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Load harmonized trait/allometry data

Source: R/load_harmonized.R
get_trait_data.Rd

Functions to load harmonized trait data and harmonized allometry data

Usage

load_harmonized_trait_tables(
  harmonized_trait_path,
  check = TRUE,
  progress = TRUE
)

load_harmonized_allometry_tables(
  harmonized_allometry_path,
  check = TRUE,
  progress = TRUE
)

get_trait_data(
  harmonized_trait_path,
  trait_name,
  output_format = "long",
  progress = TRUE
)

get_allometry_data(harmonized_allometry_path, response, progress = TRUE)

get_taxon_data(harmonized_trait_path, accepted_name, progress = TRUE)

get_taxon_trait_means(
  harmonized_trait_path,
  taxon_level = "species",
  traits = NULL,
  progress = TRUE
)

Arguments

harmonized_trait_path

The path to harmonized trait data files (.rds or .csv format).

check

A boolean flag to check harmonization and exclude non-acceptable data.

progress

A boolean flag to prompt progress.

harmonized_allometry_path

The path to harmonized allometry data files (.rds or .csv format).

trait_name

A string of an accepted trait name, according to HarmonizedTraitDefinition.

output_format

Either "long" or "wide", to indicate output format for trait columns.

response

String indicating a response variable for allometric equations.

accepted_name

String of an accepted taxon name.

taxon_level

Taxon level for grouping: either 'species' (acceptedName), 'genus' or 'family'

traits

A character vector with the set of traits to summarize. If NULL, then all available traits are summarized.

Value

Function load_harmonized_trait_tables() returns the list with all harmonized trait data tables.

Function load_harmonized_allometry_tables() returns the list with all harmonized allometry data tables.

Function get_trait_data() returns a data frame (in long trait format) with the pooled information for a given trait, or an empty data frame if not found.

Function get_taxon_data() returns a data frame (in long trait format) with the pooled information for a given taxon, or an empty data frame if not found.

Function get_taxon_trait_means() returns a data frame with taxon averages (or most frequent values) for the set of indicated traits.

Function get_allometry_data() returns a data frame with allometric equations.

Details

Function load_harmonized_trait_tables() allows loading all kinds of trait data tables, including those that do not pass harmonization check, if check = FALSE. In contrast, functions get_trait_data(), get_taxon_data() and get_taxon_trait_means() only return data from data sets passing harmonization checks (see function check_harmonized_trait).

See also

check_harmonized_trait

Examples

if (FALSE) { # \dontrun{
 # List harmonized trait files
 DB_path <- "~/OneDrive/mcaceres_work/model_development/medfate_parameterization/traits_and_models/"
 harmonized_trait_path <- paste0(DB_path,"data/harmonized_trait_sources")
 list.files(path = harmonized_trait_path)

 # Load all harmonized trait data
 l <- load_harmonized_trait_tables(harmonized_trait_path)
 head(l[[1]])

 # Get data for one specific trait
 get_trait_data(harmonized_trait_path, "SLA")

 # Get trait data for one specific taxon
 get_taxon_data(harmonized_trait_path, "Pinus halepensis")

 # List harmonized allometry files
 harmonized_allometry_path = "~/OneDrive/EMF_datasets/AllometryDatabases/Products/harmonized"
 list.files(path = harmonized_allometry_path)

 # Load all harmonized allometry data
 l <- load_harmonized_allometry_tables(harmonized_allometry_path)
 head(l[[1]])

 # Get allometry data for one specific response
 get_allometry_data(harmonized_allometry_path, "FoliarBiomass")
} # }