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breedR

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Welcome to this discussion group about breedR.

You can subscribe to this group with any email address, but you need to sign in with a google account.

Please ask your questions here. It is likely they would help others as well.
You are also encouraged to expand on questions from others.

However, if you want to report a bug, please file an issue at GitHub.

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Javier Marcuzzi

11/21/24

That's great, more than 10 years ago I used blupf90. And I would have loved to have this

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That's great, more than 10 years ago I used blupf90. And I would have loved to have this

11/21/24

Brianna Banting, lefevref...@gmail.com3

8/23/24

plotting residuals for spatial models

Hi again, solved by re-installing breedR from scracth on version of R4.3.1 Cheers, François Le

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plotting residuals for spatial models

Hi again, solved by re-installing breedR from scracth on version of R4.3.1 Cheers, François Le

8/23/24

7/15/24

Installing problem breedR

Hi, I have problem with installing breedR. It seems there is nothing on this page: https://famuvie.

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Installing problem breedR

Hi, I have problem with installing breedR. It seems there is nothing on this page: https://famuvie.

7/15/24

6/22/24

failed to load breedR

Dear Facundo, thank you very much for your creation. I got helped a lot by breedR. I recently bought

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failed to load breedR

Dear Facundo, thank you very much for your creation. I got helped a lot by breedR. I recently bought

6/22/24

5/29/24

Competition model

Dear Facundo, Thanks a lot for your great efforts on breedR package. Now I would like to use the

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Competition model

Dear Facundo, Thanks a lot for your great efforts on breedR package. Now I would like to use the

5/29/24

3/26/24

multi-trait model without repeated individual observations

Dear Facundo, I would like to fit a model with 2 traits, corresponding to the circumference of the

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multi-trait model without repeated individual observations

Dear Facundo, I would like to fit a model with 2 traits, corresponding to the circumference of the

3/26/24

12/13/23

Random regression models

Can breedR fit RR models? If so, does it have ASreml-R style in-built functions for Legendre

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Random regression models

Can breedR fit RR models? If so, does it have ASreml-R style in-built functions for Legendre

12/13/23

Victor Papin, Facundo Muñoz3

8/4/23

check convergence in BreedR

Perfect, thank you very much! Best, Victor Le 3 août 2023 à 15:54, Facundo Muñoz <facundo.munoz@

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check convergence in BreedR

Perfect, thank you very much! Best, Victor Le 3 août 2023 à 15:54, Facundo Muñoz <facundo.munoz@

8/4/23

Victor Papin, Facundo Muñoz2

7/26/23

var.init for generic effect

Dear Victor, Include the specification for the initial variance of the generic component as a third

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var.init for generic effect

Dear Victor, Include the specification for the initial variance of the generic component as a third

7/26/23

Fathur Rachman, Facundo Muñoz2

5/9/23

breedR package install issues

Dear Fathur, From the error message, it seems that you need to install Rtools [1] if you are using R

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breedR package install issues

Dear Fathur, From the error message, it seems that you need to install Rtools [1] if you are using R

5/9/23

Toni K Clarke, Facundo Muñoz4

11/7/22

estimating family blups

Thanks for replying - this makes sense. I will just fit family as a random effect for estimating the

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estimating family blups

Thanks for replying - this makes sense. I will just fit family as a random effect for estimating the

11/7/22

Nannuru Vinay, Facundo Muñoz2

9/26/22

An error with function "remlf90"

Dear Vinay, If you provided a reproducible example, I would be able to see exactly what happens. But

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An error with function "remlf90"

Dear Vinay, If you provided a reproducible example, I would be able to see exactly what happens. But

9/26/22

lefevref...@gmail.com, Facundo Muñoz10

9/12/22

variance estimates by levels of a fixed effect

Great! thanks for the feedback. ƒacu.- On 12/09/2022 13:53, lefevref...@gmail.com wrote: Dear Facundo

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variance estimates by levels of a fixed effect

Great! thanks for the feedback. ƒacu.- On 12/09/2022 13:53, lefevref...@gmail.com wrote: Dear Facundo

9/12/22

Jared Anderson, Facundo Muñoz4

1/26/22

Interactive terms in model formulae

Jared, There is a toy example [1] in breedR's "Overview" which briefly explains how to

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Interactive terms in model formulae

Jared, There is a toy example [1] in breedR's "Overview" which briefly explains how to

1/26/22

BT, Facundo Muñoz3

9/6/21

Competition model with GRM

Hi Facundo, Thank you. I'll try as you suggested. Regards, BT On Monday, 6 September 2021 at 23:

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Competition model with GRM

Hi Facundo, Thank you. I'll try as you suggested. Regards, BT On Monday, 6 September 2021 at 23:

9/6/21

shuyi yang, Facundo Muñoz6

6/28/21

Spatial analysis within site

Dear Zoe, > "... how shall we choose the best methods for our model and dataset?" In

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Spatial analysis within site

Dear Zoe, > "... how shall we choose the best methods for our model and dataset?" In

