Spatial modelling improves genomic evaluation in Tanzanian smallholder admixed dairy cattle

Houaga et al. (2025)

Preprint: https://doi.org/10.1101/2025.03.01.640883

This repository contains R scripts used to analyse the data and generate results as presented in the manuscript.

Please note the input performance and genotype data are not publicly available. The data are available from the Africa Asia Dairy Genetic Gains (AADGG) programme AADGG Website based on a research project application.

1. 01_Spatial_Modelling.R: This file contains the code used to generate the mesh, model definition and model fitting.

2. 02_Model_Validation.R: This file contains the code used for cross-validation and forward validation of the models.

3. 03_PCA_Correlations.R: This file contains the code used for Principal Components Analysis, Multi-variate analysis of Variance (MANOVA), and the correlation between estimated genomic breeding values and model components.