Add files for AGEC-LCI tutorial

README.md

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-This is a minimal example of a book based on R Markdown and **bookdown** (https://github.com/rstudio/bookdown). Please see the page "[Get Started](https://bookdown.org/yihui/bookdown/get-started.html)" at https://bookdown.org/yihui/bookdown/ for how to compile this example into HTML. You may generate a copy of the book in `bookdown::pdf_book` format by calling `bookdown::render_book('index.Rmd', 'bookdown::pdf_book')`. More detailed instructions are available here https://bookdown.org/yihui/bookdown/build-the-book.html.
+This is a tutorial for AGEC-LCI.
 
-You can find the preview of this example at https://bookdown.org/yihui/bookdown-demo/.
+This document can be accessed following this link.

_bookdown.yml

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 language:
   ui:
     chapter_name: "Section "
+output_dir: docs
 delete_merged_file: true
 new_session: yes
 rmd_files:

agec-lci-tutorial.log

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-This is XeTeX, Version 3.14159265-2.6-0.999991 (TeX Live 2019/W32TeX) (preloaded format=xelatex 2020.3.31)  8 APR 2020 23:09
+This is XeTeX, Version 3.14159265-2.6-0.999991 (TeX Live 2019/W32TeX) (preloaded format=xelatex 2020.3.31)  8 APR 2020 23:44
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docs/01-intro.md

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+
+
+# Introduction
+
+AGEC-LCI is a VBA application hosted in Microsoft Excel that computes emissions generated from the application of soil amendments, fertilizers and metal-based fungicides in agriculture (Figure \@ref(fig:agec-lci-emissions)).
+
+<div class="figure" style="text-align: center">
+<img src="Figures/agec_lci_emissions.png" alt="Emissions Computed by AGEC-LCI" width="95%" />
+<p class="caption">(\#fig:agec-lci-emissions)Emissions Computed by AGEC-LCI</p>
+</div>
+
+
+A state of the art analysis of the models for computing direct field emission from fertilizers, pesticides and soil amendments was carried out. Acknowledging that agricultural emissions are site- and time dependent, a parsimonious approach was considered for the selection of the models (Table \@ref(tab:agec-models)). See [Section](#selected-methods) \@ref(selected-methods) for more details on the selected models.
+
+Table: (\#tab:agec-models) Selected models for calculating agricultural emissions and comparison with LCI databases
+
+
+|Emission|![](Figures/agri-footprint.png) [agri footprint](https://www.agri-footprint.com/){target="_blank"} [@durlinger2017]|![](Figures/ecoinvent.png) [ecoinvent v3](https://www.ecoinvent.org/){target="_blank"} [@nemecek2011]|![](Figures/agribalyse.png) [AGRIBALYSE ®](https://www.ademe.fr/en/expertise/alternative-approaches-to-production/agribalyse-program){target="_blank"} [@Koch2015]|![](Figures/WFLDB.png) [WFLDB](https://quantis-intl.com/tools/databases/wfldb-food/){target="_blank"} [@nemecek2014]|![](Figures/agec_lci_logo.png) AGEC-LCI|
+|------------|----------------|------------|-------------|------------|-----------------|
+|Ammonia (NH~3~)|IPCC (2006)|Agrammon (Tier 3 methodology for Switzerland)|EMEP Tier 2 (EEA 2009)|EMEP Tier 2 (EEA 2013)|EMEP Tier 2 (EEA 2009 & EEA 2013)| 
+|Nitrous oxide (N~2~O)|IPCC (2006)|IPCC (2006) crops: Tier 1 animals: Tier 2|IPCC (2006) crops: Tier 1 animals: Tier 2|IPCC (2006) crops: Tier 1 animals: Tier 2|"IPCC (2006) crops: Tier 1^(a)^|
+|Nitrate (NO~3~^-^)|IPCC (2006)|Europe: SALCA-Nitrate (Richner et al. 2014), Other countries: SQCB (Faist et al, 2009)|Annual French crops: COMIFER 2001 adjusted (Tailleur et al. 2012),Permanent crops: SQCB (Faist et al, 2009)|Europe: SALCA-Nitrate (Richner et al. 2014), Other countries: SQCB (Faist et al, 2009)|SQCB (Faist et al, 2009)|
+|Phosphorus (P,PO~4~^3-^)|(Struijs, Beusen, Zwart, & Huijbregts, 2011)|SALCA-P (Prasuhn, 2006)|SALCA-P (Prasuhn, 2006)|SALCA-P (Prasuhn, 2006)|SALCA-P (Prasuhn, 2006)|SALCA-P (Prasuhn, 2006)|
+|Heavy metals (Cd, Cr, Cu, Hg, Ni, Pb, Zn)|(Mels et al., 2008, Romkens & Rietra, 2008, Nemecek & Schnetzer, 2012)|SALCA method (Freiermuth, 2006)|SALCA method (Freiermuth, 2006)|SALCA method (Freiermuth, 2006)|SALCA method (Freiermuth, 2006)|
+|Methane (CH~4~)|Dutch National Inventory Reports|IPCC (2006) Tier 2|IPCC (2006) Tier 2|IPCC (2006) Tier 2|-|
+|Synthetic pesticides|100 % of the substance emitted to agricultural soil|100 % of the substance emitted to agricultural soil|100 % of the substance emitted to agricultural soil|100 % of the substance emitted to soil^(b)^|-|
+
+
+(a): The AGEC-LCI tool does not compute enteric emissions of livestock.
+
+(b): Rule followed in the first and second release of the WFLDB. The third release will follow the rules defined in Glasgow workshops [@nemecek2014].
+
+
+
+
+
+

