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covariance_structure_of_correlated_random_effects_for_multiple_traits [2018/03/29 18:52] – andrescovariance_structure_of_correlated_random_effects_for_multiple_traits [2018/03/29 18:55] – andres
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-The documentation is  bit confusing on how to declare several correlated effects for several traits. Whereas ''renumf90'' does this automatically for maternal effects models, it is not so obvious if one does it by itself. +The documentation is  bit confusing on how to declare several correlated effects for several traits. Whereas ''renumf90'' does this automatically for maternal effects models, it is not so obvious if one does it by itself. Llibertat Tusell and I put this together.
  
 For instance terminal crosses models (e.g. [[https://gsejournal.biomedcentral.com/articles/10.1186/s12711-016-0211-3||here]]) use: For instance terminal crosses models (e.g. [[https://gsejournal.biomedcentral.com/articles/10.1186/s12711-016-0211-3||here]]) use:
  
-  * trait_pure: **y = u + e** (animal)  +  * trait_pure: **y = hys u + e** (animal)  
-  * trait_crossbred : **y = s + e** (sire of crossbred)+  * trait_crossbred : **y = hys s + e** (sire of crossbred)
  
-Thus we have two traits, purebred and crossbred performance, but effect **u** only affects purebreds and effect **s** only affects crossbreds. Data file has "animal" in column 4 and "sire" in column 5. +Thus we have two traits, purebred and crossbred performance, but effect **u** only affects purebreds and effect **s** only affects crossbreds. Data file has "animal" in column 4 and "sire" in column 5. Effect **hys** has respectively 12 and 25 levels. 
  
 <file> <file>
-...+1 0  12 cross 
 +0 2  25 cross
 4 0  3084 cross 4 0  3084 cross
 0 5  3084 cross 0 5  3084 cross
 ... ...
 RANDOM_GROUP RANDOM_GROUP
-4 5+3 4
 RANDOM_TYPE RANDOM_TYPE
 add_animal add_animal
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 Where we have a 4x4 matrix for covariances. In fact this corresponds to  Where we have a 4x4 matrix for covariances. In fact this corresponds to 
  
-^      ^ ^Effect 4^Effect 4^Effect 5^Effect 5|+^      ^ ^Effect 3^Effect 3^Effect 4^Effect 4|
 ^      ^ ^Trait 1 ^Trait2^Trait1 ^Trait2| ^      ^ ^Trait 1 ^Trait2^Trait1 ^Trait2|
-^Effect 4^Trait 1|Var(u)|     0 | 0|Cov(u,s)| +^Effect 3^Trait 1|Var(u)|     0 | 0|Cov(u,s)| 
-^Effect 4^Trait 2 |0 |     0 | 0| 0| +^Effect 3^Trait 2 |0 |     0 | 0| 0| 
-^Effect 5^Trait 1|0 |     0 |      0| 0| +^Effect 4^Trait 1|0 |     0 |      0| 0| 
-^Effect 5^Trait 2|Cov(s,u)| 0| 0|Var(s)|+^Effect 4^Trait 2|Cov(s,u)| 0| 0|Var(s)|
covariance_structure_of_correlated_random_effects_for_multiple_traits.txt · Last modified: 2024/03/25 18:22 by 127.0.0.1
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