---
title: "SoilManageR"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{SoilManageR}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
```

## Introduction

This R package is a compilation of functions to calculate numerical agricultural soil management indicators from on a management timeline of an arable field. The functions can also be used independently of the management timeline to calculate some indicators or parts thereof. Throughout the package, many assumptions were made (e.g. on time to crop establishment). These assumptions are, whenever possible, based on the literature that is cited within the function descriptions. The assumptions are considered to be representative for temperate agroecosystems, for example the Swiss midlands. ![Fig. 1: Contents of the SoilManager package](SoilManager_graphic.png){width="700"} SoilManageR organizes management data in management data frames `management_df()`, from this the indicators can then be calculated. For the calculations there are main functions and helper functions that are called by the main functions (Fig. 1). Both type of functions rely on reference data for their calculations. The package is distributed with some supporting documents.

## Suggested Workflow

### Load and check management data frame

We suggest to start the workflow with importing a `management_df()` from a XLSX template.

```{r import data, eval=FALSE}
library(SoilManageR)

#define path to excel template in the SoilManageR package
internal_path <- "/extdata/SoilManageR_mgmt_data_template_V2.5.xlsx"

#create local path
path_to_xlsx_template <- system.file(internal_path, package = "SoilManageR")

#load management_df
mgmt_data <- management_df_from_excel(path_to_xlsx_template)

```

Then the `management_df()` can be checked for internal consistency with the `check_management_df()` function.

```{r check data, eval=FALSE}
#create management_df from example data (delivered with the package)
mgmt_data <- EXAMPLE_data

#check the consistency of the example data
check_management_df(mgmt_data)
```

### Calculate indicators

When the `management_df()` shows no issues, then all indicators can be calcualted with `calculate_indicators()`

```{r calculate all indicators, eval=FALSE}
calculate_indicators(mgmt_data)
```

Alternatively, the indicators could be calculated individually

```{r calculate some indicators, eval=FALSE}
C_input(mgmt_data)
tillage_intensity(mgmt_data)
soil_cover(mgmt_data)
plant_diversity(mgmt_data,2013,2023)
```

### Access helper functions

All helper functions can be called directly, please check the description of the functions for more information on them.

## Contact

For further information on SoilManageR please contact [olivier.heller\@agroscope.admin.ch](mailto:olivier.heller@agroscope.admin.ch){.email}.