flux_gep

<a href="https://lifecycle.r-lib.org/articles/stages.html#deprecated"><img src="figures/lifecycle-deprecated.svg?package=fluxible&version=1.3.6" alt="[Deprecated]"></a>
<code>flux_gep</code> was renamed <code>flux_gpp</code> out of consistency with the literature.
Calculate gross ecosystem production (GEP) from net ecosystem
(NEE) exchange and ecosystem respiration (ER) as GEP = NEE - ER.
Datetime and other variables to keep will be taken from the NEE measurement.
Fluxes presents in the dataset that are neither NEE nor ER
(soilR, LRC or other) are not lost.

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_gep function

<dl><dt>fluxes_df</dt>
<dd>a dataframe containing NEE and ER</dd>
<dt>type_col</dt>
<dd>column containing type of flux (NEE or ER)</dd>
<dt>f_datetime</dt>
<dd>column containing start of measurement as datetime</dd>
<dt>f_flux</dt>
<dd>column containing flux values</dd>
<dt>id_cols</dt>
<dd>columns used to identify each pair of ER and NEE</dd>
<dt>nee_arg</dt>
<dd>argument designating NEE fluxes in type column</dd>
<dt>er_arg</dt>
<dd>argument designating ER fluxes in type column</dd>
<dt>cols_keep</dt>
<dd>columns to keep from <code>fluxes_df</code>. Values from NEE row will
be filled in GEP row. <code>none</code> (default) keeps only the columns in <code>id_cols</code>,
flux, type and datetime columns; <code>all</code> keeps all the columns;
can also be a vector of column names.</dd></dl>

Arguments

<a href='https://lifecycle.r-lib.org/articles/stages.html#deprecated'><img src='figures/lifecycle-deprecated.svg' alt='[Deprecated]' /></a>
<code>flux_gep</code> was renamed <code>flux_gpp</code> out of consistency with the literature.
Calculate gross ecosystem production (GEP) from net ecosystem
(NEE) exchange and ecosystem respiration (ER) as GEP = NEE - ER.
Datetime and other variables to keep will be taken from the NEE measurement.
Fluxes presents in the dataset that are neither NEE nor ER
(soilR, LRC or other) are not lost.

Calculates GEP — flux_gep

<dl>

<dt>fluxes_df</dt>
<dd>a dataframe containing NEE and ER</dd>


<dt>type_col</dt>
<dd>column containing type of flux (NEE or ER)</dd>


<dt>f_datetime</dt>
<dd>column containing start of measurement as datetime</dd>


<dt>f_flux</dt>
<dd>column containing flux values</dd>


<dt>id_cols</dt>
<dd>columns used to identify each pair of ER and NEE</dd>


<dt>nee_arg</dt>
<dd>argument designating NEE fluxes in type column</dd>


<dt>er_arg</dt>
<dd>argument designating ER fluxes in type column</dd>


<dt>cols_keep</dt>
<dd>columns to keep from <code>fluxes_df</code>. Values from NEE row will
be filled in GEP row. <code>none</code> (default) keeps only the columns in <code>id_cols</code>,
flux, type and datetime columns; <code>all</code> keeps all the columns;
can also be a vector of column names.</dd>

</dl>

flux_gep: Calculates GEP

Description

Usage

Value

Arguments