mintyr

mintyr is a high-performance data processing toolkit designed specifically for animal breeding and genomic selection. Leveraging the zero-copy and multi-threading capabilities of data.table, it significantly simplifies the construction of automated data pipelines in large-scale commercial breeding programs (e.g., coordinating data across nucleus and multiplier farms, or handling multi-trait growth test records).

The package is not only highly optimized for iterative analysis workflows with the ASReml-R package (supporting dynamic modeling and multi-trait/multi-breed nested grouping), but is also capable of generating and batch-exporting formatted phenotypic data files required for automated pipeline analyses in other mainstream command-line breeding software (e.g., HIBLUP, DMU).

✨ Key Features

mintyr covers five critical stages in the lifecycle of breeding data analysis:

🚀 High-Performance Data Importing (import_xlsx, import_csv)

• Native support for merging multiple files and sheets simultaneously.
• Automatically appends source tracking columns (excel_name, sheet_name) to prevent data confusion across different farms or batches.
• Utilizes OpenMP multi-threading and in-place data.table conversion for a minimal memory footprint.

🔄 Automated Data Reshaping & Nesting (w2l_nest, c2p_nest, r2p_nest)

• c2p_nest: Column-to-pairs nested transformation that automatically renames feature columns, providing standard uniform inputs for iterative multi-trait genetic correlation evaluations.
• w2l_nest / w2l_split: Wide-to-long format transformations with subsetting and nesting by grouping variables (e.g., farm, breed, or line).

🧪 Cross-Validation & Model Evaluation (split_cv, nest_cv)

• Provides streamlined k-fold cross-validation and repeated CV splitting tailored for nested data.table structures, facilitating the evaluation of breeding value prediction accuracy (GP).

📊 Batch Exporting for Breeding Software (export_nest, export_list)

• Automatically builds local folder hierarchies and batch-exports data based on nested groups or list structures (e.g., tempdir()/Line/Breed/data.txt), providing seamless text-file preparation to bridge the gap with command-line driven breeding evaluation software like HIBLUP and DMU.

🛠️ Phenotypic Statistics & Preprocessing (top_perc, format_digits, get_path_info)

• Quickly extracts the top N% performing individuals for specific traits, supporting independent extraction by analytical groups (e.g., different test batches), alongside robust number formatting and path-parsing utilities.

📥 Installation

You can install this package from either CRAN or GitHub:

### From CRAN
install.packages("mintyr")
### From GitHub
pak::pak("tony2015116/mintyr")

📋️ Cheat Sheet

🤝 Acknowledgments

Special thanks to AI assistance, for helping transform the initial concepts and inspirations for the mintyr package into reality. Their contribution has been invaluable in refining ideas, improving code structure, and crafting documentation.