Open gclawson1 opened 7 months ago
This will also change a bit as well, once I update the code, but here is a boxplot to show distribution of values:
Figure 3 will show something like this, but with the proportion of habitat impacted, to get an idea of how impacts are spread by raw material and taxon. I will likely add some standard error bars to it in some way as well:
And figure 4 will be a plot which includes IUCN categories. Probably something similar to this plot from Dave Williams paper, but using quantiles of impact rather than species losing >XX% of habitat:
@cottrellr I went ahead and made adjustments that we chatted about a couple of weeks ago. Now each observation in this represents an individual species. You'll notice that we see way different things with this grouping of data.
Each white dot is the mean of that taxon and the black line is the median of that taxon. I had to limit it to the 95th quantile, because otherwise it wasn't showing up. I'm planning to add a plot on the side with anything >95th quantile on this side. This also includes any species with an impact of 0.
I think it'll be really good to see a plot of the outliers, because you'll notice the terrestrial species have mean impacts way higher than the rest, indicating that they have some large outliers compared to the rest of the taxon.
I'll probably want to visualize this in a similar way you did in the other paper, with points rather than box and whisker, but I'll update it tomorrow!
Updated figure to only include BAU FCRs and added outlier
Another option is something like this:
New barchart visualization:
Lots of different stuff when visualizing this way compared to before (and I think this is technically the "more correct" way of looking at things).
Soybean is the by far the biggest impacter and is really inefficient when compared to how much of the formulations it takes up. Forage fish impacts almost directly align with the amount of the feed they occupy, which is interesting.
In the fish-dominant diet:
For the plant-dominant diet:
Cool are these mean proportions per raw material?
Sent from my iPhone
On 9 Apr 2024, at 4:07 pm, Gage Clawson @.***> wrote:
New barchart visualization:
economic_barchart.png (view on web)https://github.com/Sustainable-Aquafeeds-Project/feed_biodiv_impact_mapping/assets/33332753/0c43b170-170a-4550-9663-5a11b2cb4ad3
Lots of different stuff when visualizing this way compared to before (and I think this is technically the "more correct" way of looking at things).
Soybean is the by far the biggest impacter and is really inefficient when compared to how much of the formulations it takes up. Forage fish impacts almost directly align with the amount of the feed they occupy, which is interesting.
In the fish-dominant diet:
For the plant-dominant diet:
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Not exactly - the plot is showing the proportion of habitat impacted per raw material and taxon grouping. For example its showing that of the Marine Plant species assessed, 0.00001 of their total habitat is impacted by forage fish raw material pressure. Or that of amphibians, regardless of raw material, ~0.00002 of their habitat is impacted.
In regards to the efficiency comparison numbers I provided, I just looked at how much of the impact shown on the plot is allocated to each raw material
Its a bit different from the boxplot shown above, as that is showing individual species compared to their own habitat, whereas this barchart is showing total habitats grouped by taxon
Ah ok 👌 cool this is another nice way to chop it
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On 9 Apr 2024, at 5:03 pm, Gage Clawson @.***> wrote:
Not exactly - the plot is showing the proportion of habitat impacted per raw material and taxon grouping. For example its showing that of the Marine Plant species assessed, 0.00001 of their total habitat is impacted by forage fish raw material pressure. Or that of amphibians, regardless of raw material, ~0.00002 of their habitat is impacted.
In regards to the efficiency comparison numbers I provided, I just looked at how much of the impact shown on the plot is allocated to each raw material
Its a bit different from the boxplot shown above, as this is showing individual species compared to their own habitat, whereas this barchart is showing total habitats grouped by taxon
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IUCN Plot:
I finally figured out how to put two bars per each category and have a pattern over them... actually really really complicated. This is what I came up with. There is a lot of info and a lot of categories here... I'm thinking there might be a way to aggregate some of these groupings, but it might be important keep the taxonomic groupings consistent throughout our figures. I could also just not facet by taxon grouping, and have all of the taxon in one plot.
What do we think here? Too much info?
Also the "Not Evaluated" category are species not evaluated by the IUCN (most of the marine species from aquamaps)
Maps split by quantile values:
Going to add a histogram to the side of each plot too, something like this:
These maps are killer!
Richard S. Cottrell Research Fellow in Aquaculture Sustainability Institute for Marine and Antarctic Studies College of Sciences and Engineering University of Tasmania
Theme Co-Lead, Sustainable Futures and Planetary Health Centre for Marine Socioecology University of Tasmania
Size Ecology Labhttps://www.sizeecology.org/ | Centre for Marine Socioecologyhttps://marinesocioecology.org/themes/sustainable-futures-and-planetary-health/ Google Scholarhttps://scholar.google.com/citations?user=X1a9t90AAAAJ&hl=en&authuser=1 | ORCIDhttps://orcid.org/my-orcid?orcid=0000-0002-6499-7503 | @RichCottrell22https://twitter.com/RichCottrell22
From: Gage Clawson @.> Date: Friday, 12 April 2024 at 10:20 AM To: Sustainable-Aquafeeds-Project/feed_biodiv_impact_mapping @.> Cc: Richard Cottrell @.>, Mention @.> Subject: Re: [Sustainable-Aquafeeds-Project/feed_biodiv_impact_mapping] Publication figures (Issue #17)
Maps split by quantile values:
image.png (view on web)https://github.com/Sustainable-Aquafeeds-Project/feed_biodiv_impact_mapping/assets/33332753/3cc9c423-6c6e-4c16-816e-82011dc17d90
Going to add a histogram to the side of each plot too, something like this: image.png (view on web)https://github.com/Sustainable-Aquafeeds-Project/feed_biodiv_impact_mapping/assets/33332753/2b0e3e21-bbb1-4757-b3bb-2e10da260bf8
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I like it – maybe in the groups were there are very few species we can group into other marine or other terrestrial? Then you can provide a breakdown in the supp of what they are and explain in the text.
