monitors/DAG

[quattrinia]

Hi there, I am trying to run this tutorial https://revbayes.github.io/tutorials/clocks/ And, I have it all working up until the very end. When I type the monitors[1]=mnModel(filename="/data/mcfadden/aquattrini/ANALYSIS/Paramuricea/revbayes/output/mcmc.log", printgen=100) Error: Workspace objects cannot be used inside DAG's! You tried to access the DAG node of type 'RevObject'.

Any advice?

[wadedismukes]

Hello,

This tutorial appears to be a bit outdated. Apologies for that!

Try replacing these lines:

monitors[1] = mnModel(filename="output/TimetTree_bears_mcmc.log", printgen=10)

monitors[2] = mnFile(filename="output/TimeTree_bears_mcmc.trees",
printgen=10, timetree)

monitors[3] = mnScreen(printgen=10, root_time, tmrca_Ursidae)

with these lines:

monitors.append(mnModel(filename="output/TimetTree_bears_mcmc.log",
printgen=10))

monitors.append(mnFile(filename="output/TimeTree_bears_mcmc.trees",
printgen=10, timetree))

monitors.append(mnScreen(printgen=10, root_time, tmrca_Ursidae))

Hope this helps!

Wade

On Tue, Feb 9, 2021 at 10:36 AM quattrinia notifications@github.com wrote:

Hi there, I am trying to run this tutorial https://revbayes.github.io/tutorials/clocks/ And, I have it all working up until the very end. When I type the monitors[1]=mnModel(filename="/data/mcfadden/aquattrini/ANALYSIS/Paramuricea/revbayes/output/mcmc.log", printgen=100) Error: Workspace objects cannot be used inside DAG's! You tried to access the DAG node of type 'RevObject'.

Any advice?

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Wade Dismukes EEB PhD candidate | Heath Lab Iowa State University | EEOB

[quattrinia]

Thanks. These all seemed to work, but then I got this error upon adding mymcmc = mcmc(mymodel, monitors, moves)

Error: Unable to connect monitor to DAG copy because variable name was lost

here is my entire code: D <- readDiscreteCharacterData(file="/data/mcfadden/aquattrini/ANALYSIS/Paramuricea/parajan21.nex") n_sites <- D.nchar() mi = 1 source("/data/mcfadden/aquattrini/ANALYSIS/Paramuricea/revbayes/scripts/m_BDP.Rev") source("/data/mcfadden/aquattrini/ANALYSIS/Paramuricea/revbayes/scripts/uncl.Rev") mymodel=model(er) monitors.append(mnModel(filename="/data/mcfadden/aquattrini/ANALYSIS/Paramuricea/revbayes/output/mcmc.log", printgen=100)) monitors.append(mnFile(filename="/data/mcfadden/aquattrini/ANALYSIS/Paramuricea/revbayes/output/mcmc.trees", printgen=100, timetree)) monitors.append(mnScreen(printgen=100, root_time, tmrca_clav)) mymcmc = mcmc(mymodel, monitors, moves) mymcmc.burnin(generations=5000,tuningInterval=100) mymcmc.run(generations=25000)

[Imsolaris]

I seem to have similar error but out of the moves I was trying to use this tutorial:https://revbayes.github.io/tutorials/ctmc/

br_len_lambda=10 psi := dnUniformTopologyBranchLength(taxa,branchLengthDistribution=dnExponential(br_len_lambda)) Error: Workspace objects cannot be used inside DAG's! You tried to access the DAG node of type 'RevObject'.