---
title: "Package Overview"
author: "Elham Ebrahimi"
description: "An overview of the camtrapReport workflow, package architecture, core functionality, and the data quality checks and ecological reports it produces."
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Package Overview}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---
## Introduction

`camtrapReport` is a modular R package for turning camera-trap data into structured, reproducible ecological reports. The package brings together data preparation, data-quality diagnostics, ecological analysis, visualisation, and report generation in a single workflow.

The workflow is built around a central `camReport` object, created with `camData()`. This object stores the input data, metadata, user settings, intermediate outputs, report sections, and analytical modules. From this object, users can generate a Data Status Check report using `status()` and an Ecological Report using `report()`.

```{r package-overview-workflow, echo=FALSE, out.width="100%", fig.align="center", fig.cap="Figure 1. Overview of the camtrapReport workflow, from input camera-trap data to the central camReport object and final report outputs."}
knitr::include_graphics("figures/Figure1.png")
```

Figure 1 summarises the main `camtrapReport` workflow. Camera-trap data are imported with `camData()` and stored in a central `camReport` object. This object supports data-status checks, ecological analyses, visualisation, report customisation, and automated report generation.

## What `camtrapReport` is designed to do

`camtrapReport` is designed to bridge the gap between standardised camera-trap data and reproducible ecological reporting. It helps users assess whether a dataset is complete and internally consistent, and supports the generation of ecological outputs through an automated and reproducible workflow.

The package is intended to support researchers, monitoring practitioners, conservation managers, and the wider camera-trap community by reducing manual reporting effort and improving consistency across projects, sites, survey periods, and species groups.

## Input data

The workflow requires a camera-trap dataset in Camtrap-DP format, provided as a ZIP archive. Optional supporting data, such as habitat information and study-area boundaries, can be added to improve visualisation, ecological analysis, and interpretation.


## Key outputs

### Data Status Check Report

The Data Status Check report evaluates whether a camera-trap dataset is complete, internally consistent, and suitable for ecological analysis and report generation. It summarises data-quality dimensions such as completeness, consistency, annotation quality, validation status, temporal mismatches, spatial outliers, and observation types.


### Ecological Report

The Ecological Report is a structured, article-style document assembled from selected analytical modules. It combines ecological summaries, tables, figures, maps, and narrative text into a reproducible report.


## Modular workflow

`camtrapReport` is built as a modular system. Each report section is generated from one or more modules. A module may contain text, R code, tables, figures, maps, or ecological summaries.

This structure allows users to select, remove, reorder, modify, or add report modules depending on the aims of the project.

New modules can also be added using YAML templates or custom R code, allowing users to extend the report workflow without changing the package core.

## Conclusion

`camtrapReport` provides a unified workflow for moving from camera-trap data to reproducible ecological outputs. By combining data preparation, quality assessment, ecological analysis, visualisation, and report generation in a modular framework, the package helps users produce transparent and consistent reports from camera-trap datasets.

The two main outputs are the Data Status Check report and the Ecological Report. Together, they help users assess data readiness, identify potential issues, and translate camera-trap records into interpretable ecological information.

To learn more, continue to the [Data Status Report](data-status-report.html), [Ecological Report](ecological-report.html), and [How to add new modules?](modules.html) articles.