6/28/21

fj lario, Facundo Muñoz2

6/8/21

douglas GXE analysis row and columns within site

Dear Paco, Congratulations! you've found a bug :) Unfortunately however, it seems to be in the

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douglas GXE analysis row and columns within site

Dear Paco, Congratulations! you've found a bug :) Unfortunately however, it seems to be in the

6/8/21

Richard Whittet, … H G D9

6/23/20

Re: [breedR] Multi-trait model not working

Dear Facundo, I found that removing one of the response values (AUWP or AUWPS) fixes the problem,

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Re: [breedR] Multi-trait model not working

Dear Facundo, I found that removing one of the response values (AUWP or AUWPS) fixes the problem,

6/23/20

H G D, Facundo Muñoz5

6/18/20

remlf90: intercept and random versus fixed effects

Dear Facundo, thank you for maintaining this great package anyways, I very much appreciate your help.

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remlf90: intercept and random versus fixed effects

Dear Facundo, thank you for maintaining this great package anyways, I very much appreciate your help.

6/18/20

Jaime Alberto Zapata Valenzuela, Facundo Muñoz4

4/27/20

Interpreting the variogram

Dear Facundo I still not sure If am interpreting the variogram correctly. I understand the definition

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Interpreting the variogram

Dear Facundo I still not sure If am interpreting the variogram correctly. I understand the definition

4/27/20

Jaime Alberto Zapata Valenzuela, Facundo Muñoz3

4/27/20

Genetic model with clonal data, additive and dominance components

Facundo, thanks a million I will check the pedigree specification. I will check the paper information

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Genetic model with clonal data, additive and dominance components

Facundo, thanks a million I will check the pedigree specification. I will check the paper information

4/27/20

jesus valdes hernandez, Facundo Muñoz5

4/5/20

Initial (co)variance specification with included factor random in multi-trait models, and possibility of working with a repeatability model

Dear Jesús, Thank you for your patience: I'm not having much time these days (less than usual!).

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Initial (co)variance specification with included factor random in multi-trait models, and possibility of working with a repeatability model

Dear Jesús, Thank you for your patience: I'm not having much time these days (less than usual!).

4/5/20

Gabriel Maurin, Facundo Muñoz3

12/10/19

AR model computation time, spatial effect and genetics effect

Thank for the quick answer. It works with fixed rho = (.9,.9) ! and the results are quite similar to

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AR model computation time, spatial effect and genetics effect

Thank for the quick answer. It works with fixed rho = (.9,.9) ! and the results are quite similar to

12/10/19

Gab Diesel, Facundo Muñoz3

6/13/19

Animal Model with SNP Based Relatedness NOT pedigree

Dear Facundo, Many thanks for the reply. It makes sense now and I understood how to use a marker

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Animal Model with SNP Based Relatedness NOT pedigree

Dear Facundo, Many thanks for the reply. It makes sense now and I understood how to use a marker

6/13/19

Pamela Villalba, Facundo Muñoz6

3/11/19

Using Bootstrap estimation for a Spline model

Dear Pamela, sorry for the late reply. It is not possible to do it within the breedR.sample.phenotype

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Using Bootstrap estimation for a Spline model

Dear Pamela, sorry for the late reply. It is not possible to do it within the breedR.sample.phenotype

3/11/19

Maurizio Marchi, Facundo Muñoz2

11/14/18

Indeed, it is. Best wishes ƒacu.- On 11/13/18 11:13 PM, Maurizio Marchi wrote: Hi all, is this group

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Indeed, it is. Best wishes ƒacu.- On 11/13/18 11:13 PM, Maurizio Marchi wrote: Hi all, is this group

11/14/18

Francisco Joel Jahuey Martínez, Facundo Muñoz2

9/25/18

maternal genetic and permanent environment effect

Dear Francisco, How is the "maternal genetic effect" different from the direct additive (

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maternal genetic and permanent environment effect

Dear Francisco, How is the "maternal genetic effect" different from the direct additive (

9/25/18

robert...@usp.br, Facundo Muñoz3

5/23/18

multi-trait by a generic model

Perfect! Thanks On Tuesday, May 22, 2018 at 9:56:53 PM UTC-3, robert...@usp.br wrote: For most

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multi-trait by a generic model

Perfect! Thanks On Tuesday, May 22, 2018 at 9:56:53 PM UTC-3, robert...@usp.br wrote: For most

5/23/18

wimgo...@hotmail.com, Facundo Muñoz5

4/13/18

Include maternal effect in animal model

Yes. If you can compute de correlation matrix for the dams, then you can feed it into a generic model

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Include maternal effect in animal model

Yes. If you can compute de correlation matrix for the dams, then you can feed it into a generic model

4/13/18

Marnin Wolfe, Facundo Muñoz4

12/28/17

Highly variable results from BreedR and disagreement with other mixed model solvers!?

Dear Martin, Would you please repeat the tests with each of the following modifications? 1. Remove

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Highly variable results from BreedR and disagreement with other mixed model solvers!?

Dear Martin, Would you please repeat the tests with each of the following modifications? 1. Remove

12/28/17

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