[x] Line 8: As a non-expert this makes so much more sense with an example!
[x] Line 13: There is a difference between an encounter and an interaction isn’t there?
Is the point that:
the chance of encountering is rare,
species that encounter are not guaranteed to interact, for species to interact thier traits must be compatible
on a local scale species may not be compatible, even if elsewhere in their range they are
I feel it would help to emphasise that species need to be compatible to go from encountering to interacting?
[x] Line 22: Just to check this isn’t limited to trophic interactions?
[x] Line 80: Is it worth mentioning the distinction between direct and indirect interactions earlier?
The start of the second paragraph mentions variability in interactions and probabilistic networks,
Do probabilistic networks work for indirect interactions but this work just isn’t applicable? Or do they not and this distinction needs to be made at the start
[x] Line 86: Is this key difference here the type of data that goes into the probabilistic networks of potential or realised interactions is different? I feel like this paragraph could be clearer as to why there is a problem when assuming the type of probabilistic network
Though it is mentioned briefly in the previous one on line 66?
[x] Line 94: I’ve never heard of an interaction score, is this analagous to interaction strength in some way?
[x] Line 99: This section is really clearly explained in my opinion!
[x] Line 155: Is this worth mentioning in the metadata section earlier? I don’t think this possibility is mentioned.
[x] Line 165: This section makes sense but feels overly long because it keeps specifying that the method uses discrete time and space.
I’ve written an example below to see what you think:
In contrast, time is defined as the specific time period within which interactions were either observed or predicted. Even though space and time are continuous variables, where edge values represent probability densities (i.e., relative likelihoods of interactions occurring at infinitesimal locations and instants in time), these definitions enable them to be conceptualised as distinct patches or time segments. Treating space and time as discrete dimensions aligns with the common sampling methods of ecological networks and provides actual probabilities of interactions, which can be obtained by integrating probability densities. Furthermore, we can quantify both an area 𝐴 and a duration 𝑡, which can be readily used in spatiotemporal analyses of ecological networks. For example, when studying network-area relationships…
[x] Table 1 (after line 209): I think this is a great table, and really helps to sum up the above text. However there’s again a brief reference to the probability of observing interactions without going into any detail.
It just feels a bit lopsided; here’s all this information about what how different local interaction probabilities may be interpreted, but they could represent something completely different which we won’t talk about but reference twice in the introduction and once in the conclusion.
I think it might be worth a sentence to say we won’t focus on probability of observation in this paper, same as has been said regarding interaction strengths as opposed to presence absence.
[x] Line 313: I’m not sure what you mean by conditional variables here but my knowledge of probability is a bit rusty.
Does this mean that P(i -> j) can be any phylogenetic scale you want, it just depends how you define it?
[x] Line 382: Good job making this make good sense without the figure, I can imagine what it looks like and why!
[x] Line 414: Is this true? You mentioned earlier the difference between encountering and interacting which now seems to be overridden…
as repeated on line 401: “probability of interaction given co-occurrence and their probability of co-occurrence”. Whereas this seems to say if we watch two species in the same place for long enough they’ll interact.
[x] Line 499: Is this why we assume that every species that co-occurs and is monitored for a sufficient length of time will interact (line 414)?
Is the point that:
I feel it would help to emphasise that species need to be compatible to go from encountering to interacting?
The start of the second paragraph mentions variability in interactions and probabilistic networks, Do probabilistic networks work for indirect interactions but this work just isn’t applicable? Or do they not and this distinction needs to be made at the start
Though it is mentioned briefly in the previous one on line 66?
I’ve written an example below to see what you think:
In contrast, time is defined as the specific time period within which interactions were either observed or predicted. Even though space and time are continuous variables, where edge values represent probability densities (i.e., relative likelihoods of interactions occurring at infinitesimal locations and instants in time), these definitions enable them to be conceptualised as distinct patches or time segments. Treating space and time as discrete dimensions aligns with the common sampling methods of ecological networks and provides actual probabilities of interactions, which can be obtained by integrating probability densities. Furthermore, we can quantify both an area 𝐴 and a duration 𝑡, which can be readily used in spatiotemporal analyses of ecological networks. For example, when studying network-area relationships…
It just feels a bit lopsided; here’s all this information about what how different local interaction probabilities may be interpreted, but they could represent something completely different which we won’t talk about but reference twice in the introduction and once in the conclusion.
I think it might be worth a sentence to say we won’t focus on probability of observation in this paper, same as has been said regarding interaction strengths as opposed to presence absence.
Does this mean that P(i -> j) can be any phylogenetic scale you want, it just depends how you define it?
as repeated on line 401: “probability of interaction given co-occurrence and their probability of co-occurrence”. Whereas this seems to say if we watch two species in the same place for long enough they’ll interact.