Did you use ggpattern for the shading?
Could also use different alpha’s if that’s any clearer?
Richard S. Cottrell Research Fellow in Aquaculture Sustainability Institute for Marine and Antarctic Studies College of Sciences and Engineering University of Tasmania
Theme Co-Lead, Sustainable Futures and Planetary Health Centre for Marine Socioecology University of Tasmania
Size Ecology Labhttps://www.sizeecology.org/ | Centre for Marine Socioecologyhttps://marinesocioecology.org/themes/sustainable-futures-and-planetary-health/ Google Scholarhttps://scholar.google.com/citations?user=X1a9t90AAAAJ&hl=en&authuser=1 | ORCIDhttps://orcid.org/my-orcid?orcid=0000-0002-6499-7503 | @RichCottrell22https://twitter.com/RichCottrell22
From: Gage Clawson @.> Date: Thursday, 11 April 2024 at 12:56 PM To: Sustainable-Aquafeeds-Project/feed_biodiv_impact_mapping @.> Cc: Richard Cottrell @.>, Mention @.> Subject: Re: [Sustainable-Aquafeeds-Project/feed_biodiv_impact_mapping] Publication figures (Issue #17)
IUCN Plot:
iucn_plot.2.png (view on web)https://github.com/Sustainable-Aquafeeds-Project/feed_biodiv_impact_mapping/assets/33332753/318ef47d-caf5-49fa-83e6-b6895ac019ff
I finally figured out how to put two bars per each category and have a pattern over them... actually really really complicated. This is what I came up with. There is a lot of info and a lot of categories here... I'm thinking there might be a way to aggregate some of these groupings, but it might be important keep the taxonomic groupings consistent throughout our figures. I could also just not facet by taxon grouping, and have all of the taxon in one plot.
What do we think here? Too much info?
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Just realised it would just be ‘Other marine species’. I like the data deficient part – real gaps in knowledge!
Also – amphibians! Not too crash hot for them.
Richard S. Cottrell Research Fellow in Aquaculture Sustainability Institute for Marine and Antarctic Studies College of Sciences and Engineering University of Tasmania
Theme Co-Lead, Sustainable Futures and Planetary Health Centre for Marine Socioecology University of Tasmania
Size Ecology Labhttps://www.sizeecology.org/ | Centre for Marine Socioecologyhttps://marinesocioecology.org/themes/sustainable-futures-and-planetary-health/ Google Scholarhttps://scholar.google.com/citations?user=X1a9t90AAAAJ&hl=en&authuser=1 | ORCIDhttps://orcid.org/my-orcid?orcid=0000-0002-6499-7503 | @RichCottrell22https://twitter.com/RichCottrell22
From: Richard Cottrell @.> Date: Friday, 12 April 2024 at 11:09 AM To: Sustainable-Aquafeeds-Project/feed_biodiv_impact_mapping @.>, Sustainable-Aquafeeds-Project/feed_biodiv_impact_mapping @.> Cc: Mention @.> Subject: Re: [Sustainable-Aquafeeds-Project/feed_biodiv_impact_mapping] Publication figures (Issue #17) I like it – maybe in the groups were there are very few species we can group into other marine or other terrestrial? Then you can provide a breakdown in the supp of what they are and explain in the text.
Did you use ggpattern for the shading?
Could also use different alpha’s if that’s any clearer?
Richard S. Cottrell Research Fellow in Aquaculture Sustainability Institute for Marine and Antarctic Studies College of Sciences and Engineering University of Tasmania
Theme Co-Lead, Sustainable Futures and Planetary Health Centre for Marine Socioecology University of Tasmania
Size Ecology Labhttps://www.sizeecology.org/ | Centre for Marine Socioecologyhttps://marinesocioecology.org/themes/sustainable-futures-and-planetary-health/ Google Scholarhttps://scholar.google.com/citations?user=X1a9t90AAAAJ&hl=en&authuser=1 | ORCIDhttps://orcid.org/my-orcid?orcid=0000-0002-6499-7503 | @RichCottrell22https://twitter.com/RichCottrell22
From: Gage Clawson @.> Date: Thursday, 11 April 2024 at 12:56 PM To: Sustainable-Aquafeeds-Project/feed_biodiv_impact_mapping @.> Cc: Richard Cottrell @.>, Mention @.> Subject: Re: [Sustainable-Aquafeeds-Project/feed_biodiv_impact_mapping] Publication figures (Issue #17)
IUCN Plot:
iucn_plot.2.png (view on web)https://github.com/Sustainable-Aquafeeds-Project/feed_biodiv_impact_mapping/assets/33332753/318ef47d-caf5-49fa-83e6-b6895ac019ff
I finally figured out how to put two bars per each category and have a pattern over them... actually really really complicated. This is what I came up with. There is a lot of info and a lot of categories here... I'm thinking there might be a way to aggregate some of these groupings, but it might be important keep the taxonomic groupings consistent throughout our figures. I could also just not facet by taxon grouping, and have all of the taxon in one plot.
