gasanalyzer (version 0.4.3)

export_ess_dive: 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)

Value

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

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.

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)

.old_wd <- setwd(tempdir())
# 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")
setwd(.old_wd)