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noctiluc3nt committed Sep 17, 2024
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2 changes: 1 addition & 1 deletion docs/index.html
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Expand Up @@ -236,7 +236,7 @@ <h1><span class="header-section-number">1</span> Introduction<a href="index.html
This gitbook provides an overview about the setup, post-processing and meteorological evaluation of EC measurements, which can be used for research and teaching. The structure of this gitbook is detailed in figure 1. All described functions are implemented in the R-package Reddy, which was specially developed to allow a reproducible and comprehensive analysis of EC measurements.
Each chapter covers one topic and is also available as jupyter notebook, which can be downloaded <a href="https://github.com/noctiluc3nt/ec_analyze/tree/main/notebooks">here</a>.</p>
<div class="figure">
<img src="./figures/schema/schema.png" alt="" />
<img src="figures/schema/schema2.png" alt="" />
<p class="caption">Figure 1: Overview of the topics in this gitbook and the functionality of the Reddy package</p>
</div>
<p><strong>Installation of the Reddy package:</strong> The Reddy package can be installed directly from github:</p>
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2 changes: 1 addition & 1 deletion docs/quadrant-analysis.html
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Expand Up @@ -346,7 +346,7 @@ <h3> References<a href="references.html#references" class="anchor-section" aria-
<p>Jimenez, J. 2018. “Coherent structures in wall-bounded turbulence.” <em>J Fluid Mech</em> 842 (P1). <a href="https://doi.org/10.1017/jfm.2018.144">https://doi.org/10.1017/jfm.2018.144</a>.</p>
</div>
<div id="ref-Katul1997">
<p>Katul, G., G. Kuhn, J. Schieldge, and C.-I. Hsieh. 1997. “The ejection-sweep character of scalar fluxes in the unstable surface layer.” <em>Boundary-Layer Meteorol</em> 83: 1–26.</p>
<p>Katul, G., G. Kuhn, J. Schieldge, and C.-I. Hsieh. 1997. “The ejection-sweep character of scalar fluxes in the unstable surface layer.” <em>Boundary-Layer Meteorol</em> 83: 1–26. <a href="https://doi.org/10.1023/A:1000293516830">https://doi.org/10.1023/A:1000293516830</a>.</p>
</div>
<div id="ref-Li2011">
<p>Li, D., and E. Bou-Zeid. 2011. “Coherent Structures and the Dissimilarity of Turbulent Transport of Momentum and Scalars in the Unstable Atmospheric Surface Layer.” <em>Boundary-Layer Meteorol</em> 140: 243–62. <a href="https://doi.org/10.1007/s10546-011-9613-5">https://doi.org/10.1007/s10546-011-9613-5</a>.</p>
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2 changes: 1 addition & 1 deletion docs/references.html
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Expand Up @@ -245,7 +245,7 @@ <h1><span class="header-section-number">9</span> References<a href="references.h
<p>Jimenez, J. 2018. “Coherent structures in wall-bounded turbulence.” <em>J Fluid Mech</em> 842 (P1). <a href="https://doi.org/10.1017/jfm.2018.144">https://doi.org/10.1017/jfm.2018.144</a>.</p>
</div>
<div>
<p>Katul, G., G. Kuhn, J. Schieldge, and C.-I. Hsieh. 1997. “The ejection-sweep character of scalar fluxes in the unstable surface layer.” <em>Boundary-Layer Meteorol</em> 83: 1–26.</p>
<p>Katul, G., G. Kuhn, J. Schieldge, and C.-I. Hsieh. 1997. “The ejection-sweep character of scalar fluxes in the unstable surface layer.” <em>Boundary-Layer Meteorol</em> 83: 1–26. <a href="https://doi.org/10.1023/A:1000293516830">https://doi.org/10.1023/A:1000293516830</a>.</p>
</div>
<div>
<p>Kljun, N., P. Calanca, M. W. Rotach, and H. P. Schmid. 2015. “A simple two-dimensional parameterisation for Flux Footprint Prediction (FFP).” <em>Geosci Model Dev</em> 8: 3695–3713. <a href="https://doi.org/10.5194/gmd-8-3695-2015">https://doi.org/10.5194/gmd-8-3695-2015</a>.</p>
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344 changes: 344 additions & 0 deletions figures/schema/schema.tex
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Expand Up @@ -72,6 +72,8 @@
\definecolor{lila}{rgb}{0.5,0,0.5}
\definecolor{gray}{rgb}{0.85,0.85,0.85}



