index.qmd

:::{.callout-note}
This repo is still very much work in progress.
:::

This site contains the documentation for the process rate estimator.
For a detailed (scientific) description of the process rate estimator, see @decock2022process.

The project was done for the [sustainable agro-ecosystems group at ETH Zurich](https://sae.ethz.ch/). While the project documentation is presented on this website, the source code for the process rate estimator in contained in an R package called `PRE`. You can explore said package in [this GitHub repository](https://github.com/damian-oswald/PRE/). A brief instruction of the installation of `PRE` is provided in the next chapter. Meanwhile, the scripts for running the process rate estimator on some collected data are contained by the [main GitHub repository `process-rate-estimator`](https://github.com/damian-oswald/process-rate-estimator/), which also contains this documentation page.

# Introduction

Denitrification is the natural process by which nitrate (NO~3~^-^) in the soil are converted by bacteria into nitrous oxide (N~2~O) or pure nitrigen (N~2~). The latter is called *total denitrification* --- the full process described in @eq-denitrification takes place.

$$
\ce{NO3^- ->[\text{Nitrate}][\text{reductase}] NO2^- ->[\text{Nitrite}][\text{reductase}] NO ->[\text{Nitrite oxide}][\text{reductase}] N2O^- ->[\text{Nitrous oxide}][\text{reductase}] N2}
$${#eq-denitrification}

Denitrification occurs in conditions where oxygen is limited, such as waterlogged soils. It is part of the nitrogen cycle, where nitrogen is circulated between the atmosphere, organisms and the earth.