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I don’t think the warning was the issue, but I pushed a fix for that. Try re-installing the package and see if the warning and errors go away. From: Yansen...

That is not what I was expecting! Can you re-post the warning you get? Is it exactly the same? From: Yansen CHEN ***@***.***> Date: Tuesday, March 14, 2023 at 8:41...

Hi Yansen, I think you also need to re-attach the posterior database: MegaLMM_state$Posterior = readRDS(file.path(MegaLMM_state$run_ID,'Posterior/Posterior_base.rds')) See if that works. You should see the number of posterior_samples listed when you print...

Hi Yansen, Yes, if the posterior_base file is gone, I think you can re-generate it by running: MegaLMM_state = clear_Posterior(MegaLMM_state) Dan From: Yansen CHEN ***@***.***> Date: Wednesday, April 19, 2023...

Hi Yansen, Sorry that it is not faster. I would like to try these types of ideas, but haven’t had the time to fully explore them. I think the challenge...

Hi Timothy, Thanks for these comments. Yes, I agree that convergence of MegaLMM is an issue. I believe that the problem is that two aspects of the factors are only...

Hi Yansen, Yes, you can by specifying a model like `~(1|Family) + (1|ID) + ...`. Each `(1|X)` term specifies a random effect with group `X`. Each random effect can be...

Are `AG` and `PE` both covariance matrices with #rows and #columns equal to the number of levels of `ID`? If so you'd want to switch around the arguments: `formula =...

Hi Yan-Cheng, Thanks for the question. I think partial environmental covariate data is a challenge that we haven’t fully explored yet. MegaLMM does require that each environmental covariate has a...