%\theoremstyle{definition}
%\newtheorem{theorem}{Theorem}
%\newtheorem{definition}{Definition}
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\centering

\end{figure}



%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\newpage
\begin{figure}[H]
\small
\fontfamily{lmss}\selectfont
\begin{tikzpicture}
\node(data) [text width = 4cm,madrid,anchor=north west] at (0,0) { \textbf{Data acquisition and post-processing}} ;
\node(analysis) [text width = 4cm, orange,anchor=north west] at (5,0) { \textbf{Turbulence analysis \\ and diagnostics} };
\node(application) [text width = 4.5cm,darkred,anchor=north west] at (10,0) { \textbf{Turbulence modelling and energy balance} };

%----------------------------------------------------------------
\draw [arrows = {-Computer Modern Rightarrow[line cap=round]},gray,line width=1.6mm]
(3.9,-0.5) -- (4.9,-0.5);
\draw [arrows = {-Computer Modern Rightarrow[line cap=round]},gray,line width=1.6mm]
(8.9,-0.5) -- (9.9,-0.5);

\draw [gray,line width=0.5mm,dashed]
(4.6,-1.23) -- (4.6,-5.2);
\draw [gray,line width=0.5mm,dashed]
(9.6,-1.23) -- (9.6,-5.2);
\draw [gray,line width=0.5mm,dashed]
(0,-1.1) -- (14.2,-1.1);
\draw [gray,line width=0.5mm,dashed]
(0,-5.3) -- (14.2,-5.3);

%--------------------------------------------------------------------
\node(raw) [text width = 4cm,madrid,draw,anchor=north west] at (0,-1.3) { \textbf{Raw data processing } \\
$\cdot$ correction methods \\
$\cdot$ quality control / flagging \\
$\cdot$ time averaging \\
$\cdot$ flux calculation \\
$\cdot$ gap-filling

% $\cdot$ despiking \\
% $\cdot$ lag-time correction \\
% $\cdot$ detrending \\
% $\cdot$ coordinate rotation \\
% $\cdot$ time averaging $\rightarrow$ mean \\
% $\cdot$ calculation of covariances \\
% $\cdot$ WPL correction \\
% $\cdot$ SND correction \\
% $\cdot$ unit conversion $\rightarrow$ flux \\
% $\cdot$ quality flagging \\
% $\cdot$ flux gap-filling \\
% $\cdot$ spectral corrections
} ;

\node(download) [below=0.09cm of raw, text width = 4cm,madrid,draw] { \textbf{Eddy-covariance output} \\
% $\cdot$ from FLUXNET
} ;


%---------------------------------------------------------------------
\node(diagnostics) [text width = 4cm,orange,draw,anchor=north west] at (5,-1.3) { \textbf{Turbulence diagnostics} \\
% $\cdot$ stability parameter \\
% $\cdot$ TKE, friction velocity, ...
} ;
\node(qa) [text width = 4cm,orange,draw,below=0.233cm of diagnostics] { \textbf{Quadrant analysis} \\
% $\cdot$ coherent structures \\
% $\cdot$ organization ratio
} ;
\node(spectra) [text width = 4cm,orange,draw,below=0.233cm of qa] { \textbf{Spectra} \\
% $\cdot$ averaged FFT spectra\\
% $\cdot$ MRD spectra / wavelets
} ;
\node(aniso) [text width = 4cm,orange,draw,below=0.233cm of spectra] { \textbf{Anisotropy analysis} \\
% $\cdot$ Reynolds stress tensor\\
% %$\cdot$ turbulence anisotropy \\
% $\cdot$ barycentric map
} ;
\node(footprint) [text width = 4cm,orange,draw,below=0.233cm of aniso] { \textbf{Flux footprint} \\
% $\cdot$ 2D flux footprint
} ;

