export_ess_dive {gasanalyzer}

Export a subset of the data into the ESS-DIVE reporting format for leaf-level gas exchange data.

Description

Ely et al. (2021) proposed a standardized nomenclature for reporting gas-exchange data and metadata within the framework of the Environmental System Science Data Infrastructure for a Virtual Ecosystem (ESS-DIVE) repository. This method converts data frames or tibbles created with gasanalyzer to this standardized format. Note that the scope of the proposed standard is limited, and therefore only a subset of the data is exported. Users should add relevant additional columns and provide relevant metadata.

Usage

export_ess_dive(df, filename = "", extra_cols = NULL)

Arguments

df

a tibble with gas-exchange data.

filename

path to the output file. If none provided the method returns the data as a tibble.

extra_cols

a character vector specifying additional columns (not specified in the standard specified by Ely et al. 2021) to include in the returned data or saved files.

Details

If a filename is given as argument, the data is written into a comma separated, UTF-8 encoded file without BOM and with CRLF line headings. In addition, a data dictionary file ("_dd" is inserted at the end of the filename, before the file extension). If no filename is provided, the converted data is returned.

Value

Nothing if a filename is provided. Otherwise, a tibble with variables and headings specified by the ESS-DIVE gas-exchange standard is returned.

References

Ely KS, Rogers A, Agarwal DA, et al (2021) A reporting format for leaf-level gas exchange data and metadata. Ecol Inform 61:101232. https://doi.org/10.1016/j.ecoinf.2021.101232

Examples

example <- system.file("extdata", "d13C.tsv", package = "gasanalyzer")

# read data and recalculate using default gas-exchange equations:
df <- read_gasexchange(example) |>
  recalculate(create_equations("default"))

# view df in ess_dive format:
export_ess_dive(df)


# save the data and a data dictionary:
export_ess_dive(df, "ess_dive_test.csv")
# read and show the dictionary:
readLines("ess_dive_test_dd.csv")