PCLM-D-22-00189

TrenchR: an R package for modular and accessbile microclimate and biophysical ecology

PLOS Climate

Dear Dr. Buckley,

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Academic Editor

PLOS Climate

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Reviewer #1: Yes

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Reviewer #1: Yes

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Reviewer #1: Yes

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Reviewer #1: Yes

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5. Review Comments to the Author

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Reviewer #1: This is a nice paper that introduces the TrenchR package. While not as sophisticated as several other microclimate and biophysical models, including NIcheMapR which the package seeks to complement, I can see the merit in keeping things simple, accessible, open source and replicable, and particularly as an education tool, there is a lot of merit in this. I flag education, as one of the key barriers to biophysical approaches to ecology is not the state of the science itself, but rather awareness and understanding of the basic principles among ecological researchers.

I am a new reviewer of this manuscript, which I see has already been through one round of peer-review with three reviewers. I have borne this in mind when reviewing this, as I appreciate that satisfying four or more reviewers is a tall order! Partly a reflection of this, but mostly a reflection of the way the manuscript is written and presented, my comments are relatively minor.

Lines 36-38. Not just height above ground – also that that their body temperature = shade temperature measured inside a screen

Lines 72-82. One of the things that TrenchR doesn’t really handle properly within-canopy microclimates. As I understand it, the user can manipulate ‘shade’ outside the TrenchR environment and get some handle on it this way (and a quick look at the source code suggests that e.g. its effects on soil temperature is just handled by reducing incoming solar by 50%). However, it doesn’t explicitly permit modelling of canopy radiation transmission or, perhaps more importantly, the convective heat exchange processes within the canopy which are more complex then when modelling microclimate above a vegetated surface, as heat emanates from multiple sources, and one gets counter gradient fluxes and the like. I think this is worth stating more clearly up front, as roughly 2/3 or more of the world’s animal species live inside forests. One could point to other resources for this (e.g. the microclimc R package, or e.g. Raupach 1989’s localised near-field theory model).

Line 82. You state that some components of TrenchR is best suited for ectotherms, but you could be a bit more specific here. Do you actually mean small ectotherms? I.e. it seems that body temperature is assumed uniform and at steady-state (in terms of energy fluxes) – so not really suited to something like a crocodile, where there is likely to be significant heat storage and a more complex model that considers thermal gradients in body temperature and heat storage would be needed to quantify the (surface temperature-dependent) energy fluxes.

My generally, with the focus on ‘keeping things simple’ quite a few aspects of the modelling, particularly the microclimate modelling, are understandably behind the state of the art. It would be useful to be a bit more upfront about this, as users could then make more informed choices about which approaches to use. It might, for example, be that a user opts to use NicheMapR for some aspects and not for others.

Ilya Maclean

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Reviewer #1: Yes: Ilya Maclean

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TrenchR: an R package for modular and accessbile microclimate and biophysical ecology

PCLM-D-22-00189R1

Dear Dr. Buckley,

We are pleased to inform you that your manuscript 'TrenchR: an R package for modular and accessbile microclimate and biophysical ecology' has been provisionally accepted for publication in PLOS Climate.

Before your manuscript can be formally accepted you will need to complete some formatting changes, which you will receive in a follow-up email from a member of our team. 

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Thank you again for supporting Open Access publishing; we are looking forward to publishing your work in PLOS Climate.

Best regards,

Vincent Olanrewaju Ajayi, Ph.D

Academic Editor

PLOS Climate

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Reviewer Comments (if any, and for reference):