Package Overview

Introduction

camtrapReport provides a reproducible workflow for turning standardised camera-trap data into structured ecological reports. It brings data-quality checks, ecological summaries, visualisation, and report generation together so that users can move from a Camtrap DP dataset to a documented report without having to assemble each step separately.

The workflow starts with camData(), which creates a camReport object from the input data. The same object is then used to generate two main outputs:

a Data Status Check, created with status(), which helps users identify issues in the data before interpretation or analysis; and
an Ecological Report, created with report(), which combines selected analyses, figures, tables, maps, and explanatory text in a single document.

Input data

The main input is a camera-trap dataset in Camtrap DP format, supplied either as a ZIP archive or as an extracted Camtrap DP directory.

Optional supporting data can also be provided. These include habitat information and a study-area boundary, which can be used in relevant summaries, maps, and ecological analyses.

Bundled example data

The package includes a relationship-preserving subset of the GMU8_LEUVEN Camtrap DP dataset for examples, demonstrations, and automated tests. It contains eight derived camera locations, 87 deployments, 15,492 retained media records, and 11,092 observation records. Bundled habitat data and a derived study-area boundary provide optional inputs for exercising those parts of the workflow. The subset is a software fixture and should not be used for ecological inference; its provenance and transformations are documented in inst/external/README-Leuven-dataset.md in the source repository.

Key outputs

Data Status Check

The Data Status Check is intended to help users inspect the quality and completeness of a dataset before moving on to ecological interpretation. It summarises issues such as missing information, annotation and validation status, temporal inconsistencies, spatial outliers, observation types, and other aspects of data readiness.

It is generated with:

status(cm)

The report is diagnostic rather than inferential: passing the checks does not mean that a sampling design is suitable for every ecological analysis.

Ecological Report

The Ecological Report brings together selected ecological summaries, analyses, figures, tables, maps, and explanatory text in an article-style document.

It is generated with:

report(cm)

The content of the report depends on the selected sections, available data, and analytical settings. Users can therefore adapt the report to the purpose and scope of a particular monitoring project.

Both status() and report() create an HTML file together with the intermediate R Markdown file used to render it. With their default relative filenames, these files are written beside the writable camera-trap data used to create the object. Supply an explicit file stem or an existing output directory through filename to control where the files are written. Package examples copy the bundled data and write generated reports to temporary directories.

Working with the `camReport` object

The camReport object keeps the input data, metadata, settings, and report outputs together during the workflow. For most users, the important point is that the same object can be inspected, adjusted, and then used to regenerate reports with updated settings.

For example, metadata can be viewed or changed with info():

info(cm)

info(cm, name = "authors")

info(cm, name = "authors") <- c(
  "Elham Ebrahimi",
  "Patrick Jansen"
)

Users can also change the taxonomic focus, select years, adjust filters, or choose which report sections should be included before regenerating the report.

A modular reporting workflow

camtrapReport is modular in the sense that a report is assembled from separate sections rather than from one fixed template. Users can keep only the sections relevant to their data and reporting needs, and can omit or reorder sections when needed.

For example:

# Inspect available report sections
section_names()

# Keep only selected sections
n <- section_names(
  keep = c(
    "introduction",
    "methods",
    "study_area"
  )
)

# Apply the selection
sections(cm, n)

# Generate the report
report(cm)

This makes it possible to use the same overall workflow for projects that differ in species, survey duration, spatial extent, available covariates, or reporting objectives.

Users who want to develop or manage additional report modules can find more detail in the Module management and extension guide.

Reproducibility, interpretation, and scope

camtrapReport supports reproducible reporting by applying a consistent workflow from data checking through ecological analysis to report generation. Analytical modules use established ecological and statistical methods, with default settings that provide a common starting point across camera-trap datasets.

Because the workflow is modular, users can select relevant analyses and adjust module-specific settings, species groups, and thresholds according to their data, study design, and analytical objectives. Results should therefore be interpreted in relation to the characteristics of the dataset, sampling design, and assumptions of the selected methods.

General guidance on recording computational environments and managing reproducible research workflows is available from the Reproducible Research CRAN Task View.

Relationship to other camera-trap packages

camtrapReport is intended to complement, rather than replace, existing camera-trap and ecological analysis packages. Different packages address different parts of the workflow.

Area	Examples	Relationship to `camtrapReport`
Standardised camera-trap data	`camtrapdp`	`camtrapReport` uses Camtrap DP as its main input format.
Data management and exploration	`camtrapR`, `ct`, `camtraptor`	These packages provide complementary tools for preparing, exploring, and summarising camera-trap data.
Activity, diversity, abundance, and density analyses	`activity`, `overlap`, `iNEXT`, `camtrapDensity`, `Distance`	Specialised methods can support individual analyses used within a reporting workflow.
Hierarchical and spatial modelling	`unmarked`, `secr`	These packages provide specialised modelling frameworks outside the main reporting role of `camtrapReport`.

The main role of camtrapReport is therefore not to reproduce every specialised method. Its focus is on bringing data checks, selected ecological analyses, visual outputs, metadata, and explanatory text together in a consistent report generated from a standardised dataset.

Conclusion

camtrapReport provides a structured workflow for moving from standardised camera-trap data to quality-checked and reproducible ecological reporting. Its modular design allows the workflow to be adapted to different datasets, monitoring objectives, and analytical needs.

For more detail, see the Data Status Check, Ecological Report, and Module management and extension articles.

Elham Ebrahimi