jpwrobinson / grazing-gradients

Collaborative OS project on herbivore grazing gradients.
2 stars 0 forks source link

Turf and rubble regime categories #15

Closed jpwrobinson closed 5 years ago

jpwrobinson commented 6 years ago

@JanDajka the benthic man. Can you help me identify which categories should be included in our new rubble and turf regime covariates? The benthic taxa vary between regions, with some surveys including dead coral (this should be included as rubble, right?) and turf recorded under different names (EAM, turf).

If we're thinking about alternate regimes that are neither hard coral or macroalgal, should we also include sand in the turf regime? This was one of 3 Pacific regimes identified by JB Jouffray et al. (2015, Proc B).

We should run our selections by Nick at some point, but we can select the groups here and start incorporating into models straightaway.

Seychelles

 [1] "struc.complexity"      "total"                 "Coraline.algae"       
 [4] "Sand"                  "Soft"                  "Rubble"               
 [7] "Rock"                  "Branch.dead"           "Massive.dead"         
[10] "Sargassum"             "Asparagopsis"          "Caulerpa"             
[13] "Red.corticated"        "Galaxora"              "Lobophyta"            
[16] "turtle.grass"          "Halimeda"              "Turbinaria_macroalgae"
[19] "Dictyota"              "Dictyopteris"          "Padina"               
[22] "Acanthastrea"          "Acropora"              "Astreopora"           
[25] "Coscinarea"            "Cyphastrea"            "Diplastrea"           
[28] "Echimopora"            "Euphyllia"             "Favia"                
[31] "Favites"               "Fungia"                "Galaxea"              
[34] "Goniastrea"            "Goniopora"             "Hydnophora"           
[37] "Leptatsrea"            "Leptoria"              "Lobopyhlia"           
[40] "Millipora"             "Montastrea"            "Montipora"            
[43] "Pavona"                "Platygyra"             "Pocilopora"           
[46] "Porites"               "Porites.branching"     "Psamocra"             
[49] "Stylophora"            "Symphilia"             "Tubiastrea"           
[52] "Tubipora"              "Turbinaria"            "sponge"               
[55] "Palythoa"              "seagrass"              "Heliopora"            
[58] "Alveopora"             "Herpolitha"            "Isopora"              
[61] "Leptoseris"            "Physogyra"             "Siderastrea"          
[64] "Stylocoeniella"        "Coralimorph"           "cyanobacteria"  

Maldives

Chagos

 [1] "Acanthastrea"              "Acropora - branching"     
 [3] "Acropora - tables"         "Alveopora"                
 [5] "Anemone"                   "Astreopora"               
 [7] "CCA"                       "Clionia sponge"           
 [9] "Ctenellia"                 "Cyphastrea"               
[11] "Dead Acropora - branching" "Dead Acropora - table"    
[13] "Diploastrea"               "Echinophyllia"            
[15] "Echinopora - encrusting"   "Echinopora - plating"     
[17] "Favia (plocoid)"           "Favites (ceriod)"         
[19] "Fungiidae"                 "Galaxea"                  
[21] "Goniastrea"                "Goniopora"                
[23] "Green Sponge"              "Halimeda"                 
[25] "Heliopora"                 "Hydonophora"              
[27] "Isopora"                   "Leptastrea"               
[29] "Leptoria"                  "Lobophyllia"              
[31] "Lobophytum"                "Millepora - encrusting"   
[33] "Millepora - erect"         "Montastrea"               
[35] "Montipora - encrusting"    "Nepthea"                  
[37] "Palythoa"                  "Pavement"                 
[39] "Pavona - encrusting"       "Pectinia"                 
[41] "Platygyra"                 "Pocillopora"              
[43] "Porites - branching"       "Porites - massive"        
[45] "Psammacora"                "Rubble"                   
[47] "Sand"                      "Sarcophyton"              
[49] "Seriatopora"               "Sinularia"                
[51] "Stylocoeniella"            "Stylophora"               
[53] "Symphyllia"                "Total hard coral cover"   
[55] "Turbinaria"                "Ulva"                     
[57] "Xenia" 

