Error computing predicted values

[elslabbert]

Dear Hmsc team,

The Hmsc model I have run as a test round looks as follows:
'mod_input = Hmsc(Y = Y_past, XData = XData_p, XFormula = XFormula, Tr = past_traits, phyloTree = past_tree_only, YScale = TRUE, studyDesign = studyDesign_p, ranLevels = list("Site"=rL1,"Plot_ID"=rL2,"Subplot_ID"=rL3))
mod = sampleMcmc(mod_input, thin = thin, samples = samples, transient = transient,
nChains = nChains, verbose = verbose)'

In following up on the model to check the model fit I want to use the function 'computePredictedValues(mod)' but get the following error:

Error in PiNew[, r] <- sapply(dfPiNew[, r], function(s) which(rowNames == :
incorrect number of subscripts on matrix

As my model is running without an issue I suspect the issue lies elsewhere... I tried looking up sections of the this error in the function, but could not find is there explicitly to understand how to address the issue. Any ideas as to how to address this error?

Looking forward to your inputs

[ovaskain]

Difficult to say what's the problem without seeing the details. Can you send e.g. by email the (un-fitted) model object mod_input? Otso

…

On 28.7.2020 17.47, elslabbert wrote: Dear Hmsc team, The Hmsc model I have run as a test round looks as follows: 'mod_input = Hmsc(Y = Y_past, XData = XData_p, XFormula = XFormula, Tr = past_traits, phyloTree = past_tree_only, YScale = TRUE, studyDesign = studyDesign_p, ranLevels = list("Site"=rL1,"Plot_ID"=rL2,"Subplot_ID"=rL3)) mod = sampleMcmc(mod_input, thin = thin, samples = samples, transient = transient, nChains = nChains, verbose = verbose)' In following up on the model to check the model fit I want to use the function 'computePredictedValues(mod)' but get the following error: Error in PiNew[, r] <- sapply(dfPiNew[, r], function(s) which(rowNames == : incorrect number of subscripts on matrix As my model is running without an issue I suspect the issue lies elsewhere... I tried looking up sections of the this error in the function, but could not find is there explicitly to understand how to address the issue. Any ideas as to how to address this error? Looking forward to your inputs — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#56>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEIYMZUDFBJJP63CRUJXWNLR53QIJANCNFSM4PKTF6MA>.

[jarioksa]

Same error message was reported in issue #47: see if it offers any useful information.

[elslabbert]

Hi Osto, Hi Jarioksa,
Thanks for your respective responses. I have spent the last days going over all my data and fixing some inconsistencies.
I also worked though the issue #47, this was helpful in getting the random levels correct, but did not solve the error previously reported.

'Error in PiNew[, r] <- sapply(dfPiNew[, r], function(s) which(rowNames == :
incorrect number of subscripts on matrix'

Furthermore, I now have my Phylogeny not being included in the model anymore, although it was previously not an issues. The set-up for this section has not changed. So its odd that there is not a mismatch: 'Setting updater$Gamma2=FALSE due to specified phylogeny matrix'.

[elslabbert]

Closing comment to this issue with input from package collaborators:
The issue here was linked indeed to the random levels. It, however, had to be solved by correcting both the levels of the random factors as specified in issue #47, as well as the structure of the studyDesgin to specify factor levels:

studyDesign = data.frame(Site = as.factor(S$Site), Plot_ID = as.factor(S$Plot_ID), Subplot_ID = as.factor(S$Subplot_ID))