mass sla wood_density
#> 1 AALB 49.64162 67.866923 7.483978 0.4490821
#> 2 ACEP 25.87500 64.703750 NA NA
#> 3 ANEB 15.00000 NA 3.420603 NA
#> 4 APIN 27.33333 55.520000 3.420603 0.4586508
#> 5 CLIB 35.63636 86.872600 NA 0.4500000
#> 6 CSEM 24.69231 7.608125 5.824112 0.5184729