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Welcome to the NIMBLE users discussion group. Feel free to ask questions about using NIMBLE to do analyses, programming algorithms in NIMBLE, or setting NIMBLE up on your machine. And of course please feel free to comment on and answer others' questions.

Our list has been spam-free for most of its existence. However, recently, we have had some spam problems. As a result, we are moderating posts from new users. Thanks for understanding.

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Kavir Narsai, Perry de Valpine5

1:05 PM

Bayesian Adaptive Regression Splines

Hi Perry Below is a simple example in which I would like to fit a bayesian adaptive regression spline

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Bayesian Adaptive Regression Splines

Hi Perry Below is a simple example in which I would like to fit a bayesian adaptive regression spline

1:05 PM

Christopher Jackson, Perry de Valpine2

11:13 AM

Compile errors with derivatives

Hi Chris, Thanks for the question. The answer is in section 16.5.2.2 of the User Manual, but I get it

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Compile errors with derivatives

Hi Chris, Thanks for the question. The answer is in section 16.5.2.2 of the User Manual, but I get it

11:13 AM

PierGianLuca, Daniel Turek3

10:22 AM

Possible bug with `as.list(...$mvSamples2)`?

Hi Daniel, Thank you for confirming this, and for the fixing tips! "as.list" is a life-

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Possible bug with `as.list(...$mvSamples2)`?

Hi Daniel, Thank you for confirming this, and for the fixing tips! "as.list" is a life-

10:22 AM

Chris Paciorek, … Daniel Turek6

Jul 19

NIMBLE version 1.1.0 released

Heather, I'm sorry it's taken a few days to respond. Let me try to give a brief view of the

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NIMBLE version 1.1.0 released

Heather, I'm sorry it's taken a few days to respond. Let me try to give a brief view of the

Jul 19

EN Pete, … Chris Paciorek4

Jul 18

summing a vector of changing lengths

Yes, thanks for noticing my omission, Daniel. One needs to use `summation` in the model. -Chris On

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summing a vector of changing lengths

Yes, thanks for noticing my omission, Daniel. One needs to use `summation` in the model. -Chris On

Jul 18

Juan Xie, Chris Paciorek5

Jul 18

parallelize nested for loop

Got it, thank you for the clarification, very helpful! Best~ On Thursday, July 18, 2024 at 10:32:35

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parallelize nested for loop

Got it, thank you for the clarification, very helpful! Best~ On Thursday, July 18, 2024 at 10:32:35

Jul 18

Lawson, Andrew B., Chris Paciorek2

Jul 17

WAIC calculation for joint models

hi Andrew, This isn't something we've considered. WAIC is calculated based on the full

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WAIC calculation for joint models

hi Andrew, This isn't something we've considered. WAIC is calculated based on the full

Jul 17

Chris Bodily, Daniel Turek2

Jul 16

Parallel chains error with nimble function

Chris, great question. Unfortunately, with the present system of nimble's compilation, you'll

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Parallel chains error with nimble function

Chris, great question. Unfortunately, with the present system of nimble's compilation, you'll

Jul 16

Daniel Turek, Jimmy Hickey2

Jul 15

Re: Using nimbleRcall and the example given in the documentation

Whoops, that's a silly mistake! Thanks, Daniel! I have tried to remove the original post since

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Re: Using nimbleRcall and the example given in the documentation

Whoops, that's a silly mistake! Thanks, Daniel! I have tried to remove the original post since

Jul 15

Dusit Ngoprasert, Cyril Milleret3

Jul 14

regularly save output in nimble

Hi Dusit, It is possible to save the state of the model following this vignette: https://danielturek.

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regularly save output in nimble

Hi Dusit, It is possible to save the state of the model following this vignette: https://danielturek.

Jul 14

Qing Zhao, Benjamin R Goldstein4

Jul 10

reversible jump mcmc

Hi Qing-- I was working on a similar problem recently (RJMCMC when one indicator variable is

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reversible jump mcmc

Hi Qing-- I was working on a similar problem recently (RJMCMC when one indicator variable is

Jul 10

Cherie Yu, Chris Paciorek2

Jul 10

Error: Failed to create the shared library On Slurm Cluster

Hi Cherie, If you look at the files in `/nfs/work/agap_id-bin/img/R/4.0.2/lib/nimble/CppCode`, do you

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Error: Failed to create the shared library On Slurm Cluster

Hi Cherie, If you look at the files in `/nfs/work/agap_id-bin/img/R/4.0.2/lib/nimble/CppCode`, do you

Jul 10

raffaele liguori, Perry de Valpine2

Jul 9

nimble error Failed to create the shared library

Hi Raffaele, Thanks for the message. This looks like a system configuration issue, and it is hard for

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nimble error Failed to create the shared library

Hi Raffaele, Thanks for the message. This looks like a system configuration issue, and it is hard for

Jul 9

Quresh Latif, … Daniel Turek9

Jul 5

log density functions

Well, the mystery may be mostly solved. It seems that JAGS provides those functions, and I did start

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log density functions

Well, the mystery may be mostly solved. It seems that JAGS provides those functions, and I did start

Jul 5

Jul 5

modeling a left skewed distribution

Not really. Actually, since posting my message yesterday, I've identified the reason for the

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modeling a left skewed distribution

Not really. Actually, since posting my message yesterday, I've identified the reason for the