What do we think here? Too much info?
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Yeah I used ggpattern for the shading!
The trickiest part was figuring out how to put two bars for each impact category. ggplot doesn't actually have that functionality built in.. so had to be a bit hacky and plot two separate geom_cols and nudge the bars to the left and right a bit and layer them onto each other.
I think that's a good idea to group into other marine species. I wonder if we should do the same for the other plots (like the box plots)? I kind of like having all of the categories in the other plots, as it doesn't necessarily make them too cluttered, but consistency throughout might be better?
For the "other marine species group", I guess I would group everything but arthropods, molluscs, and finfish and cnidaria (or elasmobranchs) maybe? That would leave it with 8 grouping total, instead of 15.
Also, here's an option for the map plot with histograms on the side to show distributions of values. Will definitely need to increase text size and other things if wanted to do something like this:
these are great. but I can't help but want to see a difference map. They look so similar, it's hard to see where the differences are.
Nice idea. Maybe the difference map could be the main plot with these two maps below? This goes to the idea that this paper will really focus on relative differences in impacts between the two feeds rather than absolute values.
Not sure the distribution of impacts tell us too much based on a quick view but could be useful in the supp. Look the same for both feeds too.
Richard S. Cottrell Research Fellow in Aquaculture Sustainability Institute for Marine and Antarctic Studies College of Sciences and Engineering University of Tasmania
Theme Co-Lead, Sustainable Futures and Planetary Health Centre for Marine Socioecology University of Tasmania
Size Ecology Labhttps://www.sizeecology.org/ | Centre for Marine Socioecologyhttps://marinesocioecology.org/themes/sustainable-futures-and-planetary-health/ Google Scholarhttps://scholar.google.com/citations?user=X1a9t90AAAAJ&hl=en&authuser=1 | ORCIDhttps://orcid.org/my-orcid?orcid=0000-0002-6499-7503 | @RichCottrell22https://twitter.com/RichCottrell22
From: bshalpern @.> Date: Friday, 12 April 2024 at 12:09 PM To: Sustainable-Aquafeeds-Project/feed_biodiv_impact_mapping @.> Cc: Richard Cottrell @.>, Mention @.> Subject: Re: [Sustainable-Aquafeeds-Project/feed_biodiv_impact_mapping] Publication figures (Issue #17) these are great. but I can't help but want to see a difference map. They look so similar, it's hard to see where the differences are.
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I think the quantile maps are important for describing the geographic pattern of impacts i.e., “we see the greatest impacts in XX and YY for the fish-dominant and AA and BB for the plant-dominant” (or maybe for each they are the same)… “with the greatest differences between diets seen in XYZ”
Richard S. Cottrell Research Fellow in Aquaculture Sustainability Institute for Marine and Antarctic Studies College of Sciences and Engineering University of Tasmania
Theme Co-Lead, Sustainable Futures and Planetary Health Centre for Marine Socioecology University of Tasmania
Size Ecology Labhttps://www.sizeecology.org/ | Centre for Marine Socioecologyhttps://marinesocioecology.org/themes/sustainable-futures-and-planetary-health/ Google Scholarhttps://scholar.google.com/citations?user=X1a9t90AAAAJ&hl=en&authuser=1 | ORCIDhttps://orcid.org/my-orcid?orcid=0000-0002-6499-7503 | @RichCottrell22https://twitter.com/RichCottrell22
From: Richard Cottrell @.> Date: Friday, 12 April 2024 at 12:17 PM To: Sustainable-Aquafeeds-Project/feed_biodiv_impact_mapping @.>, Sustainable-Aquafeeds-Project/feed_biodiv_impact_mapping @.> Cc: Mention @.> Subject: Re: [Sustainable-Aquafeeds-Project/feed_biodiv_impact_mapping] Publication figures (Issue #17) Nice idea. Maybe the difference map could be the main plot with these two maps below? This goes to the idea that this paper will really focus on relative differences in impacts between the two feeds rather than absolute values.
Not sure the distribution of impacts tell us too much based on a quick view but could be useful in the supp. Look the same for both feeds too.
