LTER Synthesis working group -- The Flux Gradient Project: Understanding the methane sink-source capacity of natural ecosystems

PIs:

• Sparkle L. Malone, Assistant Professor, Yale University
• Jackie H. Matthes, Senior Scientist, Harvard University

Project Summary

• https://lternet.edu/working-groups/the-flux-gradient-project/

Data Frame Organization

• Column name should use snake case include units, last "_" proceeds units (i.e. var_molperm3)
• no "- or /" in column names

Workflow Folder

1. flow.neon.data.download.R Downloads and unzips NEON HDF5 (eddy covariance files) files for all sites and time periods of interest. ALSO downloads all required MET data products that are not in the bundled HDF5 file.
2. flow.neon.data.unzip.R Unzips all downloaded NEON data files.
3. flow.neon.data.extract.R Extracts and stacks downloaded and unzipped data into R objects for each data averaging interval, saved in their own RData file. These are currently min9.list (9-min/6-min concentrations), min30.list (30-min met and flux data), and min1.list (1-min met data), WS2D (2D wind speed data). Also extracts and saves site attributes from the HDF5 files into an R object called attr.df.
4. flow.neon.data.format.conc.diffs.R Aligns and differences the concentration data among adjacent tower levels (and also the bottom-top levels). Aggregates, interpolates, and computes related meteo and flux quantities to the window of the paired concentration differences. Saves output as SITE_aligned_conc_flux_9min.RData.
5. flow.calc.flag.windprof.R Grab aligned concentration & flux data from Google Drive and calculate the fluxes using wind profile method and adds quality flag columns, month, hour, residual, rmse for calculated fluxes. Save output as SITE_METHOD.RData, where SITE is NEON site code, METHOD is the computation method (e.g. MBR=modified bowen ratio, aero = aerodynamic, windprof=wind profile).
6. flow.calc.flag.aero.R Grab aligned concentration & flux data from Google Drive and calculate the fluxes using aerodynamic method and adds quality flag columns, month, hour, residual, rmse calculated fluxes. Save output as SITE_METHOD.RData, where SITE is NEON site code, METHOD is the computation method (e.g. MBR=modified bowen ratio, aero = aerodynamic, windprof=wind profile).
7. flow.calc.flag.mbr.R Grab aligned concentration & flux data from Google Drive and calculate the fluxes using modified bowen ratio method and adds quality flag columns, month, hour, residual, rmse calculated fluxes. Save output as SITE_METHOD.RData, where SITE is NEON site code, METHOD is the computation method (e.g. MBR=modified bowen ratio, aero = aerodynamic, windprof=wind profile).
8. flow.flag.flux.stats.R Grab SITE_METHOD.Rdata from Google Drive and adds quality flag columns, month, hour, residual, rmse. MOVE TO CALL THESE FUNCTIONS WHEN FLUXES ARE CALCULATED
9. flow.eval.plots.R Grad SITE_METHOD.Rdata and make 1to1 plots, bar plots, light response curves, temperature response curves, dirurnal plots. MOVE TO EXPLORATORY

Function Folder

• Use hierarchical naming with the active verb first, i.e. "flag.iqr.R"
• This is where all functions called by flow. scripts in Workflow Folder are stored

Exploratory Folder

• Wild West, this is where preliminary functions and workflows are stored

Deprecated Folder

• This is where unused workflows and functions are stored

NOTE: Feel free to contact Nick and Angel during their office hours for coding/git help

NEON Data Products

ADD LINKS TO NEON DATA PRODUCTS PAGE

Supplementary Resources

NCEAS Scientific Computing Support Team page link