%---------------------------------------------------------------

\node(param) [text width = 4cm,darkred,draw,anchor=north west] at (10,-1.3) { \textbf{Turbulence modelling / \\ parameterizations} \\
% $\cdot$ bulk closures \\
% $\cdot$ eddy-diffusivity closures \\
% $\cdot$ flux-variance relations \\
% $\cdot$ flux-profile relations
} ;
\node(comp) [text width = 4cm,darkred,draw,below=0.175cm of param] { \textbf{Model comparison / \\ verification\\}
% $\cdot$ model data processing
} ;
\node(seb) [text width = 4cm,darkred,draw,below=0.175cm of comp] { \textbf{Surface energy balance} \\
% $\cdot$ radiative fluxes \\
% $\cdot$ residual and closure ratio
} ;
\node(hyrdo) [text width = 4cm,darkred,draw,below=0.175cm of seb] { \textbf{Ecohydrology} \\
% $\cdot$ Bowen ratio \\
% $\cdot$ evaporative fraction\\
% $\cdot$ flux partitioning
} ;


%----------------------------------------------------------
\node(meteo) [text width = 14cm,lila,anchor=north west,draw,align=center] at (0,-5.5) { \textbf{Meteorological and environmental contextualization} \\
% $\cdot$ wind speed profiles, gradients, Richardson number, clear-sky index, ...
} ;


%\draw[->, >=stealth',line width=1.5pt,text width=5cm, align=left] (start) -- (rans) node[midway,right] {\textbf{apply}: \\Reynolds average \\ Boussinesq approximation\\hydrostatic approximation} ;

\end{tikzpicture}
\centering

\end{figure}




\vspace{2cm}
\begin{figure}[H]
\small
\fontfamily{lmss}\selectfont
\begin{tikzpicture}
\node(data) [text width = 4cm,madrid,anchor=north west] at (0,0) { \textbf{Data acquisition and post-processing}} ;
\node(analysis) [text width = 4cm, darkred,anchor=north west] at (5,0) { \textbf{Turbulence analysis \\ and diagnostics} };
\node(application) [text width = 4.5cm,orange,anchor=north west] at (10,0) { \textbf{Turbulence modelling \\ and energy balance} };

%----------------------------------------------------------------
\draw [arrows = {-Computer Modern Rightarrow[line cap=round]},gray,line width=1.6mm]
(3.9,-0.5) -- (4.9,-0.5);
\draw [arrows = {-Computer Modern Rightarrow[line cap=round]},gray,line width=1.6mm]
(8.9,-0.5) -- (9.9,-0.5);

\draw [gray,line width=0.5mm,dashed]
(4.6,-1.23) -- (4.6,-5.2);
\draw [gray,line width=0.5mm,dashed]
(9.6,-1.23) -- (9.6,-5.2);
\draw [gray,line width=0.5mm,dashed]
(0,-1.1) -- (14.2,-1.1);
\draw [gray,line width=0.5mm,dashed]
(0,-5.3) -- (14.2,-5.3);

%--------------------------------------------------------------------
\node(raw) [text width = 4cm,madrid,draw,anchor=north west] at (0,-1.3) { \textbf{Raw data processing } \\
$\cdot$ correction methods \\
$\cdot$ quality control / flagging \\
$\cdot$ time averaging \\
$\cdot$ flux calculation \\
$\cdot$ gap-filling

% $\cdot$ despiking \\
% $\cdot$ lag-time correction \\
% $\cdot$ detrending \\
% $\cdot$ coordinate rotation \\
% $\cdot$ time averaging $\rightarrow$ mean \\
% $\cdot$ calculation of covariances \\
% $\cdot$ WPL correction \\
% $\cdot$ SND correction \\
% $\cdot$ unit conversion $\rightarrow$ flux \\
% $\cdot$ quality flagging \\
% $\cdot$ flux gap-filling \\
% $\cdot$ spectral corrections
} ;

\node(download) [below=0.09cm of raw, text width = 4cm,madrid,draw] { \textbf{Eddy-covariance output} \\
% $\cdot$ from FLUXNET
} ;