Richard S. Cottrell Research Fellow in Aquaculture Sustainability Institute for Marine and Antarctic Studies College of Sciences and Engineering University of Tasmania
Theme Co-Lead, Sustainable Futures and Planetary Health Centre for Marine Socioecology University of Tasmania
Size Ecology Labhttps://www.sizeecology.org/ | Centre for Marine Socioecologyhttps://marinesocioecology.org/themes/sustainable-futures-and-planetary-health/ Google Scholarhttps://scholar.google.com/citations?user=X1a9t90AAAAJ&hl=en&authuser=1 | ORCIDhttps://orcid.org/my-orcid?orcid=0000-0002-6499-7503 | @RichCottrell22https://twitter.com/RichCottrell22
From: bshalpern @.> Date: Friday, 12 April 2024 at 12:09 PM To: Sustainable-Aquafeeds-Project/feed_biodiv_impact_mapping @.> Cc: Richard Cottrell @.>, Mention @.> Subject: Re: [Sustainable-Aquafeeds-Project/feed_biodiv_impact_mapping] Publication figures (Issue #17) these are great. but I can't help but want to see a difference map. They look so similar, it's hard to see where the differences are.
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So maybe these two in a top row followed by a big difference map between the two?
Richard S. Cottrell Research Fellow in Aquaculture Sustainability Institute for Marine and Antarctic Studies College of Sciences and Engineering University of Tasmania
Theme Co-Lead, Sustainable Futures and Planetary Health Centre for Marine Socioecology University of Tasmania
Size Ecology Labhttps://www.sizeecology.org/ | Centre for Marine Socioecologyhttps://marinesocioecology.org/themes/sustainable-futures-and-planetary-health/ Google Scholarhttps://scholar.google.com/citations?user=X1a9t90AAAAJ&hl=en&authuser=1 | ORCIDhttps://orcid.org/my-orcid?orcid=0000-0002-6499-7503 | @RichCottrell22https://twitter.com/RichCottrell22
From: Richard Cottrell @.> Date: Friday, 12 April 2024 at 12:20 PM To: Sustainable-Aquafeeds-Project/feed_biodiv_impact_mapping @.>, Sustainable-Aquafeeds-Project/feed_biodiv_impact_mapping @.> Cc: Mention @.> Subject: Re: [Sustainable-Aquafeeds-Project/feed_biodiv_impact_mapping] Publication figures (Issue #17) I think the quantile maps are important for describing the geographic pattern of impacts i.e., “we see the greatest impacts in XX and YY for the fish-dominant and AA and BB for the plant-dominant” (or maybe for each they are the same)… “with the greatest differences between diets seen in XYZ”
Richard S. Cottrell Research Fellow in Aquaculture Sustainability Institute for Marine and Antarctic Studies College of Sciences and Engineering University of Tasmania
Theme Co-Lead, Sustainable Futures and Planetary Health Centre for Marine Socioecology University of Tasmania
Size Ecology Labhttps://www.sizeecology.org/ | Centre for Marine Socioecologyhttps://marinesocioecology.org/themes/sustainable-futures-and-planetary-health/ Google Scholarhttps://scholar.google.com/citations?user=X1a9t90AAAAJ&hl=en&authuser=1 | ORCIDhttps://orcid.org/my-orcid?orcid=0000-0002-6499-7503 | @RichCottrell22https://twitter.com/RichCottrell22
From: Richard Cottrell @.> Date: Friday, 12 April 2024 at 12:17 PM To: Sustainable-Aquafeeds-Project/feed_biodiv_impact_mapping @.>, Sustainable-Aquafeeds-Project/feed_biodiv_impact_mapping @.> Cc: Mention @.> Subject: Re: [Sustainable-Aquafeeds-Project/feed_biodiv_impact_mapping] Publication figures (Issue #17) Nice idea. Maybe the difference map could be the main plot with these two maps below? This goes to the idea that this paper will really focus on relative differences in impacts between the two feeds rather than absolute values.
Not sure the distribution of impacts tell us too much based on a quick view but could be useful in the supp. Look the same for both feeds too.
Richard S. Cottrell Research Fellow in Aquaculture Sustainability Institute for Marine and Antarctic Studies College of Sciences and Engineering University of Tasmania
Theme Co-Lead, Sustainable Futures and Planetary Health Centre for Marine Socioecology University of Tasmania
Size Ecology Labhttps://www.sizeecology.org/ | Centre for Marine Socioecologyhttps://marinesocioecology.org/themes/sustainable-futures-and-planetary-health/ Google Scholarhttps://scholar.google.com/citations?user=X1a9t90AAAAJ&hl=en&authuser=1 | ORCIDhttps://orcid.org/my-orcid?orcid=0000-0002-6499-7503 | @RichCottrell22https://twitter.com/RichCottrell22
From: bshalpern @.> Date: Friday, 12 April 2024 at 12:09 PM To: Sustainable-Aquafeeds-Project/feed_biodiv_impact_mapping @.> Cc: Richard Cottrell @.>, Mention @.> Subject: Re: [Sustainable-Aquafeeds-Project/feed_biodiv_impact_mapping] Publication figures (Issue #17) these are great. but I can't help but want to see a difference map. They look so similar, it's hard to see where the differences are.
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This all makes sense to me! Here is a revised plot, with the delta plot at the bottom. I just categorized the impact as having greater impact or not for each diet type:
this is great! I love the delta plot. if there is enough spread in the data in the delta plot, it could be good to split into quartiles or similar to show where differences were higher/lower...
That's a good idea, I'll see if I can come up with a good way to visualise that!
