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hmecology: Hierarchical Modeling in Ecology

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This is an email list for discussion of hierarchical modeling in ecology and especially related to the book by Royle and Dorazio (2008), Kery and Schaub (2012) and forthcoming.

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Mathilde, Jeffrey Royle2

Aug 25

Question on variable significance in dynamic occupancy model (unmarked)

hi Mathilde, Unfortunately you're out of luck in this situation -- complete separation means that

unread,

Question on variable significance in dynamic occupancy model (unmarked)

hi Mathilde, Unfortunately you're out of luck in this situation -- complete separation means that

Aug 25

Aug 19

Bayesian Population Analysis with NIMBLE

Dear all, We are currently working on a 2 nd edition of the BPA book from back in 2012, which will be

unread,

Bayesian Population Analysis with NIMBLE

Dear all, We are currently working on a 2 nd edition of the BPA book from back in 2012, which will be

Aug 19

Aug 14

Fw: Statistical Scientist / Research Associate position at the Cornell Lab of Ornithology

Perhaps of interest to some on this list. Best regards --- Marc From: Daniel Fink <daniel.fink@

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Fw: Statistical Scientist / Research Associate position at the Cornell Lab of Ornithology

Perhaps of interest to some on this list. Best regards --- Marc From: Daniel Fink <daniel.fink@

Aug 14

Michael Schaub, Perry de Valpine2

Aug 14

Cautionary note for using categorical or multinomial distributions

Hi Michael, Thanks for sharing this. It is quite interesting. As you explain at the end, nimble (and

unread,

Cautionary note for using categorical or multinomial distributions

Hi Michael, Thanks for sharing this. It is quite interesting. As you explain at the end, nimble (and

Aug 14

Marc Kery, Matthijs Hollanders3

Jul 8

why it's not enough to scan values of (simple) Rhat blindly

Dear Matt, to be honest, I can't remember :( I think I have never seen this sort of pathology,

unread,

why it's not enough to scan values of (simple) Rhat blindly

Dear Matt, to be honest, I can't remember :( I think I have never seen this sort of pathology,

Jul 8

Jul 7

Capture-recapture workshop in Mallorca/Spain, 24-28 Nov 2025

Dear colleagues, Giacomo Tavecchia and his group at the IMEDEA in Esporles/Spain are offering a

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Capture-recapture workshop in Mallorca/Spain, 24-28 Nov 2025

Dear colleagues, Giacomo Tavecchia and his group at the IMEDEA in Esporles/Spain are offering a

Jul 7

Marc Kery, falaf...@gmail.com3

Jun 27

Cautionary note on the use of Rhat alone to decide on sufficient chain length

Dear Jeff, thanks a lot ! Will try out sometimes (I am still mostly a JAGS user ;)...). This is

unread,

Cautionary note on the use of Rhat alone to decide on sufficient chain length

Dear Jeff, thanks a lot ! Will try out sometimes (I am still mostly a JAGS user ;)...). This is

Jun 27

falaf...@gmail.com2

Jun 25

Density dependence in an integrated population model with prior parameter estimates

Update: issue fixed, with a great assist from Dr. Heather Gaya in the NIMBLE group. Thanks, Jeff On

unread,

Density dependence in an integrated population model with prior parameter estimates

Update: issue fixed, with a great assist from Dr. Heather Gaya in the NIMBLE group. Thanks, Jeff On

Jun 25

Perry de Valpine

Jun 22

Fwd: Quantitative Ecologist Position at CDFW

The California Department of Fish and Wildlife has a position that will be of interest to some on

unread,

Fwd: Quantitative Ecologist Position at CDFW

The California Department of Fish and Wildlife has a position that will be of interest to some on

Jun 22

Carlos, … Matthijs Hollanders5

Jun 18

Occupancy models with latent variables in both occupancy and detection submodels

Hi Matt and John. It's good to know that there are already simulations and publications exploring

unread,

Occupancy models with latent variables in both occupancy and detection submodels

Hi Matt and John. It's good to know that there are already simulations and publications exploring

Jun 18

Jun 12

Bayesian Population Analysis Workshop @ Sempach, Dec 2025

Dear Julia, sorry, but no. We are just not fans of online/hybrid courses. Admittedly, an online

unread,

Bayesian Population Analysis Workshop @ Sempach, Dec 2025

Dear Julia, sorry, but no. We are just not fans of online/hybrid courses. Admittedly, an online

Jun 12

May 23

Applied Hierarchical Modeling workshop, OSU, October 2025 (registration open now !)

Dear all, as announced previously, Joshua Twining, Ken Kellner, Andy Royle and myself will teach a 1-

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Applied Hierarchical Modeling workshop, OSU, October 2025 (registration open now !)

Dear all, as announced previously, Joshua Twining, Ken Kellner, Andy Royle and myself will teach a 1-

May 23

May 8

Use of the correlation coefficient to study effects of demographic rates on population growth rate in an IPM

Dear all, in the attached memo, we describe our current understanding of the issue brought up by

unread,

Use of the correlation coefficient to study effects of demographic rates on population growth rate in an IPM

Dear all, in the attached memo, we describe our current understanding of the issue brought up by

May 8

May 2

possible AHM workshop at OSU in the fall

Dear all, We (Andy Royle, Josh Twining, Ken Kellner, and I) are hoping to run an in-person Applied

unread,

possible AHM workshop at OSU in the fall

Dear all, We (Andy Royle, Josh Twining, Ken Kellner, and I) are hoping to run an in-person Applied