%---------------------------------------------------------------------
\node(diagnostics) [text width = 4cm,darkred,draw,anchor=north west] at (5,-1.3) { \textbf{Turbulence diagnostics} \\
% $\cdot$ stability parameter \\
% $\cdot$ TKE, friction velocity, ...
} ;
\node(qa) [text width = 4cm,darkred,draw,below=0.233cm of diagnostics] { \textbf{Quadrant analysis} \\
% $\cdot$ coherent structures \\
% $\cdot$ organization ratio
} ;
\node(spectra) [text width = 4cm,darkred,draw,below=0.233cm of qa] { \textbf{Spectra} \\
% $\cdot$ averaged FFT spectra\\
% $\cdot$ MRD spectra / wavelets
} ;
\node(aniso) [text width = 4cm,darkred,draw,below=0.233cm of spectra] { \textbf{Anisotropy analysis} \\
% $\cdot$ Reynolds stress tensor\\
% %$\cdot$ turbulence anisotropy \\
% $\cdot$ barycentric map
} ;
\node(footprint) [text width = 4cm,darkred,draw,below=0.233cm of aniso] { \textbf{Flux footprint} \\
% $\cdot$ 2D flux footprint
} ;

%---------------------------------------------------------------

\node(param) [text width = 4cm,orange,draw,anchor=north west] at (10,-1.3) { \textbf{Turbulence modelling / \\ parameterizations} \\
% $\cdot$ bulk closures \\
% $\cdot$ eddy-diffusivity closures \\
% $\cdot$ flux-variance relations \\
% $\cdot$ flux-profile relations
} ;
\node(comp) [text width = 4cm,orange,draw,below=0.175cm of param] { \textbf{Model comparison / \\ verification\\}
% $\cdot$ model data processing
} ;
\node(seb) [text width = 4cm,orange,draw,below=0.175cm of comp] { \textbf{Surface energy balance} \\
% $\cdot$ radiative fluxes \\
% $\cdot$ residual and closure ratio
} ;
\node(hyrdo) [text width = 4cm,orange,draw,below=0.175cm of seb] { \textbf{Ecohydrology} \\
% $\cdot$ Bowen ratio \\
% $\cdot$ evaporative fraction\\
% $\cdot$ flux partitioning
} ;


%----------------------------------------------------------
\node(meteo) [text width = 14cm,lila,anchor=north west,draw,align=center] at (0,-5.5) { \textbf{Meteorological and environmental contextualization} \\
% $\cdot$ wind speed profiles, gradients, Richardson number, clear-sky index, ...
} ;


%\draw[->, >=stealth',line width=1.5pt,text width=5cm, align=left] (start) -- (rans) node[midway,right] {\textbf{apply}: \\Reynolds average \\ Boussinesq approximation\\hydrostatic approximation} ;

\end{tikzpicture}
\centering

\end{figure}






\vspace{2cm}
\begin{figure}[H]
\small
\fontfamily{lmss}\selectfont
\begin{tikzpicture}
\node(data) [text width = 4cm,lila,anchor=north west] at (0,0) { \textbf{Data acquisition and post-processing}} ;
\node(analysis) [text width = 4cm, darkred,anchor=north west] at (5,0) { \textbf{Turbulence analysis \\ and diagnostics} };
\node(application) [text width = 4.5cm,orange,anchor=north west] at (10,0) { \textbf{Turbulence modelling \\ and energy balance} };

%----------------------------------------------------------------
\draw [arrows = {-Computer Modern Rightarrow[line cap=round]},gray,line width=1.6mm]
(3.9,-0.5) -- (4.9,-0.5);
\draw [arrows = {-Computer Modern Rightarrow[line cap=round]},gray,line width=1.6mm]
(8.9,-0.5) -- (9.9,-0.5);

\draw [gray,line width=0.5mm,dashed]
(4.6,-1.23) -- (4.6,-5.2);
\draw [gray,line width=0.5mm,dashed]
(9.6,-1.23) -- (9.6,-5.2);
\draw [gray,line width=0.5mm,dashed]
(0,-1.1) -- (14.2,-1.1);
\draw [gray,line width=0.5mm,dashed]
(0,-5.3) -- (14.2,-5.3);

%--------------------------------------------------------------------
\node(raw) [text width = 4cm,lila,draw,anchor=north west] at (0,-1.3) { \textbf{Raw data processing } \\
$\cdot$ correction methods \\
$\cdot$ quality control / flagging \\
$\cdot$ time averaging \\
$\cdot$ flux calculation \\
$\cdot$ gap-filling