Here is an updated IUCN category plot:
Superrrrrrr!
Richard S. Cottrell Research Fellow in Aquaculture Sustainability Institute for Marine and Antarctic Studies College of Sciences and Engineering University of Tasmania
Theme Co-Lead, Sustainable Futures and Planetary Health Centre for Marine Socioecology University of Tasmania
Size Ecology Labhttps://www.sizeecology.org/ | Centre for Marine Socioecologyhttps://marinesocioecology.org/themes/sustainable-futures-and-planetary-health/ Google Scholarhttps://scholar.google.com/citations?user=X1a9t90AAAAJ&hl=en&authuser=1 | ORCIDhttps://orcid.org/my-orcid?orcid=0000-0002-6499-7503 | @RichCottrell22https://twitter.com/RichCottrell22
From: Gage Clawson @.> Date: Friday, 12 April 2024 at 3:51 PM To: Sustainable-Aquafeeds-Project/feed_biodiv_impact_mapping @.> Cc: Richard Cottrell @.>, Mention @.> Subject: Re: [Sustainable-Aquafeeds-Project/feed_biodiv_impact_mapping] Publication figures (Issue #17)
That's a good idea, I'll see if I can come up with a good way to visualise that!
Here is an updated IUCN category plot:
iucn_plot.png (view on web)https://github.com/Sustainable-Aquafeeds-Project/feed_biodiv_impact_mapping/assets/33332753/8cb51769-e3c8-4a2b-90e4-a26180db2ab4
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Still need to sort out the legends on the delta plot, but here it is with quantiles!
You’re a wizard! This looks stunning. I think we have figure 1?
Richard S. Cottrell Research Fellow in Aquaculture Sustainability Institute for Marine and Antarctic Studies College of Sciences and Engineering University of Tasmania
Theme Co-Lead, Sustainable Futures and Planetary Health Centre for Marine Socioecology University of Tasmania
Size Ecology Labhttps://www.sizeecology.org/ | Centre for Marine Socioecologyhttps://marinesocioecology.org/themes/sustainable-futures-and-planetary-health/ Google Scholarhttps://scholar.google.com/citations?user=X1a9t90AAAAJ&hl=en&authuser=1 | ORCIDhttps://orcid.org/my-orcid?orcid=0000-0002-6499-7503 | @RichCottrell22https://twitter.com/RichCottrell22
From: Gage Clawson @.> Date: Friday, 12 April 2024 at 4:56 PM To: Sustainable-Aquafeeds-Project/feed_biodiv_impact_mapping @.> Cc: Richard Cottrell @.>, Mention @.> Subject: Re: [Sustainable-Aquafeeds-Project/feed_biodiv_impact_mapping] Publication figures (Issue #17)
Still need to sort out the legends on the delta plot, but here it is with quantiles!
economic_mean_prop_quantiles_delta.png (view on web)https://github.com/Sustainable-Aquafeeds-Project/feed_biodiv_impact_mapping/assets/33332753/4047e956-1e5b-4b02-953d-65448e4a3090
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Alright, here are the 4 figures that I have so far. Not sure if 5 figures would be too much, but it could be a good idea to visualize standard deviations and add in some efficiency stuff (although perhaps this can just be added in text somehow).
The order is this way because I imagine the flow of the paper to be 1) Hotspots of impact, here is how the scenarios differ globally on a map 2) Impacts are small (even the outliers), here is the distribution 3) Here is how each raw material impacts taxanomic groupings 4) Are at risk species impacted?
Figure 1. (A) Map of average proportion of habitat impacted per aquafeed formulation. Impacts are split by quantile group. (B) Map of impact deltas between the feed formulation scenarios. The magnitude of the difference is split into quantile groups, where darker shades indicate larger differences.
Figure 2. Distribution of proportion of habitat area impacted by taxon. Each point represents an individual species. White points indicate mean across all species in taxon. Boxes represent median and interquartile range (IQR, quartile Q1 to Q3); whiskers indicate observations 1.5x IQR below (above) Q1 (Q3) the box. Plot on the right shows points >95th quantile.
Figure 3. Contribution of impacts on total taxon AOH by raw material for each aquafeed scenario.
Figure 4. Number of species within each impact quantile, split by current IUCN status and feed formulation scenario.
These look fab, Gage!
Couple of questions:
Couple of suggestions:
Richard S. Cottrell Research Fellow in Aquaculture Sustainability Institute for Marine and Antarctic Studies College of Sciences and Engineering University of Tasmania
Theme Co-Lead, Sustainable Futures and Planetary Health Centre for Marine Socioecology University of Tasmania
Size Ecology Labhttps://www.sizeecology.org/ | Centre for Marine Socioecologyhttps://marinesocioecology.org/themes/sustainable-futures-and-planetary-health/ Google Scholarhttps://scholar.google.com/citations?user=X1a9t90AAAAJ&hl=en&authuser=1 | ORCIDhttps://orcid.org/my-orcid?orcid=0000-0002-6499-7503 | @RichCottrell22https://twitter.com/RichCottrell22
From: Gage Clawson @.> Date: Monday, 15 April 2024 at 1:37 PM To: Sustainable-Aquafeeds-Project/feed_biodiv_impact_mapping @.> Cc: Richard Cottrell @.>, Mention @.> Subject: Re: [Sustainable-Aquafeeds-Project/feed_biodiv_impact_mapping] Publication figures (Issue #17)
Alright, here are the 4 figures that I have so far. Not sure if 5 figures would be too much, but it could be a good idea to visualize standard deviations somehow as well.
