1. 1a submissão
   1. Título: Estimating abundance at age with Bayesian geostatistics and compositional data analysis
   2. Autores:
      • Ernesto Jardim
      • Paulo Justiniano RIBEIRO JUNIOR
   3. Periódico:
      • Canadian Journal of Fisheries & Aquatic Sciences (CJFAS)
      • submetido em 24/Jan/2008, Texto Submetido: versão submetida
      • Status: rejeitado pelos editores (ver resposta abaixo)
2. 2a submissão
   1. Pedido de reconsideração e reavaliação feito por Ernesto ao CJFAS e aceito em 10/04/2008
   2. Título: Modelling spatio-temporal abundance at age with Bayesian geostatistics and compositional data analysis
   3. Autores:
      • Ernesto Jardim
      • Paulo Justiniano RIBEIRO JUNIOR
   4. Periódico:
      • resubmissão após contacto com editor: Canadian Journal of Fisheries & Aquatic Sciences (CJFAS)
   5. Versões do texto:
      • arquivos fonte versão 20080411
      • arquivo com sugestões de PJ, 17/04/2008, 22:40 (BRT)
      • Versão enviada à revista (submetido em 18/04/2008)

1. 3a submissão
   • Documento sobre NBGM (latest version PJ, 05.11.2008, 01:10)
   • Revisão da PJ - Sessões 1 e 2 (18/11/2008)
   • Revisão de PJ - Sessões 3 até final (20/11/2008)
     • Sugestão para texto de ressubmissão: (needs to be revised)

In this current revision of the paper we have made a major attempt to present a more objective MS

 compared to the previous version, focusing on the essence of hte propose methodology and 
 removing aspects is the previous work which were diverting the text from its mais goal without 
 substantially improving the findings or even bringing unnecessary complications if not biasing results.

Dear Dr. Jardim,

20383 - Estimating abundance at age with Bayesian geostatistics and compositional data analysis

We very much regret that we cannot consider this manuscript for publication in CJFAS. The problem concerns a conflict with our editorial policy, and does not reflect upon the quality of your science. Upon receipt of your submission, we sought advice from an Associate Editor. The consensus is that, while we recognise the importance of the study, it presents a heavier emphasis on the statistics and modelling than we typically consider for CJFAS, and therefore we believe it would be better suited to a journal such as Biometrics.

It has become evident that we must restrict the scope and size of the Journal in some way, while trying to preserve its general multi-disciplinary character. The most equitable solution, we believe, is to refer to other more specialised outlets reports that are basically descriptive, or whose novelty relates only to new data or to the particular situation studied, or methods papers that apply standard techniques without breaking new methodological ground. In other words, we attempt to select work that leads to a conceptual advance or a refined understanding of general processes or phenomena (see our policy statement inside the front cover of each Journal issue and an editorial in CJFAS 55(1): 1-2).

We trust you will appreciate that an initial editorial decision avoids the delays of the peer review process, and will allow you to re-submit your manuscript elsewhere. We thank you for your interest in CJFAS and wish you well in finding another outlet for your work.

Yours sincerely,

Don Jackson Editor

Dear Don Jackson,

Recently the CJFAS published several papers with a strong statistical emphasis. Among others you have published in 2008:

Can. J. Fish. Aquat. Sci. 65(1): 17?26 (2008) | doi:10.1139/F07-141 | © 2008 NRC Canada A statistical modeling method for estimating mortality and abundance of spawning salmon from a time series of counts R. Glenn Szerlong and David E. Rundio

Can. J. Fish. Aquat. Sci. 65(1): 117?133 (2008) | doi:10.1139/F07-153 | © 2008 NRC Canada Hierarchical Bayesian modelling with habitat and time covariates for estimating riverine fish population size by successive removal method Etienne Rivot, Etienne Prévost, Anne Cuzol, Jean-Luc Baglinière, and Eric Parent

Can. J. Fish. Aquat. Sci. 65(2): 176?197 (2008) | doi:10.1139/F07-138 | © 2008 NRC Canada Estimating abundance of spatially aggregated populations: comparing adaptive sampling with other survey designs Kathryn L. Mier and Susan J. Picquelle

All this papers have a stronger statistical burden than the paper we submitted and you rejected base on “a heavier emphasis on the statistics and modelling than we typically consider for CJFAS” and, as you said, without considering the quality of our science.

My opinion is that this paper is good and tackles an important issue for marine science, the estimation of the population structure from survey data, and I'd like to have it evaluated by the quality of the science. We revised the manuscript and added a flowchart with a visual representation of the algorithm to make it easier to understand by those not very familiar with statistics.

I really believe CJFAS is the right journal for this paper exactly because you manage, along the years, to balance between theoretical papers presenting important advances to science and holistic views that make those advances useful.

Once more I'd like to ask you to reconsider and accept this manuscript to be revised by my peers.

Sorry to bother you again, but looking at the recent CJFAS numbers made me reconsider this submission.

Best regards

EJ

Holly Foster wrote: Dear Dr. Jardim,

Thank you again for your interest in CJFAS for this work. If you have revised your work to make it more accessible to those less familiar with the statistics, we would be pleased to consider it again. You may send the revised version to me by email in Word or PDF format for an informal evaluation of its suitability for CJFAS, or you may resubmit through Osprey as a new submission for a formal evaluation. I look forward to hearing from you soon.

Best regards,

Holly Foster

Dear Holly Foster,

Thanks for the opportunity of resubmitting our work for an informal evaluation. We did a deeper revision than we foreseen initially to improve its readability which took longer than we expected. You'll notice we also changed the title.

Best regards.

EJ

The work itself looks pretty good to me and if you wish I'll make a few suggestions about technical additions as well. Spatial notions and ideas are nor foreign to the stock assessment community, and nor are Bayesian ideas now, but *few if any* handle it well. That's the real gap. The idea of a joint spatial-age composition parametric model seems to me likely to be exportable to many other stock assessment projects, so it is important you get this work published and widely read.

Há dois comentários relevantes feitos em apresentações no IPIMAR e num curso do Paulo

1. Existe um viés entre as estimativas amostrais e as geoestatísticas da abundância por ano ! Esta questão está relacionada com o efeito do GLM que produz a abundância calibrada e com a utilização do \beta do modelo espacial para estimar a abundundância. Na prática esta é uma medida diferente da média amostral e não tem que ter a mesma magnitude. Por outro lado o modelo espacial reduz a influência dos clusters de observações muito elevadas o que não acontece com a média amostral, que é muito influenciada por observações extremas. Isto está incuido no paper.

1. Na modelação das composições podia utilizar-se a profundidade para melhorar o ajuste do modelo ! É um desenvolvimento do modelo que deve sr considerado no futuro. Neste trabalho não foi incluido porque a profundidade é redundante com a longitude/latidude devido à forma da costa portuguesa e achei que não deviamos utilizar a mesma informação duas vezes. No entanto, sendo os dois modelos independentes esse não seria um problema. Deviamos incluir um comentário a esta questão.

primeira revisão