1. 20 million
data points
can’t be
wrong?
Aur´lien
e
Madouasse
20 million data points can’t be wrong?
Background
Data
Using milk recording data to make better decision on cow
Milk
health
Production
Somatic Cell
Count
Aur´lien Madouasse
e
Reproduction
10th March 2010

2. Fifty Million Frenchmen Can’t Be Wrong
20 million
data points
can’t be They say the French are naughty
wrong?
They say the French are bad
Aur´lien
e
Madouasse They all declare that over there
The French are going mad.
Background
Data
They have a reputation of being very gay
Milk
I just got back from Paris, and I just want to say:
Production
Somatic Cell
...
Count
Reproduction
In Viva la France
They’re full of romance
You’ll find policemen with embroidery on their pants.
And when they start to sing the Marseillaise
They sing it forty different ways
Fifty million Frenchmen can’t be wrong.

3. Fifty Million Frenchmen Can’t Be Wrong
20 million
data points
can’t be
wrong?
Aur´lien
e
Madouasse
Background
Data
Milk
Production
Somatic Cell
Count
Reproduction

4. A cow’s life
20 million
data points
can’t be
wrong?
Aur´lien
e
Madouasse
Background
Data
Milk
Production
Somatic Cell
Count
Reproduction

5. What is Milk Recording?
20 million
data points
can’t be
wrong?
Aur´lien
e
Madouasse
Milk recording is the regular collection of a milk sample
from all lactating cows of a dairy herd
Background
What is measured:
Data
Milk
Milk yield
Production % butterfat, % protein, % lactose
Somatic Cell Somatic cell count
Count
Reproduction
Information collected
Date of birth
Date of calving
Parity

6. What is Milk Recording?
20 million
data points
can’t be
wrong?
Aur´lien
e
Madouasse
Farmers pay for milk recording, in order to:
Background
Data
Adapt management
Identify cows likely to have mastitis
Milk
Production Identify the best producers
Somatic Cell
Count
The information is also used for
Reproduction
Genetic evaluation
Epidemiologic studies

7. Dataset
20 million
data points
can’t be
wrong?
Aur´lien
e
Madouasse The National Milk Records: main provider of milk
Background recording in England and Wales
Data All the data collected by the NMR between January 2004
Milk and December 2006 were purchased:
Production
19,893,093 recordings
Somatic Cell
Count 1,247,427 cows
Reproduction 5,714 herds
⇒ Big!!!

8. Dataset
20 million
data points
can’t be
wrong?
Aur´lien
e
Madouasse The National Milk Records: main provider of milk
Background recording in England and Wales
Data All the data collected by the NMR between January 2004
Milk and December 2006 were purchased:
Production
19,893,093 recordings
Somatic Cell
Count 1,247,427 cows
Reproduction 5,714 herds
⇒ Big!!!

9. Data selection
20 million
data points
can’t be
wrong?
Aim: Obtain a homogeneous dataset and discard unreliable
Aur´lien
e
data
Madouasse
Herds recording:
Background For the 3 complete years
Data On a monthly basis
Milk At least 80 % of Holstein-Friesian cows
Production
Somatic Cell
Milk samples collected on 2 consecutive milkings
Count
Reproduction

10. Data selection
20 million
data points
can’t be
wrong?
Aim: Obtain a homogeneous dataset and discard unreliable
Aur´lien
e
data
Madouasse
Herds recording:
Background For the 3 complete years
Data On a monthly basis
Milk At least 80 % of Holstein-Friesian cows
Production
Somatic Cell
Milk samples collected on 2 consecutive milkings
Count
Reproduction
Final dataset
8,211,988 recordings
483,747 cows
2,128 herds
⇒ Reasonably big!!!

11. Amelia’s problem
20 million
data points
can’t be
wrong?
Aur´lien
e
Madouasse
Background
Data
Milk
Production
Somatic Cell
Count
Reproduction

12. Amelia’s problem
20 million
data points
can’t be
wrong?
Aur´lien
e
Madouasse
Background
Data 50 million Frenchmen
Milk
Production
can’t be wrong!
Somatic Cell What about one
Count
Reproduction
Frenchman with a few
million data points?

13. Amelia’s problem
20 million
data points
can’t be
wrong?
Aur´lien
e
Madouasse
Background
Data
Milk
Production
Somatic Cell
Count
Reproduction

14. Milk Yield
Variation
20 million
data points
can’t be
wrong?
Milk Yield Distribution
Aur´lien
e
Madouasse Milk Yield
Background
Mean ∼ 27 kg/day
Data
Standard deviation ∼ 8.5 kg
Milk
Production
Somatic Cell
Count
Reproduction
0 10 20 30 40 50 60 70
Milk Yield

15. Milk Yield
Variation
20 million
data points
can’t be
wrong?
Milk Yield Distribution
Aur´lien
e
Madouasse Milk Yield
Background
Mean ∼ 27 kg/day
Data
Standard deviation ∼ 8.5 kg
Milk Using a model notation we
Production
could write:
Somatic Cell
Count
Yi = µ + i
Reproduction
Where
µ = 27 kg
2
0 10 20 30 40 50 60 70 i ∼ Normal(0, 8.5 )
Milk Yield

16. Milk Yield
Variation
20 million
data points
can’t be
wrong?
Aur´lien
e
Madouasse
Background
Data We can do better than that by
Milk
Production
Somatic Cell
incorporating other sources of
Count
Reproduction variation!!!