The order is this way because I imagine the flow of the paper to be
economic_mean_prop_quantiles_delta.png (view on web)https://github.com/Sustainable-Aquafeeds-Project/feed_biodiv_impact_mapping/assets/33332753/209443ca-3944-4803-8fc3-a4089e37777a
Figure 1. (A) Map of average proportion of habitat impacted per aquafeed formulation. Impacts are split by quantile group. (B) Map of impact deltas between the feed formulation scenarios. The magnitude of the difference is split into quantile groups, where darker shades indicate larger differences.
economic_boxplot_prop.png (view on web)https://github.com/Sustainable-Aquafeeds-Project/feed_biodiv_impact_mapping/assets/33332753/d03028de-589e-456f-8b27-89ea5938c250
Figure 2. Distribution of proportion of habitat area impacted by taxon. Each point represents an individual species. White points indicate mean across all species in taxon. Boxes represent median and interquartile range (IQR, quartile Q1 to Q3); whiskers indicate observations 1.5x IQR below (above) Q1 (Q3) the box. Plot on the right shows points >95th quantile.
economic_barchart.png (view on web)https://github.com/Sustainable-Aquafeeds-Project/feed_biodiv_impact_mapping/assets/33332753/5ffd1e57-655d-4378-9ef4-afbc4b0bad2f
Figure 3. Contribution of impacts on total taxon AOH by raw material for each aquafeed scenario.
iucn_plot.png (view on web)https://github.com/Sustainable-Aquafeeds-Project/feed_biodiv_impact_mapping/assets/33332753/fdef07f0-05bd-44de-9fe6-d804fda7637c
Figure 4. Number of species within each impact quantile, split by current IUCN status and feed formulation scenario.
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Thanks!
Yes, as in a description of what the quantiles represent. These quantiles are different from the maps above so you need to distinguish. One is the “Impact quantile” and the other is something like “Greater impact (% difference)” or something to that effect.
Richard S. Cottrell Research Fellow in Aquaculture Sustainability Institute for Marine and Antarctic Studies College of Sciences and Engineering University of Tasmania
Theme Co-Lead, Sustainable Futures and Planetary Health Centre for Marine Socioecology University of Tasmania
Size Ecology Labhttps://www.sizeecology.org/ | Centre for Marine Socioecologyhttps://marinesocioecology.org/themes/sustainable-futures-and-planetary-health/ Google Scholarhttps://scholar.google.com/citations?user=X1a9t90AAAAJ&hl=en&authuser=1 | ORCIDhttps://orcid.org/my-orcid?orcid=0000-0002-6499-7503 | @RichCottrell22https://twitter.com/RichCottrell22
From: Gage Clawson @.> Date: Monday, 15 April 2024 at 2:56 PM To: Sustainable-Aquafeeds-Project/feed_biodiv_impact_mapping @.> Cc: Richard Cottrell @.>, Mention @.> Subject: Re: [Sustainable-Aquafeeds-Project/feed_biodiv_impact_mapping] Publication figures (Issue #17)
Thanks!
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Quick reminder to check out the reason soy impacts are higher under fish-dominant diet and associated biomass estimates for each diet.
Updated boxplot per request to make mean and median more visible
Updated map plots with new methodology, as described in #18
Although the spatial distribution of impacts looks the same, we actually see some pretty drastic differences in the actual values of proportion of habitat impacted. For example, here is the plot showing the actual values, with the dark red being areas above the 99.9th quantile of proportion of habitat impacted:
Notice the scale on the side, previously this was an order of magnitude lower. And if we look at the plant-dominant, regular, there are about 2000 cells which are above the 99.9th quantile in that plot (0.0038). The max value for plant-dominant, regular is 0.22, meaning that on average in that particular cell, 22% of the species in that cell habitat is displaced.
I think partially this is because I filter out the species which have 0 impact. There could be more than one species in that cell with 22% displacement, but some of those species might not be vulnerable to the pressure, therefore are not impacted, and excluded from the calculation. I think this is the right approach though, because if a species isn't vulnerable, then it should really matter whether we have crops or fishing there or not (if its not, I will definitely have a problem with computational power to try to include those 0 impact).
The vast majority of values are still very small (given that 99.9th quantile is 0.003, or 0.3% of habitat)
Well done Gage! The maps make a lot more sense now 0 and v interesting about the 22% of habitat
just a quick question/note on this: "I think this is the right approach though, because if a species isn't vulnerable, then it should really matter whether we have crops or fishing there or not." Are there species that are vulnerable in the plant-based diet but not the fish-based, or vice verse? If so, do you drop the zero when it is not vulnerable? That would influence the assessment of the difference between the diets and doesn't seem right. But maybe these cases don't exist.
