r-InsectLabelR

Create Labels for Insect in Collection.

InsectLabelR: Generate Labels for Insect Pinning

Overview

InsectLabelR is an R package designed to streamline the creation of high-quality labels for insect pinning. By taking a dataset as input, InsectLabelR generates printable labels in PDF format, helping researchers and entomologists maintain accurate and standardized specimen records.

For enhanced accessibility, the package includes a user-friendly Shiny application, which provides a graphical interface for generating labels without requiring programming expertise and detailed user guides in both English and French .

Features

• Create insect pinning labels from dataset inputs.
• Output labels as PDF files, ready for printing.
• Flexible label formatting options.
• User-friendly GUI via the Shiny app InsectLabelR.

Installation

To install the InsectLabelR package, use the following command in R:

# Install from GitHub
devtools::install_github("Nmoiroux/InsectLabelR")

Usage

Using the Shiny App:

The Shiny app provides an intuitive interface for generating insect pinning labels. You can access it online at InsectLabelR or run it locally:

InsectLabelR_App()

Steps to Use the Shiny App:

1. Upload Data: Upload a .csv, .xlsx, or .ods file containing your insect data.
   • If using .xlsx or .ods, select the appropriate sheet containing the dataset.
   • Example datasets are available in the InsectLabelR repository.
2. Configure Printing Parameters: Use a pre-configured table or manually fill out a printing parameters table, specifying:
   • Which fields to print
   • Number of labels per individual
   • Printing order
   • Text formatting (e.g., italics for genus/species).
3. Customize Labels: Adjust label width, height, font size, and more.
4. Generate PDF: Download the formatted labels as a PDF file.

Input Format

Your dataset must include:

1. Data Table: A table with one row per insect and columns describing attributes (e.g., species, collection date).
   • Supported formats: .csv (tab-delimited), .xlsx, .ods.
   • Column names are flexible.
2. Printing Parameters Table: Specifies how data fields appear on labels.
   • Formats: as a sheet in the .xlsx or .ods file containing the Data table, or as a .csv file (tab-delimited).
   • Includes the following columns: field_name, print, label_no, order_lab, and more.
   • Can be configured offline or within the app.

Example data and parameter tables are provided in the InsectLabelR repository.

Example Workflow

1. Download the example dataset: liste_ind_coll_ex.ods.
2. Upload the file and select the sheet "Table_data".
3. Set printing parameters by selecting "Print_parameters_ex1" sheet or configure them manually.
4. Adjust label size, font, and layout as needed.
5. Generate and download the PDF labels.

Usage in R

InsectLabelR provides programmatic access to its core functionality. Below is an example using the create_pdf() function with a dataset embedded in the package.

Example: Generating Labels with Embedded Dataset

# Example dataset path (included in the package)
data_path <- system.file("extdata", "liste_ind_coll_ex.ods", package = "InsectLabelR")

# Load data table
data_table <- readODS::read_ods(data_path, sheet = "Table_data")

# Load print parameter data
par_table <- readODS::read_ods(data_path, sheet = "Print_parameters_ex1")

# Define output file path for the PDF
output_pdf <- "example_labels.pdf"

# Generate labels
InsectLabelR::create_pdf(
  file_out = output_pdf,            # Name of pdf file
  ind_list = data_table ,           # Table of data
  print_info = par_table,           # Table of printing parameters
  font_size = 5,                    # Font size
  lab_width = 15,                   # Width of the labels in mm
  lab_height =12,                   # Height of the labels in mm
  n_col = 8,                        # Number of label columns per row
  hl_col = "orange"                 # Color for highlighted text
) 

This script:

1. Loads an example .ods dataset included in the package.
2. Configures the data and parameter sheets.
3. Defines label size, font, and layout.
4. Outputs the generated labels as a PDF file.

Expected Output

The generated example_labels.pdf file will contain insect pinning labels formatted according to the specified parameters.

Dependencies

• R version >= 4.0.0
• Required packages: dplyr, purrr, stringr, magrittr, shiny

Troubleshooting

• Ensure your dataset and parameters follow the specified structure.
• Avoid special characters in field names to prevent LaTeX rendering issues.
• Ensure you have a compatible installation of pdflatex see https://www.latex-project.org/get/. For Debian or Debian-based (Ubuntu...) Linux distributions, the following commands should ensure a compatible pdflatex install:

sudo apt-get install texlive-latex-base
sudo apt-get install texlive-latex-extra