17. Milk Yield
Days in milk
20 million
data points
can’t be
wrong?
Yield increases from calving
Aur´lien
e
until a peak and decreases
40
Madouasse
Background
afterwards
35
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0 100 200 300 400 Yi = µ + β1 Dimi + β2 Dimi2 + ...
Days in Milk
+ i

18. Milk Yield
Parity
20 million
data points
can’t be
wrong?
Aur´lien
e
40
Madouasse
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Background
35
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Mean Milk Yield
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Milk q
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Somatic Cell q
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... + γParityi +
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0 100 200 300 400
i
Days in Milk

19. Milk Yield
Season
20 million
data points
can’t be
wrong? Parity 1 Parity > 1
Aur´lien
e
Madouasse
Background
Data
Milk
Production
Somatic Cell
Count
Reproduction

20. Milk Yield
Season
20 million
data points
can’t be
wrong? Parity 1 Parity > 1
Aur´lien
e
Madouasse
Background
Data
Milk
Production
Somatic Cell
Count
Reproduction

21. Milk Yield
Season
20 million
data points
can’t be
wrong? Parity 1 Parity > 1
Aur´lien
e
Madouasse
Background
Data
Milk
Production
Somatic Cell
Count
Reproduction

22. Milk Yield
Season
20 million
data points
can’t be
wrong? Parity 1 Parity > 1
Aur´lien
e
Madouasse
Background
Data
Milk
Production
Somatic Cell
Count
Reproduction

23. Milk Yield
Season
20 million
data points
can’t be
wrong? Parity 1 Parity > 1
Aur´lien
e
Madouasse
Background
Data
Milk
Production
Somatic Cell
Count
Reproduction

24. Milk Yield
Season
20 million
data points
can’t be
wrong? Parity 1 Parity > 1
Aur´lien
e
Madouasse
Background
Data
Milk
Production
Somatic Cell
Count
Reproduction

25. Milk Yield
Season
20 million
data points
can’t be
wrong? Parity 1 Parity > 1
Aur´lien
e
Madouasse
Background
Data
Milk
Production
Somatic Cell
Count
Reproduction

26. Milk Yield
Season
20 million
data points
can’t be
wrong? Parity 1 Parity > 1
Aur´lien
e
Madouasse
Background
Data
Milk
Production
Somatic Cell
Count
Reproduction

27. Milk Yield
Season
20 million
data points
can’t be
wrong? Parity 1 Parity > 1
Aur´lien
e
Madouasse
Background
Data
Milk
Production
Somatic Cell
Count
Reproduction

28. Milk Yield
Season
20 million
data points
can’t be
wrong? Parity 1 Parity > 1
Aur´lien
e
Madouasse
Background
Data
Milk
Production
Somatic Cell
Count
Reproduction

29. Milk Yield
Season
20 million
data points
can’t be
wrong? Parity 1 Parity > 1
Aur´lien
e
Madouasse
Background
Data
Milk
Production
Somatic Cell
Count
Reproduction

30. Milk Yield
Season
20 million
data points
can’t be
wrong?
Parity 1 Parity > 1
Aur´lien
e
Madouasse
Background
Data
Milk
Production
Somatic Cell
Count
Reproduction

31. Milk Yield
Season
20 million
data points
can’t be
wrong?
Parity 1 Parity > 1
Aur´lien
e
Madouasse
Background
Data
Milk
Production
Somatic Cell
Count
Reproduction

32. Solving the problem
20 million
data points
can’t be
wrong?
Aur´lien
e
Madouasse
Summary values for milk production were extracted for
Background
groups of cows stratified by:
Data
Days in milk
Milk
Production Parity (1 vs. > 1)
Somatic Cell Average herd production
Count
Month of calving
Reproduction
⇒ 168 lactation curves were produced

33. Amelia is happy
20 million
data points
can’t be
wrong?
Aur´lien
e
Madouasse
Her model factored in
Background details of variables such
Data as the number of cows
Milk calving and heifers
Production
Somatic Cell
calving, cows to be dried
Count off per month and cows in
Reproduction milk exiting the herd
The new model has an
average accuracy rate of
96.83 %

34. Amelia is happy
20 million
data points
can’t be
wrong?
Aur´lien
e
Madouasse
Background
Data
Milk
Production
Somatic Cell
Count
Reproduction

35. Somatic Cell Count
20 million
data points
can’t be
wrong?
Aur´lien
e
Madouasse
Background
Data
Milk
Production
Somatic Cell
Count
Reproduction

36. Somatic Cell Count
Relation to mastitis
20 million
data points
can’t be
wrong?
Mastitis
Aur´lien
e
Madouasse One of the biggest health problems in dairy herds
Can be clinical or subclinical
Background
Causes an increase in milk somatic cell count (SCC)
Data
Milk
Production Bulk Milk Somatic Cell Count
Somatic Cell Reflects herd mastitis prevalence
Count
Penalty on milk price when it is too high
Reproduction
Contribution of individual cows to BMSCC
Can we identify the contribution of different groups of
cows to BMSCC?