Jul 5

cro...@ualberta.ca, … Abby Keller47

Jul 1

Run parallel chains and update model

Hi Chris, Thanks for your quick response, I appreciate it. And so sorry, I think I had answered my

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Run parallel chains and update model

Hi Chris, Thanks for your quick response, I appreciate it. And so sorry, I think I had answered my

Jul 1

catheri...@gmail.com, Chris Paciorek3

Jun 25

Incorrect dimensions in y data for nimbleSCR

Hi Chris, Thanks so much for the quick response - converting to a matrix did the trick to remove

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Incorrect dimensions in y data for nimbleSCR

Hi Chris, Thanks so much for the quick response - converting to a matrix did the trick to remove

Jun 25

Eduardo Guimarães Martins, … Chris Paciorek4

Jun 24

HMC and configureRJ

Hi Eduardo, Sorry about our slow response. You've caught us at a time where the developer team

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HMC and configureRJ

Hi Eduardo, Sorry about our slow response. You've caught us at a time where the developer team

Jun 24

Qianyu Li, … Chris Paciorek19

Jun 24

Nimble model failed due to the error of "Failed to create the shared library"

Hi Shivshankar, This may be difficult for us to diagnose given we don't have access to a PBS-

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Nimble model failed due to the error of "Failed to create the shared library"

Hi Shivshankar, This may be difficult for us to diagnose given we don't have access to a PBS-

Jun 24

Cherie Yu, Perry de Valpine2

Jun 24

rror: In sizeAssignAfterRecursing: 'x' is not available or its output type is unknown.

Hi Cherie, Thanks for the question. This one is frustrating as it arises from a kind of name clash we

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rror: In sizeAssignAfterRecursing: 'x' is not available or its output type is unknown.

Hi Cherie, Thanks for the question. This one is frustrating as it arises from a kind of name clash we

Jun 24

Dave Hudson, Wei Zhang3

Jun 19

Hi Dave, You might need to change your index (t-1)*ns+(1:ns) to (1 + (t-1)*ns) : (ns + (t-1)*ns); and

unread,

Hi Dave, You might need to change your index (t-1)*ns+(1:ns) to (1 + (t-1)*ns) : (ns + (t-1)*ns); and

Jun 19

ARJUN BANIK, … Perry de Valpine5

Jun 18

Error: Failed to create the shared library.

Just for thread sanity I am noting this is a duplicate (perhaps due to the moderation we had to put

unread,

Error: Failed to create the shared library.

Just for thread sanity I am noting this is a duplicate (perhaps due to the moderation we had to put

Jun 18

Alt, Ethan Mackenzie, Perry de Valpine3

Jun 17

MCEM for Mixture Cure Rate Model

Hi Ethan and all, I just wanted to circle back to this message and note that the newly released

unread,

MCEM for Mixture Cure Rate Model

Hi Ethan and all, I just wanted to circle back to this message and note that the newly released

Jun 17

Erika Anderson, Heather Gaya4

Jun 14

SCR - NA or NAN values for z[]

Hi Heather, Thanks so much for the quick reply. I took another look at the coefficients using

unread,

SCR - NA or NAN values for z[]

Hi Heather, Thanks so much for the quick reply. I took another look at the coefficients using

Jun 14

Enrico Ryunosuke Crema, Perry de Valpine7

Jun 14

checkAndPrepareDistributionInfo: random generation function rAExp is missing returnType or returnType does not match the type of the x argument to the corresponding density function.

Thanks Perry, I opted for the latter solution (ie creating the placeholder function) and it works

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checkAndPrepareDistributionInfo: random generation function rAExp is missing returnType or returnType does not match the type of the x argument to the corresponding density function.

Thanks Perry, I opted for the latter solution (ie creating the placeholder function) and it works

Jun 14

Jun 14

NIMBLE version 1.2.0 released

We're pleased to announce the release of version 1.2.0. This release provides provides extensive

unread,

NIMBLE version 1.2.0 released

We're pleased to announce the release of version 1.2.0. This release provides provides extensive

Jun 14

Colton Padilla, Chris Paciorek2

Jun 13

AFT Model - logProb of data node is.censored[8]: logProb is -Inf

Hi Colton, It looks like you need valid (ie, consistent with the censoring value) initial values for

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AFT Model - logProb of data node is.censored[8]: logProb is -Inf

Hi Colton, It looks like you need valid (ie, consistent with the censoring value) initial values for

Jun 13

Ryan Burner, Daniel Turek11

Jun 13

Options for discrete/custom priors?

Ryan, are you certain you're using valid initial values for the model, prior to beginning the

unread,

Options for discrete/custom priors?

Ryan, are you certain you're using valid initial values for the model, prior to beginning the

Jun 13

SimonGE, Perry de Valpine3

Jun 12

reasonable initial values recalculated to impossible values in distance sampling model

Amazing! Thank you so much for such a quick and thorough reply. I am disappointed that it was exactly

unread,

reasonable initial values recalculated to impossible values in distance sampling model

Amazing! Thank you so much for such a quick and thorough reply. I am disappointed that it was exactly

Jun 12

kei, … Perry de Valpine4

Jun 11

The number of particles at first-time point for particle filter

The PMCMC should be able to use any PF you give it, including a PF that you have modified. On Sun,

unread,

The number of particles at first-time point for particle filter

The PMCMC should be able to use any PF you give it, including a PF that you have modified. On Sun,

Jun 11

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