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Bristol, United Kingdom

Heath C.A.E.,University of Bristol | Main D.C.J.,University of Bristol | Mullan S.,University of Bristol | Haskell M.J.,SRUC | And 2 more authors.
Animal | Year: 2015

Lameness in dairy cows is an important welfare issue. As part of a welfare assessment, herd level lameness prevalence can be estimated from scoring a sample of animals, where higher levels of accuracy are associated with larger sample sizes. As the financial cost is related to the number of cows sampled, smaller samples are preferred. Sequential sampling schemes have been used for informing decision making in clinical trials. Sequential sampling involves taking samples in stages, where sampling can stop early depending on the estimated lameness prevalence. When welfare assessment is used for a pass/fail decision, a similar approach could be applied to reduce the overall sample size. The sampling schemes proposed here apply the principles of sequential sampling within a diagnostic testing framework. This study develops three sequential sampling schemes of increasing complexity to classify 80 fully assessed UK dairy farms, each with known lameness prevalence. Using the Welfare Quality herd-size-based sampling scheme, the first ‘basic’ scheme involves two sampling events. At the first sampling event half the Welfare Quality sample size is drawn, and then depending on the outcome, sampling either stops or is continued and the same number of animals is sampled again. In the second ‘cautious’ scheme, an adaptation is made to ensure that correctly classifying a farm as ‘bad’ is done with greater certainty. The third scheme is the only scheme to go beyond lameness as a binary measure and investigates the potential for increasing accuracy by incorporating the number of severely lame cows into the decision. The three schemes are evaluated with respect to accuracy and average sample size by running 100 000 simulations for each scheme, and a comparison is made with the fixed size Welfare Quality herd-size-based sampling scheme. All three schemes performed almost as well as the fixed size scheme but with much smaller average sample sizes. For the third scheme, an overall association between lameness prevalence and the proportion of lame cows that were severely lame on a farm was found. However, as this association was found to not be consistent across all farms, the sampling scheme did not prove to be as useful as expected. The preferred scheme was therefore the ‘cautious’ scheme for which a sampling protocol has also been developed. © The Animal Consortium 2015

Leckie G.,Center for Multilevel Modelling | Charlton C.,Center for Multilevel Modelling
Journal of Statistical Software | Year: 2013

We illustrate how to fit multilevel models in the MLwiN package seamlessly from within Stata using the Stata program runmlwin. We argue that using MLwiN and Stata in combination allows researchers to capitalize on the best features of both packages. We provide examples of how to use runmlwin to fit continuous, binary, ordinal, nominal and mixed response multilevel models by both maximum likelihood and Markov chain Monte Carlo estimation.

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