Unfortunately the terrestrial vulnerability values don't differ across crop type. It's just if they are vulnerable to cropland agriculture or not. The marine raw materials are the same across both diets, so those don't differ either.
Yes this is a good point though. So this metric gives us an average impact value for those that are impacted. Just to clarify, did you drop the zero cells based on if there was zero impact or zero habitat? i.e., were the cells dropped when species were there but there was no impact, or when species presence in that cell = 0?
I guess both?
Cells were dropped if a species was there but there was no impact on the species (either no pressure or it is not vulnerable). If there was no species in a cell and no pressure, then that cell just wouldn't be evaluated.
Trying to make it more clear the percentage of species in the >= 95th quantile side of the plot. Does something like this work? I would have to add some explanation in the figure caption that the first percentage is the fish-dominant percentage of species in the >=95th quantile of impact. I.e., 4.5% of terrestrial mammals are in the >=95th or greater impact for fish-dominant scenario, and 8.1% for plant-dominant
I think the figure is starting to have too much information. Split plots are already hard for readers (side note: is there really no values between 0.000055 and 0.003??), and then with mean, median, box plot quantiles and N for each row, that feels like a lot. Adding in the % of species in 95th quantile, which requires two values for fish and plant dominated, starts to make my head hurt :). I think those latter numbers should just be reported in a supplementary table.
I’ll put my hand up for suggesting that, but (annoyingly for you, sorry), I think I agree. But yes, it’s all important information to be retained in the text.
Richard S. Cottrell Research Fellow in Aquaculture Sustainability Institute for Marine and Antarctic Studies College of Sciences and Engineering University of Tasmania
Theme Co-Lead, Sustainable Futures and Planetary Health Centre for Marine Socioecology University of Tasmania
Size Ecology Labhttps://www.sizeecology.org/ | Centre for Marine Socioecologyhttps://marinesocioecology.org/themes/sustainable-futures-and-planetary-health/ Google Scholarhttps://scholar.google.com/citations?user=X1a9t90AAAAJ&hl=en&authuser=1 | ORCIDhttps://orcid.org/my-orcid?orcid=0000-0002-6499-7503 | @RichCottrell22https://twitter.com/RichCottrell22
From: bshalpern @.> Date: Tuesday, 7 May 2024 at 12:36 AM To: Sustainable-Aquafeeds-Project/feed_biodiv_impact_mapping @.> Cc: Richard Cottrell @.>, Mention @.> Subject: Re: [Sustainable-Aquafeeds-Project/feed_biodiv_impact_mapping] Publication figures (Issue #17) I think the figure is starting to have too much information. Split plots are already hard for readers (side note: is there really no values between 0.000055 and 0.003??), and then with mean, median, box plot quantiles and N for each row, that feels like a lot. Adding in the % of species in 95th quantile, which requires two values for fish and plant dominated, starts to make my head hurt :). I think those latter numbers should just be reported in a supplementary table.
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Haha no worries! I agree, it is a bit crowded this way. Supplementary table/in text it is!
@bshalpern There are values between 0.000055 and 0.0003. The second panel starts at the 95th quantile cutoff value (0.00005431971). If I didn't split it that way and have a separate scale for the larger values all the smaller ones get washed out. Does adding the value at that 95th quantile line make it more clear? :
hmm, I guess I've never seen split plots that don't show some values. So yes I like this new version much better.
Before I dive too deep into making this look nice, is this kind of what we were thinking with the legend discussion earlier (but obviously with the two legends smushed together)? The values are the right hand size of the ranges (i.e. the max of the quantile ranges)
yes, but you could stretch the colors wider so that the text could be horizontal instead of vertical
Agree.
Richard S. Cottrell Research Fellow in Aquaculture Sustainability Institute for Marine and Antarctic Studies College of Sciences and Engineering University of Tasmania
Theme Co-Lead, Sustainable Futures and Planetary Health Centre for Marine Socioecology University of Tasmania
Size Ecology Labhttps://www.sizeecology.org/ | Centre for Marine Socioecologyhttps://marinesocioecology.org/themes/sustainable-futures-and-planetary-health/ Google Scholarhttps://scholar.google.com/citations?user=X1a9t90AAAAJ&hl=en&authuser=1 | ORCIDhttps://orcid.org/my-orcid?orcid=0000-0002-6499-7503 | @RichCottrell22https://twitter.com/RichCottrell22
From: bshalpern @.> Date: Thursday, 9 May 2024 at 11:48 AM To: Sustainable-Aquafeeds-Project/feed_biodiv_impact_mapping @.> Cc: Richard Cottrell @.>, Mention @.> Subject: Re: [Sustainable-Aquafeeds-Project/feed_biodiv_impact_mapping] Publication figures (Issue #17) yes, but you could stretch the colors wider so that the text could be horizontal instead of vertical
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Cool, what do we think about these? Do we prefer a box around the legends or not?
What do we think about the title underneath the legend "[ , maximum value]". Is that needed? Is there a better way to convey that the numbers are the right hand size of the range of quantile values?
Nice plots! Think I like it without the box? The box is good but I think my eye is drawn to the legend rather than the map first. Which I would think we want the other way around..?
