David Makowski and Daniel Wallach INRA, France

1. October 2006 Bayesian methods for parameter estimation and data assimilation with crop modelsPart 2: Likelihood function and prior distribution David Makowski and Daniel Wallach INRA, France

2. Previously • Notions in probability - Joint probability - Conditional probability - Marginal probability • Bayes’ theorem

3. Objectives of part 2 • Introduce the notion of prior distribution. • Introduce the notion of likelihood function. • Show how to estimate parameters with a Bayesian method.

4. Part 2: Likelihood function and prior distributions Estimation of parameters () Parameter = numerical value not calculated by the model and not observed. Information available to estimate parameters - A set of observations (y). - Prior knowledge about parameter values.

5. Part 2: Likelihood function and prior distributions Two distributions in Bayes’ theorem • Prior parameter distribution = probability distribution describing our initial knowledge about parameter values. • Likelihood function = function relating data to parameters.

6. Part 2: Likelihood function and prior distributions Measurements Combined info about parameters Bayesian method Prior Information about parameter values

7. Part 2: Likelihood function and prior distributions Example Estimation of crop yield θby combining a measurement with expert knowledge. Plot about 5 t/ha ± 2 Measurement y = 9t/ha ± 1 Field with unknown yield  Expert

8. Part 2: Likelihood function and prior distributions Example Estimation of crop yield θby combining a measurement with expert knowledge. • One parameter to estimate: the crop yield θ. • Two types of information available: • - A measurement equal to 9 t/ha with a standard error equal to 1 t/ha. • - An estimation provided by an expert equal to 5 t/ha with a standard error equal to 2 t/ha.

9. Part 2: Likelihood function and prior distributions Prior distribution • It describes our belief about the parameter values before we observe the measurements. • It is based on past studies, expert knowledge, and litterature.

10. Part 2: Likelihood function and prior distributions Example (continued) Definition of a prior distribution θ ~ N( µ, ² ) • Normal probability distribution. • Expected value equal to 5 t/ha. • Standard error equal to 2 t/ha

11. Part 2: Likelihood function and prior distributions Example (continued) Plot of the prior distribution

12. Part 2: Likelihood function and prior distributions Likelihood function • A likelihood function is a function relating data to parameters. • It is equal to the probability that the measurements would have been observed given some parameter values. • Notation: P(y | θ)

13. Part 2: Likelihood function and prior distributions Example (continued) Statistical model y = θ +  with  ~ N( 0, σ² ) y | θ ~ N( θ, σ² )

14. Part 2: Likelihood function and prior distributions Example (continued) Definition of a likelihood function y | θ ~ N( θ, σ² ) • Normal probability distribution. • Measurement y assumed unbiaised and equal to 9 t/ha. • Standard error σ assumed equal to 1 t/ha

15. Part 2: Likelihood function and prior distributions Example (continued) Definition of a likelihood function Maximum likelihood estimate

16. Part 2: Likelihood function and prior distributions Maximum likelihood Likelihood functions are also used by frequentist to implement the maximum likelihood method. The maximum likelihood estimator is the value of θmaximizing P(y | θ) .

17. Part 2: Likelihood function and prior distributions Likelihood function Prior probability distribution

18. Part 2: Likelihood function and prior distributions Example (continued) Analytical expression of the posterior distribution θ | y ~ N( µpost, post² )

19. Part 2: Likelihood function and prior distributions Posterior probability distribution Prior probability distribution Likelihood function

20. Part 2: Likelihood function and prior distributions Example (continued) Discussion of the posterior distribution • Result is a probability distribution (posterior distr.) • Posterior mean is intermediate between prior mean and observation. • Weight of each depends on prior variance and measurement error. • Posterior variance is lower than both prior variance and measurement error variance. • Used just one data point and still got estimator.

21. Part 2: Likelihood function and prior distributions Frequentist versus Bayesian Bayesian analysis introduces an element of subjectivity: the prior distribution. But its representation of the uncertainty is easy to understand - the uncertainty is assessed conditionally to the observations, - the calculations are straightforward when the posterior distribution is known.

22. Part 2: Likelihood function and prior distributions Which is better? Bayesian methods often lead to - more realistic estimated parameter values, - in some cases, more accurate model predictions. Problems when prior information is wrong and when one has a strong confidence in it.

23. Part 2: Likelihood function and prior distributions Difficulties for estimating crop model parameters Which likelihood function ? - Unbiaised errors ? - Independent errors ? Which prior distribution ? - What do the parameters really represent ? - Level of uncertainty ? - Symmetric distribution ?

24. Part 2: Likelihood function and prior distributions Practical considerations • The analytical expression of the posterior distribution can be derived for simple applications. • For complex problems, the posterior distribution must be approximated.

25. Next part Importance sampling, an algorithm to approximate the posterior probability distribution.