flux_fitting_hm

Fits the exponential expression to the concentration evolution
<code>C(t) = C_m + (C_z - C_m) exp(-b * t)</code>

internal

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.

Joseph Gaudard

fluxible

Ecosystem Gas Fluxes Calculations for Closed Loop Chamber Setup

flux_fitting_hm function

<dl><dt>conc_df_cut</dt>
<dd>dataframe of gas concentration over time, cut</dd>
<dt>conc_df</dt>
<dd>dataframe of gas concentration over time</dd>
<dt>f_conc</dt>
<dd>column with gas concentration</dd>
<dt>f_start</dt>
<dd>column with datetime when the measurement started</dd>
<dt>f_fluxid</dt>
<dd>column with ID of each flux</dd>
<dt>cz_window</dt>
<dd>window used to calculate Cz, at the beginning of cut window</dd>
<dt>b_window</dt>
<dd>window to estimate b. It is an interval after tz
where it is assumed that C fits the data perfectly</dd>
<dt>roll_width</dt>
<dd>width of the rolling mean for CO2 when looking for tz,
ideally same as cz_window</dd>
<dt>t_zero</dt>
<dd>time at which the slope should be calculated
(for quadratic fit)</dd></dl>

Arguments

Fitting a model to the gas concentration curve and estimating the slope over
time, using the HM model
(Pedersen et al., 2010; Hutchinson and Mosier, 1981). — flux_fitting_hm

<dl>

<dt>conc_df_cut</dt>
<dd>dataframe of gas concentration over time, cut</dd>


<dt>conc_df</dt>
<dd>dataframe of gas concentration over time</dd>


<dt>f_conc</dt>
<dd>column with gas concentration</dd>


<dt>f_start</dt>
<dd>column with datetime when the measurement started</dd>


<dt>f_fluxid</dt>
<dd>column with ID of each flux</dd>


<dt>cz_window</dt>
<dd>window used to calculate Cz, at the beginning of cut window</dd>


<dt>b_window</dt>
<dd>window to estimate b. It is an interval after tz
where it is assumed that C fits the data perfectly</dd>


<dt>roll_width</dt>
<dd>width of the rolling mean for CO2 when looking for tz,
ideally same as cz_window</dd>


<dt>t_zero</dt>
<dd>time at which the slope should be calculated
(for quadratic fit)</dd>

</dl>

Fitting a model to the gas concentration curve and estimating the slope over
time, using the HM model
(Pedersen et al., 2010; Hutchinson and Mosier, 1981).

flux_fitting_hm: Fitting a model to the gas concentration curve and estimating the slope over time, using the HM model (Pedersen et al., 2010; Hutchinson and Mosier, 1981).

Description

Usage

Value

Arguments

References