Richard S. Cottrell Research Fellow in Aquaculture Sustainability Institute for Marine and Antarctic Studies College of Sciences and Engineering University of Tasmania
Theme Co-Lead, Sustainable Futures and Planetary Health Centre for Marine Socioecology University of Tasmania
Size Ecology Labhttps://www.sizeecology.org/ | Centre for Marine Socioecologyhttps://marinesocioecology.org/themes/sustainable-futures-and-planetary-health/ Google Scholarhttps://scholar.google.com/citations?user=X1a9t90AAAAJ&hl=en&authuser=1 | ORCIDhttps://orcid.org/my-orcid?orcid=0000-0002-6499-7503 | @RichCottrell22https://twitter.com/RichCottrell22
From: Gage Clawson @.> Date: Friday, 10 May 2024 at 12:19 PM To: Sustainable-Aquafeeds-Project/feed_biodiv_impact_mapping @.> Cc: Richard Cottrell @.>, Mention @.> Subject: Re: [Sustainable-Aquafeeds-Project/feed_biodiv_impact_mapping] Publication figures (Issue #17)
Cool, what do we think about these? Do we prefer a box around the legends or not?
image.png (view on web)https://github.com/Sustainable-Aquafeeds-Project/feed_biodiv_impact_mapping/assets/33332753/9b943ce2-44d0-4a73-b100-665a656d13d8
image.png (view on web)https://github.com/Sustainable-Aquafeeds-Project/feed_biodiv_impact_mapping/assets/33332753/c7f990d5-36dc-4006-b975-ee6e099eddae
What do we think about the title underneath the legend "[ , maximum value]". Is that needed? Is there a better way to convey that the numbers are the right hand size of the range of quantile values?
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One thing is that the max value probably needs to be a bit more descriptive. E.g., Maximum AOH impact
Richard S. Cottrell Research Fellow in Aquaculture Sustainability Institute for Marine and Antarctic Studies College of Sciences and Engineering University of Tasmania
Theme Co-Lead, Sustainable Futures and Planetary Health Centre for Marine Socioecology University of Tasmania
Size Ecology Labhttps://www.sizeecology.org/ | Centre for Marine Socioecologyhttps://marinesocioecology.org/themes/sustainable-futures-and-planetary-health/ Google Scholarhttps://scholar.google.com/citations?user=X1a9t90AAAAJ&hl=en&authuser=1 | ORCIDhttps://orcid.org/my-orcid?orcid=0000-0002-6499-7503 | @RichCottrell22https://twitter.com/RichCottrell22
From: Richard Cottrell @.> Date: Friday, 10 May 2024 at 1:18 PM To: Sustainable-Aquafeeds-Project/feed_biodiv_impact_mapping @.>, Sustainable-Aquafeeds-Project/feed_biodiv_impact_mapping @.> Cc: Mention @.> Subject: Re: [Sustainable-Aquafeeds-Project/feed_biodiv_impact_mapping] Publication figures (Issue #17) Nice plots! Think I like it without the box? The box is good but I think my eye is drawn to the legend rather than the map first. Which I would think we want the other way around..?
Richard S. Cottrell Research Fellow in Aquaculture Sustainability Institute for Marine and Antarctic Studies College of Sciences and Engineering University of Tasmania
Theme Co-Lead, Sustainable Futures and Planetary Health Centre for Marine Socioecology University of Tasmania
Size Ecology Labhttps://www.sizeecology.org/ | Centre for Marine Socioecologyhttps://marinesocioecology.org/themes/sustainable-futures-and-planetary-health/ Google Scholarhttps://scholar.google.com/citations?user=X1a9t90AAAAJ&hl=en&authuser=1 | ORCIDhttps://orcid.org/my-orcid?orcid=0000-0002-6499-7503 | @RichCottrell22https://twitter.com/RichCottrell22
From: Gage Clawson @.> Date: Friday, 10 May 2024 at 12:19 PM To: Sustainable-Aquafeeds-Project/feed_biodiv_impact_mapping @.> Cc: Richard Cottrell @.>, Mention @.> Subject: Re: [Sustainable-Aquafeeds-Project/feed_biodiv_impact_mapping] Publication figures (Issue #17)
Cool, what do we think about these? Do we prefer a box around the legends or not?
image.png (view on web)https://github.com/Sustainable-Aquafeeds-Project/feed_biodiv_impact_mapping/assets/33332753/9b943ce2-44d0-4a73-b100-665a656d13d8
image.png (view on web)https://github.com/Sustainable-Aquafeeds-Project/feed_biodiv_impact_mapping/assets/33332753/c7f990d5-36dc-4006-b975-ee6e099eddae
What do we think about the title underneath the legend "[ , maximum value]". Is that needed? Is there a better way to convey that the numbers are the right hand size of the range of quantile values?
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I'm going to add some things to this (like what the red areas mean, some distribution info about the high impact areas, decrease size of legends), but here is an updated figure with the average proportion of habitat impacted in each pixel. Dark red areas are areas that are above the 99th quantile of impacts. This is just showing BAU feed conversion ratios, so as not to cram too much information on the foundational figure: