flux_fitting: Fitting a model to concentration data and estimating the...

In fluxible: Ecosystem Gas Fluxes Calculations for Closed Loop Chamber Setup

Fitting a model to concentration data and estimating the slope

Description

Fits gas concentration over time data with a model (exponential, quadratic or linear) and provides the slope later used to calculate gas fluxes with flux_calc

Usage

flux_fitting(
  conc_df,
  f_conc = f_conc,
  f_datetime = f_datetime,
  f_start = f_start,
  f_end = f_end,
  f_fluxid = f_fluxid,
  fit_type,
  start_cut = 0,
  end_cut = 0,
  t_zero = 0,
  cz_window = 15,
  b_window = 10,
  a_window = 10,
  roll_width = 15
)

Arguments

conc_df	dataframe of gas concentration over time
f_conc	column with gas concentration data
f_datetime	column with datetime of each concentration measurement Note that if there are duplicated datetime in the same f_fluxid only the first row will be kept
f_start	column with datetime when the measurement started (ymd_hms)
f_end	column with datetime when the measurement ended (ymd_hms)
f_fluxid	column with ID of each flux
fit_type	exp_zhao18, exp_tz, exp_hm, quadratic or linear. exp_zhao18 is using the exponential model C(t) = C_m + a (t - t_z) + (C_z - C_m) exp(-b (t - t_z)) from Zhao et al (2018). expt_tz is a modified version which allows the user to fix t_zero: C(t) = C_m + a * t + (C_z - C_m) exp(-b * t) exp_hm is using the HM model (Pedersen et al., 2010; Hutchinson and Mosier, 1981) C(t) = C_m + (C_z - C_m) exp(-b * t) exponential is equal to exp_zhao18, for backwards compatibility
start_cut	time to discard at the start of the measurements (in seconds)
end_cut	time to discard at the end of the measurements (in seconds)
t_zero	time at which the slope should be calculated (for quadratic, exp_tz and exp_hm fits)
cz_window	window used to calculate Cz, at the beginning of cut window (exp_zhao18 and exp_tz fits)
b_window	window to estimate b. It is an interval after tz where it is assumed that the model fits the data perfectly (exp_zhao18 and exp_tz fits)
a_window	window at the end of the flux to estimate a (exp_zhao18 and exp_tz fits)
roll_width	width of the rolling mean for gas concentration when looking for tz, ideally same as cz_window (exp_zhao18 and exp_tz fits)

Value

a dataframe with the slope at t zero (f_slope), a datetime column of t zero (f_start_z), a factor column indicating the cuts (f_cut), the time in seconds since the start of the measurement (f_time), the modeled fit (f_fit), the modeled slope (f_fit_slope), the parameters of the fit depending on the model used, and any columns present in the input. The type of fit is added as an attribute for use by the other functions.

References

Pedersen, A.R., Petersen, S.O., Schelde, K., 2010. A comprehensive approach to soil-atmosphere trace-gas flux estimation with static chambers. European Journal of Soil Science 61, 888–902. https://doi.org/10.1111/j.1365-2389.2010.01291.x

Hutchinson, G.L., Mosier, A.R., 1981. Improved Soil Cover Method for Field Measurement of Nitrous Oxide Fluxes. Soil Science Society of America Journal 45, 311–316. https://doi.org/10.2136/sssaj1981.03615995004500020017x

Zhao, P., Hammerle, A., Zeeman, M., Wohlfahrt, G., 2018. On the calculation of daytime CO2 fluxes measured by automated closed transparent chambers. Agricultural and Forest Meteorology 263, 267–275. https://doi.org/10.1016/j.agrformet.2018.08.022

Examples

data(co2_conc)
flux_fitting(co2_conc, conc, datetime, fit_type = "exp_zhao18")
flux_fitting(co2_conc, conc, datetime,  fit_type = "quadratic",
t_zero = 10, end_cut = 30)

fluxible documentation built on June 25, 2025, 1:08 a.m.