GBR


  [3] "Acropora...submassive"              "Astreopora"                        
  [5] "Isopora"                            "Montipora...encrusting"            
  [7] "Montipora...foliose"                "Montipora...submassive"            
  [9] "Pocillopora"                        "Seriatopora"                       
 [11] "Stylophora"                         "Porites...branching"               
 [13] "Porites...massive"                  "Porites...encrusting"              
 [15] "Porites...submassive"               "Alveopora"                         
 [17] "Goniopora"                          "Favia..plocoid."                   
 [19] "Favites..ceriod."                   "Goniastrea"                        
 [21] "Montastrea"                         "Caulastrea"                        
 [23] "Platygyra"                          "Cyphastrea"                        
 [25] "Oulaphyllia"                        "Leptoria"                          
 [27] "Echinopora...encrusting"            "Echinopora...plating"              
 [29] "Echinopora...branching"             "Diploastrea"                       
 [31] "Merulina"                           "Leptastrea"                        
 [33] "Gardinoseris"                       "Acanthastrea"                      
 [35] "Lobophyllia"                        "Symphyllia"                        
 [37] "Physogyra"                          "Plerogyra"                         
 [39] "Coscinaraea"                        "Mycedium"                          
 [41] "Cycloseris"                         "Coeloseris"                        
 [43] "Fungiidae"                          "Polyphillia"                       
 [45] "Halomitra"                          "Ctenactis"                         
 [47] "Echinophyllia"                      "Euphyllia"                         
 [49] "Pachyseris"                         "Tubastrea"                         
 [51] "Galaxea"                            "Tubipora"                          
 [53] "Oxypora"                            "Pectinia"                          
 [55] "Oulaphyllia.1"                      "Psammacora"                        
 [57] "Pavona"                             "Hydonophora...branching"           
 [59] "Hydnophora...plating"               "Turbinaria"                        
 [61] "Scolymia"                           "Soft.Coral"                        
 [63] "Millepora...encrusting"             "Millepora...erect"                 
 [65] "Anemone"                            "Heliopora"                         
 [67] "Giant.Clam"                         "Sponge"                            
 [69] "Other.Invertebrates"                "CCA"                               
 [71] "Sand"                               "Rubble"                            
 [73] "Pavement"                           "Ascidians"                         
 [75] "Turf"                               "Zooanthid"                         
 [77] "Caulerpa"                           "Filimentous.Green"                 
 [79] "Red.Filimentous"                    "Ulva"                              
 [81] "Coralline.Red.Branching.Macroalgae" "Actinotrichia"                     
 [83] "Cyanophyta"                         "Sargassum"                         
 [85] "Padina"                             "Tydemania"                         
 [87] "Dictyota"                           "Turbinaria..Algae."                
 [89] "Neomeris"                           "Halimeda"                          
 [91] "Chlorodesmis"                       "Unidentified.Macroalgae"           
 [93] "Epilithic.algal.matrix"             "Dead.Acropora...table"             
 [95] "Dead.Acropora...branching"          "Total.hard.coral.cover"            
 [97] "Soft.Coral.1"                       "Octocorals"                        
 [99] "Bare.Substrate"                     "CCA.1"                             
[101] "Turfs"                              "Macroalgae"                        
[103] "EAM"                                "Other.Invertebrates.1"             
[105] "Dead.Coral"                         "Sponge.1"                          
[107] "Total.no..points"```
JanDajka commented 6 years ago

Predictors: In general, there are three 'stages' in the breakdown of a reef that Shaun and I agreed on while on fieldwork. One example scenario to make the distinction: dead corals are still structurally intact and once physically broken become rubble and that gets eroded over time to sand. All three would have different theoretical effects on herbivores.

Dead corals still provide structure to fish, so it's unlikely to have a alternate effect on herbivores than our measure of hard coral would.

Rubble can move with wave energy and crush whatever settles on it, including corals and algae. Perhaps herbivores make us of it as protection though (e.g. by hiding in between / actively move it to create shelter and dig for plant matter).

Sand by itself doesn't provide protection anymore, unless a fish buries (short of cyptic gobies and blennies that aren't included in the UVCs, I don't know of a herbivore that buries). Sand is sometimes ingested by fish to "clean" their stomachs or because the sand is somewhat covered in algae matter that they ingest but those aren't very promising links.

Sand + turf: If sand becomes trapped in the turf algae, it deters grazers, protecting the turf algae and allowing them to grow more or less undisturbed. This often happens on patch reefs with low wave energy. But I've seen the opposite on reefs with high wave energy (e.g. granitic headlands), where the sand doesn't get trapped in the EAM and the turf algae lay bare, ready to be munched.

Soooo, depending on what type of reef we have, it will determine whether a turf + sand combo will make sense. Seeing as sand itself might not yield in anything, perhaps a combo and turf by itself if we can be sure about that distinction? Definitely should consult Nick about this.

Seychelles: Turf - you're right, no turf measure. I checked the data from our fieldtrip again, seems like Shaun didn't record it. Would be with a good reason though. Rubble - should be rubble by itself.

Maldives: EAM + sand depends on whether we can infer about the hydrodynamics somehow, I'd say. Talking with Nick should clear this up though. Rubble is rubblerubble, yes.

Chagos: Also no turf recorded, it seems. Rubble is rubblerubble, yes.

GBR: Turf is 'turf' + 'turfs' + 'EAM'. Maybe Nick changed his labels over the years. Would again wait to see what Nick says. Rubble is rubblerubble, yes.

jpwrobinson commented 6 years ago

Great ok. Hydrodynamics stuff is interesting for sure. We can 1) just include all these variables as predictors OR 2) use a multivariate analysis to identify regimes that exist in Nick's dataset.

2 is probably better, but we could also use 2 to select individual variables. I've asked Jamie if she has time to run this analysis.

Bigger problem is missing turf for Chagos and Seychelles. We can't really justify a turf category if it wasn't measured, even if there are good reasons to believe that turf cover is low at those reefs. To be honest that seems unlikely, because what else would the grazers be eating??

Anyway lets run by Nick next week.

JanDajka commented 6 years ago

Yeah, I agree - option 2 sounds great - hopefully Jamie has got time.

Yes, you're right - perhaps we can't use turf as a measure. At least for Seychelles, turf algae definitely are around, plenty of them.

Let's see what Nick says.

jpwrobinson commented 6 years ago

Ok I've added rubble and fishable biomass as predictors, and they should load directly in the Rmd. Model fits are much improved with both variables (see fitted ~ observed plots when you knit the 01_biomass_models.Rmd). Just need those scraper model predictions and I think we have the main substance of the biomass analysis now.

I'll try and catch Nick about turf this week

JanDajka commented 6 years ago

Yip, just working on the scrapers. Comin' up soon!

JanDajka commented 6 years ago

I uploaded the scraper model but for some reason, I couldn't get the curves to show. Must have to do with that I worked on it this morning while James was working on it. Tried to figure it out but can't find the mistake for the life of me. Do you have ideas?

jpwrobinson commented 6 years ago

Looks 100% correct dude! The models and predictions are working, but check the y-axis lims on those plots. If you look at the fishing figs, you see that predicted scraper biomass is > 2, and benthic plots max out at 2. The fishable biomass plot also misses the largest scraper values - the line shoots out the top before reaching max fishable biomass.

So pristine reefs have more herbivores. WHO KNEW!?

On Mon, 24 Sep 2018 at 15:47, Jan-Claas Dajka notifications@github.com wrote:

I uploaded the scraper model but for some reason, I couldn't get the curves to show. Must have to do with that I worked on it this morning while James was working on it. Tried to figure it out but can't find the mistake for the life of me. Do you have ideas?

— You are receiving this because you were assigned. Reply to this email directly, view it on GitHub https://github.com/jpwrobinson/grazing-gradients/issues/15#issuecomment-424000498, or mute the thread https://github.com/notifications/unsubscribe-auth/AE_TKts-aVbDYH0PbVK1nyZEjBzHmVOaks5uePCMgaJpZM4WzmO8 .

--

Dr. James Robinson

Senior Research Associate Lancaster Environment Centre Lancaster University, Lancaster, UK

Website http://jpwrobinson.wordpress.com | Github http://github.com/jpwrobinson | Twitter http://twitter.com/jamespwr

JanDajka commented 6 years ago

Ahhh, the axes - shit, stupid mistake. I'll do it now.

jpwrobinson commented 6 years ago

Awesome, looking good Jan. Particularly strong fishing effect there.

Just chatted with Nick and he suggested using rock + pavement as a measure of available substrate, which potentially is covered by turf. I added this variable to the master Rdata, and tested it out on the grazer model - it has the strongest effect on grazer biomass. Which is what we would expect if available substrate = turf availability.

How does that sound to you? Possibly could combine rubble, rock + pavement, but that might miss the dynamic habitat aspect of a rubble environment you mentioned.

@Jeneen @samanthajh suggestions welcome if you've missed this thread at all!

JanDajka commented 6 years ago

I think explaining the rubble effect would be hardest anyway. I like the combination idea!

samanthajh commented 6 years ago

Hi Guys! Haha can't really believe that we didn't think to explore the relationship with turf substrates before! Seems very obvious in hindsight lol. So.... I would probably also say to combine. So far from my filming of grazing behaviours here it seems like, especially here on the fore reef, rubble beds are sites of high grazing activity, so would be interesting to see how it all fits together. Keep up the good work!

On Wed, Sep 26, 2018 at 4:50 AM Jan-Claas Dajka notifications@github.com wrote:

I think explaining the rubble effect would be hardest anyway. I like the combination idea!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/jpwrobinson/grazing-gradients/issues/15#issuecomment-424374525, or mute the thread https://github.com/notifications/unsubscribe-auth/AlE5rqd4MFDoIh44mQRYSu8jC2wb_1oiks5uekLIgaJpZM4WzmO8 .

jpwrobinson commented 6 years ago

@JanDajka @Jeneen around for a meeting Thursday next week? I've got some prelim bite rate stuff I want to run past you, and hopefully we can talk to @JamieMcDevittIrwin about the PCA..then biomass models will be finished!

Jeneen commented 6 years ago

Sounds good to me! -------- Original message --------From: James Robinson notifications@github.com Date: 28/09/2018 11:51 (GMT+00:00) To: jpwrobinson/grazing-gradients grazing-gradients@noreply.github.com Cc: Jeneen jeneenhh@gmail.com, Mention mention@noreply.github.com Subject: Re: [jpwrobinson/grazing-gradients] Turf and rubble regime categories (#15) @JanDajka @Jeneen around for a meeting Thursday next week? I've got some prelim bite rate stuff I want to run past you, and hopefully we can talk to @JamieMcDevittIrwin about the PCA..then biomass models will be finished!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread. {"api_version":"1.0","publisher":{"api_key":"05dde50f1d1a384dd78767c55493e4bb","name":"GitHub"},"entity":{"external_key":"github/jpwrobinson/grazing-gradients","title":"jpwrobinson/grazing-gradients","subtitle":"GitHub repository","main_image_url":"https://assets-cdn.github.com/images/email/message_cards/header.png","avatar_image_url":"https://assets-cdn.github.com/images/email/message_cards/avatar.png","action":{"name":"Open in GitHub","url":"https://github.com/jpwrobinson/grazing-gradients"}},"updates":{"snippets":[{"icon":"PERSON","message":"@jpwrobinson in #15: @JanDajka @Jeneen around for a meeting Thursday next week? I've got some prelim bite rate stuff I want to run past you, and hopefully we can talk to @JamieMcDevittIrwin about the PCA..then biomass models will be finished!"}],"action":{"name":"View Issue","url":"https://github.com/jpwrobinson/grazing-gradients/issues/15#issuecomment-425399047"}}} [ { "@context": "http://schema.org", "@type": "EmailMessage", "potentialAction": { "@type": "ViewAction", "target": "https://github.com/jpwrobinson/grazing-gradients/issues/15#issuecomment-425399047", "url": "https://github.com/jpwrobinson/grazing-gradients/issues/15#issuecomment-425399047", "name": "View Issue" }, "description": "View this Issue on GitHub", "publisher": { "@type": "Organization", "name": "GitHub", "url": "https://github.com" } }, { "@type": "MessageCard", "@context": "http://schema.org/extensions", "hideOriginalBody": "false", "originator": "AF6C5A86-E920-430C-9C59-A73278B5EFEB", "title": "Re: [jpwrobinson/grazing-gradients] Turf and rubble regime categories (#15)", "sections": [ { "text": "", "activityTitle": "James Robinson", "activityImage": "https://assets-cdn.github.com/images/email/message_cards/avatar.png", "activitySubtitle": "@jpwrobinson", "facts": [

] } ], "potentialAction": [ { "name": "Add a comment", "@type": "ActionCard", "inputs": [ { "isMultiLine": true, "@type": "TextInput", "id": "IssueComment", "isRequired": false } ], "actions": [ { "name": "Comment", "@type": "HttpPOST", "target": "https://api.github.com", "body": "{\n\"commandName\": \"IssueComment\",\n\"repositoryFullName\": \"jpwrobinson/grazing-gradients\",\n\"issueId\": 15,\n\"IssueComment\": \"{{IssueComment.value}}\"\n}" } ] }, { "name": "Close issue", "@type": "HttpPOST", "target": "https://api.github.com", "body": "{\n\"commandName\": \"IssueClose\",\n\"repositoryFullName\": \"jpwrobinson/grazing-gradients\",\n\"issueId\": 15\n}" }, { "targets": [ { "os": "default", "uri": "https://github.com/jpwrobinson/grazing-gradients/issues/15#issuecomment-425399047" } ], "@type": "OpenUri", "name": "View on GitHub" }, { "name": "Unsubscribe", "@type": "HttpPOST", "target": "https://api.github.com", "body": "{\n\"commandName\": \"MuteNotification\",\n\"threadId\": 382624700\n}" } ], "themeColor": "26292E" } ]

JanDajka commented 6 years ago

Yes - back Thursday.

JanDajka commented 6 years ago

When are we meeting Thursday then? Just got asked whether I can show the new students around at 14:00.

jpwrobinson commented 6 years ago

10am work ok?

Jeneen commented 6 years ago

Good for me -------- Original message --------From: James Robinson notifications@github.com Date: 02/10/2018 11:18 (GMT+00:00) To: jpwrobinson/grazing-gradients grazing-gradients@noreply.github.com Cc: Jeneen jeneenhh@gmail.com, Mention mention@noreply.github.com Subject: Re: [jpwrobinson/grazing-gradients] Turf and rubble regime categories (#15) 10am work ok?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread. {"api_version":"1.0","publisher":{"api_key":"05dde50f1d1a384dd78767c55493e4bb","name":"GitHub"},"entity":{"external_key":"github/jpwrobinson/grazing-gradients","title":"jpwrobinson/grazing-gradients","subtitle":"GitHub repository","main_image_url":"https://assets-cdn.github.com/images/email/message_cards/header.png","avatar_image_url":"https://assets-cdn.github.com/images/email/message_cards/avatar.png","action":{"name":"Open in GitHub","url":"https://github.com/jpwrobinson/grazing-gradients"}},"updates":{"snippets":[{"icon":"PERSON","message":"@jpwrobinson in #15: 10am work ok?"}],"action":{"name":"View Issue","url":"https://github.com/jpwrobinson/grazing-gradients/issues/15#issuecomment-426222649"}}} [ { "@context": "http://schema.org", "@type": "EmailMessage", "potentialAction": { "@type": "ViewAction", "target": "https://github.com/jpwrobinson/grazing-gradients/issues/15#issuecomment-426222649", "url": "https://github.com/jpwrobinson/grazing-gradients/issues/15#issuecomment-426222649", "name": "View Issue" }, "description": "View this Issue on GitHub", "publisher": { "@type": "Organization", "name": "GitHub", "url": "https://github.com" } }, { "@type": "MessageCard", "@context": "http://schema.org/extensions", "hideOriginalBody": "false", "originator": "AF6C5A86-E920-430C-9C59-A73278B5EFEB", "title": "Re: [jpwrobinson/grazing-gradients] Turf and rubble regime categories (#15)", "sections": [ { "text": "", "activityTitle": "James Robinson", "activityImage": "https://assets-cdn.github.com/images/email/message_cards/avatar.png", "activitySubtitle": "@jpwrobinson", "facts": [

] } ], "potentialAction": [ { "name": "Add a comment", "@type": "ActionCard", "inputs": [ { "isMultiLine": true, "@type": "TextInput", "id": "IssueComment", "isRequired": false } ], "actions": [ { "name": "Comment", "@type": "HttpPOST", "target": "https://api.github.com", "body": "{\n\"commandName\": \"IssueComment\",\n\"repositoryFullName\": \"jpwrobinson/grazing-gradients\",\n\"issueId\": 15,\n\"IssueComment\": \"{{IssueComment.value}}\"\n}" } ] }, { "name": "Close issue", "@type": "HttpPOST", "target": "https://api.github.com", "body": "{\n\"commandName\": \"IssueClose\",\n\"repositoryFullName\": \"jpwrobinson/grazing-gradients\",\n\"issueId\": 15\n}" }, { "targets": [ { "os": "default", "uri": "https://github.com/jpwrobinson/grazing-gradients/issues/15#issuecomment-426222649" } ], "@type": "OpenUri", "name": "View on GitHub" }, { "name": "Unsubscribe", "@type": "HttpPOST", "target": "https://api.github.com", "body": "{\n\"commandName\": \"MuteNotification\",\n\"threadId\": 382624700\n}" } ], "themeColor": "26292E" } ]

jpwrobinson commented 6 years ago

screen shot 2018-10-02 at 11 40 54

why your email do dis @Jeneen

JanDajka commented 6 years ago

10:00 Boom!

jpwrobinson commented 6 years ago

screen shot 2018-10-02 at 13 55 40

kaboom

JanDajka commented 6 years ago

Hearts all around.