% $\cdot$ despiking \\
% $\cdot$ lag-time correction \\
% $\cdot$ detrending \\
% $\cdot$ coordinate rotation \\
% $\cdot$ time averaging $\rightarrow$ mean \\
% $\cdot$ calculation of covariances \\
% $\cdot$ WPL correction \\
% $\cdot$ SND correction \\
% $\cdot$ unit conversion $\rightarrow$ flux \\
% $\cdot$ quality flagging \\
% $\cdot$ flux gap-filling \\
% $\cdot$ spectral corrections
} ;

\node(download) [below=0.09cm of raw, text width = 4cm,lila,draw] { \textbf{Eddy-covariance output} \\
% $\cdot$ from FLUXNET
} ;


%---------------------------------------------------------------------
\node(diagnostics) [text width = 4cm,darkred,draw,anchor=north west] at (5,-1.3) { \textbf{Turbulence diagnostics} \\
% $\cdot$ stability parameter \\
% $\cdot$ TKE, friction velocity, ...
} ;
\node(qa) [text width = 4cm,darkred,draw,below=0.233cm of diagnostics] { \textbf{Quadrant analysis} \\
% $\cdot$ coherent structures \\
% $\cdot$ organization ratio
} ;
\node(spectra) [text width = 4cm,darkred,draw,below=0.233cm of qa] { \textbf{Spectra} \\
% $\cdot$ averaged FFT spectra\\
% $\cdot$ MRD spectra / wavelets
} ;
\node(aniso) [text width = 4cm,darkred,draw,below=0.233cm of spectra] { \textbf{Anisotropy analysis} \\
% $\cdot$ Reynolds stress tensor\\
% %$\cdot$ turbulence anisotropy \\
% $\cdot$ barycentric map
} ;
\node(footprint) [text width = 4cm,darkred,draw,below=0.233cm of aniso] { \textbf{Flux footprint} \\
% $\cdot$ 2D flux footprint
} ;

%---------------------------------------------------------------

\node(param) [text width = 4cm,orange,draw,anchor=north west] at (10,-1.3) { \textbf{Turbulence modelling / \\ parameterizations} \\
% $\cdot$ bulk closures \\
% $\cdot$ eddy-diffusivity closures \\
% $\cdot$ flux-variance relations \\
% $\cdot$ flux-profile relations
} ;
\node(comp) [text width = 4cm,orange,draw,below=0.175cm of param] { \textbf{Model comparison / \\ verification\\}
% $\cdot$ model data processing
} ;
\node(seb) [text width = 4cm,orange,draw,below=0.175cm of comp] { \textbf{Surface energy balance} \\
% $\cdot$ radiative fluxes \\
% $\cdot$ residual and closure ratio
} ;
\node(hyrdo) [text width = 4cm,orange,draw,below=0.175cm of seb] { \textbf{Ecohydrology} \\
% $\cdot$ Bowen ratio \\
% $\cdot$ evaporative fraction\\
% $\cdot$ flux partitioning
} ;


%----------------------------------------------------------
\node(meteo) [text width = 14cm,madrid,anchor=north west,draw,align=center] at (0,-5.5) { \textbf{Meteorological and environmental contextualization} \\
% $\cdot$ wind speed profiles, gradients, Richardson number, clear-sky index, ...
} ;


%\draw[->, >=stealth',line width=1.5pt,text width=5cm, align=left] (start) -- (rans) node[midway,right] {\textbf{apply}: \\Reynolds average \\ Boussinesq approximation\\hydrostatic approximation} ;

\end{tikzpicture}
\centering

\end{figure}






\end{document}
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Expand Up @@ -29,7 +29,7 @@ However, they require a thought-through technical setup and a special post-proce
This gitbook provides an overview about the setup, post-processing and meteorological evaluation of EC measurements, which can be used for research and teaching. The structure of this gitbook is detailed in figure 1. All described functions are implemented in the R-package Reddy, which was specially developed to allow a reproducible and comprehensive analysis of EC measurements.
Each chapter covers one topic and is also available as jupyter notebook, which can be downloaded <a href="https://github.com/noctiluc3nt/ec_analyze/tree/main/notebooks">here</a>.

![Figure 1: Overview of the topics in this gitbook and the functionality of the Reddy package](./figures/schema/schema.png)
![Figure 1: Overview of the topics in this gitbook and the functionality of the Reddy package](./figures/schema/schema2.png)


**Installation of the Reddy package:** The Reddy package can be installed directly from github:
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