Module Management

How to add new modules?

The Ecological Report is built from separate report sections, here referred to as modules. Each module is a small report component that can contain explanatory text, R code, or both. This modular structure allows users to extend the report by adding new sections, modifying existing ones, or changing the order in which sections appear.

A new module is defined in a YAML file and then registered with camtrapReport using add_Module(). After the module has been added, it is useful to test it before generating the full report.

The modular structure of camtrapReport allows users to extend the Ecological Report by defining new report sections, registering them as modules, selecting which modules should be included, and then generating the final report.

Figure 1. Modular workflow for defining, registering, selecting, and running report modules in camtrapReport.

Figure 1 summarises how new modules are added to the report workflow. A module can be defined using R code or a YAML file, registered in the module library, added to the main camReport object, tested separately, and then included when generating the final Ecological Report.

1. List existing modules

Before adding a new module, check which modules are already available in the package.

# List all available modules
list_Modules()

# Show all section names used in the report
section_names()

2. Create a new module YAML file

A module can be written as a YAML file. The example below defines a simple module called species_table, which adds a species summary table to the Ecological Report.

Create a file called species_table.yml and save it in your working directory.

name: species_table
title: "Species summary table"
parent: "results"
text: "This section provides a summary of the species detected in the camera-trap dataset, including their taxonomy and total number of captures."

code: |
  #| echo: false
  #| message: false
  #| warning: false
  
  species_table <- object$data_status$Species$Table
  
  if (!is.null(species_table) && nrow(species_table) > 0) {
    knitr::kable(
      species_table,
      caption = "Species detected in the camera-trap dataset."
    )
  } else {
    cat("No species table is available for this dataset.")
  }

The name field defines the internal module name. The title field controls the section title shown in the report. The parent field defines where the module belongs in the report structure, for example under methods or results. The text field adds explanatory text, and the code field contains the R code used to generate the module output.

3. Add the new module

After creating the YAML file, add the module using add_Module(). In this example, the new species_table module is placed before the richness section.

# Add a new module from a YAML file
add_Module(
  x = "species_table.yml",
  before = "richness",
  test = FALSE,
  object = cm
)

# Check whether the module has been added
list_Modules()
section_names()

You can change before = "richness" to another section name if you want the new module to appear elsewhere in the report.

4. Update the current camReport object

If the camReport object was already loaded before adding the module, run setup() again and update the report sections.

# Re-run setup after adding the new module
cm$setup()

# Get all available section names, including the new module
n <- section_names()

# Apply the updated section list to the camReport object
sections(cm, n)

# Check included sections
listReportSections(cm)

5. Test the new module

Before generating the full report, test only the new module. This is useful for checking whether the YAML structure, text, and R code work correctly.

# Test the new module only
testSection(
  cm$reportObjectElements$Modules$species_table,
  object = cm,
  view = TRUE
)

If the module opens correctly in the browser, it can be included in the full report.

6. Generate the full report

After testing, generate the full Ecological Report with the new module included.

# Generate the full report
report(cm, view = TRUE)

This workflow allows users to extend the Ecological Report with project-specific outputs, additional summaries, new figures, or custom interpretation sections.