communityPGLMM.plot.re()

[arives]

I couldn't get this to work. There were a variety of error messages, such as

Error in as(as.matrix(Y.mat), "denseMatrix")[, cov_ranef_update[[sp.var]]$tip.label] :
invalid or not-yet-implemented 'Matrix' subsetting

It would be nice if somebody could just enter a comunityPGLMM object and have the covariance matrices plotted.

[daijiang]

If the input is a model, it needs to be (x = model name, sp.var = "sp.col.name"). The argument name x is needed because it is not the first argument in the function.

[arives]

I got this:

w <- pglmm(Y ~ U2 + (1|sp__), cov_ranef=list(sp=Vsp), data=data) communityPGLMM.plot.re(x=w, sp.var="sp", site.var="trait")

Error in cov_ranef_update[[sp.var]]$tip.label : $ operator is invalid for atomic vectors From: Daijiang Li <[email protected]> Reply-To: daijiang/phyr <[email protected]> Date: Wednesday, July 31, 2019 at 6:31 AM To: daijiang/phyr <[email protected]> Cc: "Anthony R. Ives" <[email protected]>, Author <[email protected]> Subject: Re: [daijiang/phyr] communityPGLMM.plot.re() (#40) If the input is a model, it needs to be (x = model name, sp.var = "sp.col.name"). The argument name x is needed because it is not the first argument in the function. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#40?email_source=notifications&email_token=ACYX6LDLCBXZLYGQRAAOTYLQCFZZVA5CNFSM4IIFTP32YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD3G6N3Y#issuecomment-516810479>, or mute the thread<https://github.com/notifications/unsubscribe-auth/ACYX6LHWZDVUZ6H7SLNKDELQCFZZVANCNFSM4IIFTP3Q>.

[daijiang]

It is a bug. Can you try cov_randef=list(sp=phylogeny) instead of the matrix?

[arives]

I'm just going into work, so I'll try later this morning. From: Daijiang Li <[email protected]> Reply-To: daijiang/phyr <[email protected]> Date: Wednesday, July 31, 2019 at 7:17 AM To: daijiang/phyr <[email protected]> Cc: "Anthony R. Ives" <[email protected]>, Author <[email protected]> Subject: Re: [daijiang/phyr] communityPGLMM.plot.re() (#40) It is a bug. Can you try cov_randef=list(sp=phylogeny) instead of the matrix? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#40?email_source=notifications&email_token=ACYX6LCR572XNIJWYU45YDTQCF7E5A5CNFSM4IIFTP32YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD3HBUHY#issuecomment-516823583>, or mute the thread<https://github.com/notifications/unsubscribe-auth/ACYX6LCH3WMCHUMOFXVJ2U3QCF7E5ANCNFSM4IIFTP3Q>.