Applied Statistical Methods - Notebook 6

Problem 1: Sire Model

Use the following dataset to predict breeding values using a sire model. The dataset is available from

https://charlotte-ngs.github.io/asmss2023/data/asm_ped_sim_data.csv 

Hints

• The variance component \(\sigma_s^2\) of the sire effect can be assumed to be \(2.25\).
• The variance component \(\sigma_e^2\) of the random resiudals is \(36\).
• Sex is modelled as a fixed effect.
• The sire pedigree relationship can be computed using the pedigreemm package.

Your Solution

• Read the data

• Compute the inverse sire relationship matrix

• Setup the mixed model equations

• Solve mixed model equations

Problem 2: Animal Model

Use the same dataset as in Problem 1 to predict breeding values, but use an animal model instead of a sire model. The dataset is available from

https://charlotte-ngs.github.io/asmss2023/data/asm_ped_sim_data.csv 

Hints

• The variance component \(\sigma_u^2\) of the breeding value can be assumed to be \(9\).
• The variance component \(\sigma_e^2\) of the random resiudals is \(36\).
• Sex is modelled as a fixed effect.
• The numerator relationship matrix can be computed using the pedigreemm package.

Your Solution

• Read the data

• Compute the inverse sire relationship matrix

• Setup the mixed model equations

• Solve mixed model equations

Problem 3: Model Comparison

Compare the order of the predicted breeding values for the sires from the sire model and from the animal model.

Your Solution

• Compare both ordered vectors of predicted breeding values

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Latest Changes: 2023-05-14 09:02:31 (pvr)