May 2

Facundo Palacio, Marc Kery4

Apr 29

Conceptual question on N-Mixture models with data augmentation

Dear Marc, I've drafted an initial version of the model. Based on your feedback, I incorporated

unread,

Conceptual question on N-Mixture models with data augmentation

Dear Marc, I've drafted an initial version of the model. Based on your feedback, I incorporated

Apr 29

Apr 28

Two PhD and postdoc positions

Dear all, my colleague Joanie Van de Walle just asked whether it was possible for me to post two

unread,

Two PhD and postdoc positions

Dear all, my colleague Joanie Van de Walle just asked whether it was possible for me to post two

Apr 28

Trevor Davies, Michael Schaub3

Apr 24

M-array CLS model with 3 survival parameters

Hi Trevor, But I think there are still errors in your code – the time indices are not correct. I have

unread,

M-array CLS model with 3 survival parameters

Hi Trevor, But I think there are still errors in your code – the time indices are not correct. I have

Apr 24

Apr 23

Regression-to-the-mean modification in the MCMC

I'm working on an analysis that involves a regression-to-the-mean issue. I have a vague memory of

unread,

Regression-to-the-mean modification in the MCMC

I'm working on an analysis that involves a regression-to-the-mean issue. I have a vague memory of

Apr 23

Matthew Hyde, Marc Kery3

Apr 23

Creating detection matrix for n-mixture model

Hi Mark, Thank you very much for the thorough explanation! I'm trying to fit the model in JAGS,

unread,

Creating detection matrix for n-mixture model

Hi Mark, Thank you very much for the thorough explanation! I'm trying to fit the model in JAGS,

Apr 23

FelicityE, Matthew Hyde2

Apr 22

spOccupancy advice for seasonal camera trap data

Hi Felicity, What do you mean by unpick the spOccupancy options? I think if you're between model

unread,

spOccupancy advice for seasonal camera trap data

Hi Felicity, What do you mean by unpick the spOccupancy options? I think if you're between model

Apr 22

Tomas T., … Matthijs Hollanders22

Apr 12

Calculating derived statistics as in BPA 2012 seems wrong?

Hey Tim and others, I think I thought of a good example of why the empirical correlation coefficient

unread,

Calculating derived statistics as in BPA 2012 seems wrong?

Hey Tim and others, I think I thought of a good example of why the empirical correlation coefficient

Apr 12

Mar 29

post-doc position with Smithsonian Migratory Bird Center (quantitative ecologist)

hi all, here is a good post-doc position in quantitative ecology working with Scott Sillett and

unread,

post-doc position with Smithsonian Migratory Bird Center (quantitative ecologist)

hi all, here is a good post-doc position in quantitative ecology working with Scott Sillett and

Mar 29

Claudio Angelini, Manuel Marton Marc KERY3

Mar 24

residual correlation matrix from spOccupancy

Dear Marc, thanks for your answer. I was not aware of the spOccupancy group. I am going to post there

unread,

residual correlation matrix from spOccupancy

Dear Marc, thanks for your answer. I was not aware of the spOccupancy group. I am going to post there

Mar 24

Mar 20

IPM workshop, Fort Collins, 13-17 October 2025

Dear all, from 13 - 17 October 2025 we plan to teach an intermediate-level workshop (in person only)

unread,

IPM workshop, Fort Collins, 13-17 October 2025

Dear all, from 13 - 17 October 2025 we plan to teach an intermediate-level workshop (in person only)

Mar 20

Chris Sutherland

Mar 20

Post-doc in South Africa

Hello folks, My colleague, Lourens Swanepoel and I have some funding for a post-doc based at the

unread,

Post-doc in South Africa

Hello folks, My colleague, Lourens Swanepoel and I have some funding for a post-doc based at the

Mar 20

Nguvan Agaigbe, Michael Schaub3

Mar 15

Advice on handling unequal temporal coverage in IPM

Thanks for the advice. On Fri, Mar 14, 2025 at 3:28 PM Michael Schaub <michael.schaub@vogelwarte.

unread,

Advice on handling unequal temporal coverage in IPM

Thanks for the advice. On Fri, Mar 14, 2025 at 3:28 PM Michael Schaub <michael.schaub@vogelwarte.

Mar 15

Mar 10

Dealing with underdispersion in JAGs

Hi all, I am working with a JAGs model that estimates abundance from vocalizations obtained via

unread,

Dealing with underdispersion in JAGs

Hi all, I am working with a JAGs model that estimates abundance from vocalizations obtained via

Mar 10

Tomas T., … John C8

Feb 28

Calculating derived statistics as in BPA 2012 is wrong - proof by a simulation study and proposed remedy

Dear all, attached you will find an update to my simulation study. I have added: 1) The direct

unread,

Calculating derived statistics as in BPA 2012 is wrong - proof by a simulation study and proposed remedy

Dear all, attached you will find an update to my simulation study. I have added: 1) The direct

Feb 28

Thomas Duchesne, … Perry de Valpine5

Feb 18

Full dynamic occupancy model using JAGS with NA in observation matrix ans observation covariates

Hi Thomas and Marc, I'm coming to the discussion late but will chime in a few ideas. I hope I

unread,

Full dynamic occupancy model using JAGS with NA in observation matrix ans observation covariates

Hi Thomas and Marc, I'm coming to the discussion late but will chime in a few ideas. I hope I

Feb 18

Matthijs Hollanders, … Perry de Valpine11

Feb 18

Ecological modeling in Stan

Dear Matt et al, I am following up on this in slow motion. Thanks for pointing out that Twitter/X

unread,

Ecological modeling in Stan

Dear Matt et al, I am following up on this in slow motion. Thanks for pointing out that Twitter/X

Feb 18

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