flux_quality_kappamax

selecting linear slope with kappamax method

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_quality_kappamax function

<dl><dt>slopes_df</dt>
<dd>dataset containing slopes</dd>
<dt>f_slope</dt>
<dd>column containing the slope of each flux
(as calculated by the flux_fitting function)</dd>
<dt>f_fit</dt>
<dd>column containing the modeled data (exponential fits)</dd>
<dt>f_fluxid</dt>
<dd>column of ID for each measurement</dd>
<dt>f_slope_lm</dt>
<dd>column containing the linear slope of each flux</dd>
<dt>f_fit_lm</dt>
<dd>column with the fit of the linear model.</dd>
<dt>f_b</dt>
<dd>column containing the b parameter of the exponential expression</dd>
<dt>force_exp</dt>
<dd>vector of fluxIDs for which the exponential slope should be
used by the user's decision (kappamax method)</dd>
<dt>fit_type</dt>
<dd>model fitted to the data, linear, quadratic or exponential.
Will be automatically filled if <code>slopes_df</code> was produced using
flux_fitting</dd>
<dt>instr_error</dt>
<dd>error of the instrument, in the same unit as the
gas concentration</dd>
<dt>name_df</dt>
<dd>name of <code>slopes_df</code></dd></dl>

Arguments

selecting linear slope with kappamax method — flux_quality_kappamax

<dl>

<dt>slopes_df</dt>
<dd>dataset containing slopes</dd>


<dt>f_slope</dt>
<dd>column containing the slope of each flux
(as calculated by the flux_fitting function)</dd>


<dt>f_fit</dt>
<dd>column containing the modeled data (exponential fits)</dd>


<dt>f_fluxid</dt>
<dd>column of ID for each measurement</dd>


<dt>f_slope_lm</dt>
<dd>column containing the linear slope of each flux</dd>


<dt>f_fit_lm</dt>
<dd>column with the fit of the linear model.</dd>


<dt>f_b</dt>
<dd>column containing the b parameter of the exponential expression</dd>


<dt>force_exp</dt>
<dd>vector of fluxIDs for which the exponential slope should be
used by the user's decision (kappamax method)</dd>


<dt>fit_type</dt>
<dd>model fitted to the data, linear, quadratic or exponential.
Will be automatically filled if <code>slopes_df</code> was produced using
flux_fitting</dd>


<dt>instr_error</dt>
<dd>error of the instrument, in the same unit as the
gas concentration</dd>


<dt>name_df</dt>
<dd>name of <code>slopes_df</code></dd>

</dl>

flux_quality_kappamax: selecting linear slope with kappamax method

Description

Usage

Arguments