get_md: Metadata file management
In domvit81/RFlux: Eddy Covariance Flux Data Processing

Description Usage Arguments Details Value Warning Note Author(s) References See Also Examples

View source: R/get_md.R

Returns the input files required by EddyPro software (LI-COR registered trademark; Fratini and Mauder, 2014).

get_md(path_ecmd = NULL,
       path_rawdata = NULL,
       path_output = NULL,
       online,
       path_sa_file = NULL,
       path_pf_file = NULL,
       tlag_meth,
       despike_meth=c("None", "VM97", "M13"),
       detrend_meth=c("BA", "LD"),
       tilt_correction_meth=c("DR", "PF"))

`path_ecmd`	path where the CC-Xxx_ecmd.csv file containing metadata information is stored.
`path_rawdata`	path where eddy covariance rawdata files are stored.
`path_output`	path where the results of `eddypro_run` will be stored (it will be created, if any).
`online`	logical. Indicating whether the parameters of the planar fit method and the spectral correction factors are taken from results of previous processing (online=TRUE) or estimated by using the current set of EC rawdata (online=FALSE).
`path_sa_file`	path where the spectral assessment file generated by EddyPro software is stored.
`path_pf_file`	path where the planar fit file generated by EddyPro software is stored.
`tlag_meth`	time lag detection method: 0 None; 1 Constant time lag, 2 Maximum covariance with default; 3 Maximum covariance; 4 Automatic optimization.
`despike_meth`	despiking method: "None", not apply; "VM97", algorithm by Vickers and Mahrt (1997); "M13", algorithm by Mauder et al (2013).
`detrend_meth`	trend removal method: "BA" Block Average; "LD" Linear Detrending (Rannik and Vesala, 2001).
`tilt_correction_meth`	axis rotation method for tilt correction: "DR" Double Rotation; "PF" Planar Fit (Wilczak et al, 2001).

This function builds the input files required by EddyPro software to process eddy covariance rawdata files.

Returns the following files

`CC-Xxx.eddypro`
`CC-Xxx.metadata`
`CC-Xxx_dynamic_metadata.txt`

where CC-Xxx denoting the site's ID.

If online=FALSE, the number of rawdata needs to be large enough to allow robust estimates of the planar fit parameters (Wilczak et al 2001) and of the spectral correction factors (Fratini et al, 2012). In case of few rawdata, the double rotation method for sonic anemometer tilt correction and the analytical method by Moncrieff et al (1997) for spectral correction will be performed.

Rawdata must be provided as .csv file with the following name: CC-Xxx????yyyymmddHHMM????.csv, where CC-Xxx is the site's ID, yyyymmddHHMM is the ISO timestamp, and ?s denoting free characters. For example: DE-HoH_EC_201901010030_v01.csv.

Domenico Vitale, Dario Papale

Fratini, G., Mauder, M. (2014). Towards a consistent eddy-covariance processing: an intercomparison of EddyPro and TK3. Atmospheric Measurement Techniques, 7(7), 2273-2281, doi: https://doi.org/10.5194/amt-7-2273-2014.

Fratini, G., Ibrom, A., Arriga, N., Burba, G., Papale, D. (2012). Relative humidity effects on water vapour fluxes measured with closed-path eddy-covariance systems with short sampling lines. Agricultural and forest meteorology, 165, pp 53-63, doi: https://doi.org/10.1016/j.agrformet.2012.05.018.

LI-COR Biosciences: EddyPro 7.0.4: Help and User's Guide, LI-COR Biosciences, Lincoln, Nebraska USA, www.licor.com/EddyPro, 2019.

Mauder, M., Cuntz, M., Drue, C., Graf, A., Rebmann, C., Schmid, H. P., ..., Steinbrecher, R. (2013). A strategy for quality and uncertainty assessment of long-term eddy-covariance measurements. Agricultural and Forest Meteorology, 169, 122-135, doi: https://doi.org/10.1016/j.agrformet.2012.09.006.

Moncrieff, J. B., Massheder, J. M., De Bruin, H., Elbers, J., Friborg, T., Heusinkveld, B., ..., Verhoef, A. (1997). A system to measure surface fluxes of momentum, sensible heat, water vapour and carbon dioxide. Journal of Hydrology, 188, 589-611, doi: https://doi.org/10.1016/S0022-1694(96)03194-0.

Rannik, U., Vesala, T. (1999). Autoregressive filtering versus linear detrending in estimation of fluxes by the eddy covariance method. Boundary-Layer Meteorology, 91(2), 259-280, doi: https://doi.org/10.1023/A:1001840416858.

Vickers, D., Mahrt, L. (1997). Quality control and flux sampling problems for tower and aircraft data. Journal of atmospheric and oceanic technology, 14(3), 512-526, doi: https://doi.org/10.1175/1520-0426(1997)014<0512:QCAFSP>2.0.CO;2.

Wilczak, J.M., Oncley, S.P., Stage, S.A. (2001). Sonic anemometer tilt correction algorithms. Boundary-Layer Meteorology, 99(1), 127-150, doi: https://doi.org/10.1023/A:1018966204465.

closed_path_rawdata

## Not run: 
workdir <- getwd()
siteID <- "DE-HoH"
PATH_ECMD <- system.file("extdata", "DE-HoH_ecmd.csv", package = "RFlux")
PATH_RAWDATA <- system.file("extdata", package = "RFlux")
PATH_OUTPUT <- paste0(workdir, "/eddypro/processing")
PATH_SA_FILE <- system.file("extdata", "spectral_assessment.txt", package = "RFlux")
PATH_PF_FILE <- system.file("extdata", "planar_fit.txt", package = "RFlux")

MD <- get_md(path_ecmd=PATH_ECMD,
             path_rawdata=PATH_RAWDATA,
             path_output=PATH_OUTPUT,
             online=TRUE,
             path_sa_file=PATH_SA_FILE,
             path_pf_file=PATH_PF_FILE,
             tlag_meth=2,
             despike_meth="VM97",
             detrend_meth="BA",
             tilt_correction_meth="PF")
             
## End(Not run)