flux_fortify

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_fortify function

<dl><dt>slopes_df</dt>
<dd>dataset containing slopes,
with flags produced by flux_quality</dd>
<dt>f_conc</dt>
<dd>column with gas concentration</dd>
<dt>f_datetime</dt>
<dd>column with datetime of each data point</dd>
<dt>f_ylim_upper</dt>
<dd>y axis upper limit</dd>
<dt>f_ylim_lower</dt>
<dd>y axis lower limit</dd>
<dt>f_facetid</dt>
<dd>character vector of columns to use as facet IDs. Note that
they will be united, and that has to result in a unique facet ID for each
measurement. Default is <code>f_fluxid</code></dd></dl>

Arguments

Fortify fluxes for visual evaluation — flux_fortify

<dl>

<dt>slopes_df</dt>
<dd>dataset containing slopes,
with flags produced by flux_quality</dd>


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


<dt>f_datetime</dt>
<dd>column with datetime of each data point</dd>


<dt>f_ylim_upper</dt>
<dd>y axis upper limit</dd>


<dt>f_ylim_lower</dt>
<dd>y axis lower limit</dd>


<dt>f_facetid</dt>
<dd>character vector of columns to use as facet IDs. Note that
they will be united, and that has to result in a unique facet ID for each
measurement. Default is <code>f_fluxid</code></dd>

</dl>

flux_fortify: Fortify fluxes for visual evaluation

Description

Usage

Arguments