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eddy4R.york

Description

eddy4R.york is an R package that extends eddy4R by providing features and helpers that are used to build the WACL-York flux workflows.

The major feature allows for flux workflows to be defined by relatively short configuration scripts, making it simple to iterate on the parameters used, while maintaining reproducibility.

Some other features include:

  • Flexible aggregation periods - def.avg() determines what files are relevant to the user defined aggregation period so inputs can be stored in any time bins e.g. if files are organised into 30 min files, but the user wishes to to calculate fluxes hourly, the correct files will be loaded for this to occur.

  • Support for double rotation - wrap.rot() implements double rotation and wraps it with the existing planar fit capability. Additionally allows for sector or time based changes to planar fit coefficients.

  • Options to restrict time lag ranges via wrap.lag().

  • Error catching and logging

Getting Started

[!NOTE] As eddy4R is provided as a docker image and as such eddy4R.york provides updated image - currently based on the eddy4R:maps image, but this will change to the stable annual releases when available.

Installation

The docker image can be installed using:

docker pull ghcr.io/wacl-york/eddy4r.york:dev

[!NOTE] This example is for the development version of the container, which should be considered ‘unstable’. Packages with a tagged version number will be released in the future, or by request to be able to be included alongside publications.

Run the container

To run the container as an interactive session run the following:

docker run --name eddy4r.york --rm -d -p 8787:8787 -v <extDir>:/home/rstudio/data ghcr.io/wacl-york/eddy4r.york:dev

Where <extDir> is the path to the volume you wish to mount on your machine

Configuring Run Parameters

eddy4R.york uses a parameters list created using def.para(). This is the main input to wrap.towr() and defines all of the settings of the calculation. Creating this configuration looks like:

para = eddy4R.york::def.para(
  DirWrk = "/home/rstudio/data/",
  DirInp = "in/",
  siteName = "MySite",
  analysis = "nitrate_fluxes",
  runID = "standard_run",
  fileMask = "input_%y%m%d_%H%M.csv",
  species = c("NO","NO2"),
  aggregationPeriod = 3600,
  writeFastData = TRUE,
  AlgBase = "trnd",
  idepVar = "unixTime",
  MethRot = "double",
  missingMethod = "mean",
  lagApplyCorrection = TRUE,
  lagApplyRangeLimit = TRUE,
  lagRangeLimit = list(c(0,0),
                      c(0,0),
                      c(-2,-8),
                      c(-4,-10)),
  lagDefaults = c(0,0,-6, -8))

This has set up a run to calculate hourly fluxes of CO2 and O3 as well as sensible and latent heat. It will use using linear detrending, double rotation and perform a lag correction of all the scalars relative to the vertical wind. If the determined lag falls out of the ranges supplied per scalar, a fixed lag will be used instead.

Input Data

Input files contain the following columns. They should all be read by read.csv() as numeric. By default the listed units are expected, but this can be changed by using def.para(unitList = ...)

Column Header Description Unit
unixTime seconds since midnight 1970-01-01 s
veloXaxs x component of the 3D wind* m s-1
veloYaxs y component of the 3D wind* m s-1
veloZaxs z component of the 3D wind* m s-1
tempAir air temperature Kelvin
presAtm atmospheric pressure Pa
distZaxsAbl Atmospheric Boundary Layer Height m
distZaxsMeas measurement height above surface m
rtioMoleDryH2o dry mole water vapour concentration molH2O molDryAir-1
rtioMoleDry{Spc} dry mole concentration of other species “spc” mol{spc} molDryAir-1

*x/y/z == u/v/w == east/north/up

Overview of wrap.towr()

wrap.towr() is the function that contains all possible steps of the workflow which are configured .by def.para(). This consists of some initial steps, then a loop around all of the flux aggregation periods that have been defined: