Ecosystem Gas Fluxes Calculations for Closed Loop Chamber Setup
Calculates ecosystem gas fluxes
check the items inside flux_fun_check
filter cut data before calculating fluxes
Calculates difference between fluxes
wet air correction
to check the type of fit
Fitting a model to the gas concentration curve and estimating the slop...
Fitting a model to the gas concentration curve and estimating the slop...
linear fit to gas concentration over time
quadratic fit to gas concentration over time
Fitting a model to the gas concentration curve and estimating the slop...
Fitting a model to concentration data and estimating the slope
Counts quality flags
Fortify fluxes with exponential fit
Fortify fluxes with linear fit
Fortify fluxes with a quadratic fit
Fortify fluxes for visual evaluation
checking that arguments and columns are in the correct class
Calculates GEP
Calculates GPP
Standardizes CO2 fluxes at fixed PAR values
Using an already existing end column to slice measurements
Using a fixed measurement length to slice the measurements
Matching continuously measured fluxes with measurement IDs and meta da...
prepares text to print for flux_plot function
prepares text to print for flux_plot function
prepares text to print in flux_plot
prepares text to print in flux_plot
creates the flag column to be used by flux_plot
print plots in a single long pdf
print plots in pdf
Plotting fluxes for visual evaluation
Printing plot
quality assessment for the slopes estimated by flux_fitting
selecting linear slope with kappamax method
quality assessment for the slopes estimated by flux_fitting
quality assessment for the slopes estimated by flux_fitting
Assessing the quality of the fits
Unit conversion coefficient for fluxes
fluxible: Ecosystem Gas Fluxes Calculations for Closed Loop Chamber Se...
From raw gas concentration over time to clean fluxes
Toolbox to process raw data from closed loop flux chamber (or tent) setups into ecosystem gas fluxes usable for analysis. It goes from a data frame of gas concentration over time (which can contain several measurements) and a meta data file indicating which measurement was done when, to a data frame of ecosystem gas fluxes including quality diagnostics. Organized with one function per step, maximizing user flexibility and backwards compatibility. Different models to estimate the fluxes from the raw data are available: exponential as described in Zhao et al (2018) <doi:10.1016/j.agrformet.2018.08.022>, exponential as described in Hutchinson and Mosier (1981) <doi:10.2136/sssaj1981.03615995004500020017x>, quadratic, and linear. Other functions include quality assessment, plotting for visual check, calculation of fluxes based on the setup specific parameters (chamber size, plot area, ...), gross primary production and transpiration rate calculation, and light response curves.
Useful links