docs/02-instructions-pdf.md

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+
+
+# Instructions for use {#instructions}
+
+
+#### Step 1 {-}
+
+Unzip the compressed folder AGEC-LCI_v1_0.zip that you got from [this site](){target="_blank"}, then open the file AGEC-LCI_v1_0.xlsm (Figure \@ref(fig:agec-icon)).
+
+\begin{figure}[ht]
+
+{\centering \includegraphics[width=0.15\linewidth]{Figures/agec_lci_icon} 
+
+}
+
+\caption{AGEC-LCI is stored in a macro-enabbled workbook}(\#fig:agec-icon)
+\end{figure}
+
+
+
+#### Step 2 {-}
+
+Click on the Launch AGEC-LCI user interface button at the top of README-RUN worksheet of AGEC-LCI_v1_0.xlsm (Figure \@ref(fig:agec-lci-step1)). 
+
+\begin{figure}[ht]
+
+{\centering \includegraphics[width=0.85\linewidth]{Figures/agec_lci_step1} 
+
+}
+
+\caption{Launch AGEC-LCI user interface}(\#fig:agec-lci-step1)
+\end{figure}
+
+
+#### Step 3 {-}
+
+The AGEC-LCI user interface will be displayed (Figure \@ref(fig:agec-lci-step2)).
+
+\begin{figure}[ht]
+
+{\centering \includegraphics[width=0.65\linewidth]{Figures/agec_lci_step2} 
+
+}
+
+\caption{AGEC-LCI user interface}(\#fig:agec-lci-step2)
+\end{figure}
+
+AGEC-LCI allows the user to select inputs from a database composed of 25 crops, 42 fertilizers, 6 metal-based fungicides and the pedo-climatic characteristics of 5 French regions according to data from AGRIBALYSE [@Koch2015]. Furthermore, the user is allowed to add crops, regions and other inputs not available in the accompanying database. 
+
+
+#### Step 4 {-}
+
+You will be asked to give a short name for your current project. It is advised to give a short and meaningful name, because it will be part of the name of the reports and the process generated (Figure \@ref(fig:agec-lci-step3)). Click OK to finish the computations.
+
+\begin{figure}[ht]
+
+{\centering \includegraphics[width=6.76in]{Figures/agec_lci_step3} 
+
+}
+
+\caption{Name your current project}(\#fig:agec-lci-step3)
+\end{figure}
+
+#### Step 5 {-} 
+
+Three reports will be generated and stored under the Results folder accompanying this tool (Figure \@ref(fig:agec-lci-step4)). The Results folder will be automatically open at the end of the computation.  
+
+- **Report_Project_Name_YYYY-MM-DD.xlsx**: Contains the user’s inputs and the calculated emissions. The aim of this report is to keep track of the inputs that need to be entered by the LCA practitioner into a LCA software.
+
+- **Report_olca_Project_Name_YYYY-MM-DD.xlsx**: Reports the calculated emissions in an Excel file compatible with openLCA. The importation of this report was tested with openLCA 1.9.0, and the procedure is described in [Section](#import-olca) \@ref(import-olca).
+
+- **Report_SimaPro_Project_Name_YYYY-MM-DD.csv**: Reports the calculated emissions in a csv file compatible with SimaPro. The importation of this csv file was tested with SimaPro 8.5.2.2, it is not guaranteed that it will work in previous versions the software. The procedure for importing this file is described in [Section](#import-simapro) \@ref(import-simapro).
+
+
+\begin{figure}[ht]
+
+{\centering \includegraphics[width=0.95\linewidth]{Figures/age_lci_user_interface} 
+
+}
+
+\caption{Files generated by AGEC-LCI}(\#fig:agec-lci-step4)
+\end{figure}
+
+
+