Atlnts 1 biomass landings

README.Rmd

@@ -17,47 +17,26 @@ knitr::opts_chunk$set(
 
 Atlantis is a series of submodels (biological, geophysical, fishing, assessment, and management) and as a whole simulates a Management Strategy Evaluation (MSE) procedure which allows for qualitative comparisons of different management choices. We have parameterized Atlantis for the Northeast United States Continental Shelf (NEUS), including the major functional groups from an ecosystem perspective. We have also parameterized and simulated the physiographic dynamics of the ecosystem, as well as the most important fleets. Our goal was to recreate, at least in approximate terms, the biomass, catch, and effort trends in the NEUS from 1964 to the mid 2000s.
 
-### The spatial domain
-```{r neusfig, echo=F}
-knitr::include_graphics(path="https://raw.githubusercontent.com/NOAA-EDAB/neus-atlantis/master/Geometry/AtlantisNeusDomain.PNG")
-```
-
 
 ### Development team
 
-In alphabetical order:
-
-| [jcaracappa1] | [gambler1650] |
-|-|-|
-| [![][jcaracappa1-img]][jcaracappa1] | [![][gambler1650-img]][gambler1650] |
+In alphabetical
+order:
 
-
-[jcaracappa1-img]: https://avatars1.githubusercontent.com/u/57966543?s=100&v=4
-[gambler1650-img]: https://avatars1.githubusercontent.com/u/5949383?s=100&v=4
-[jcaracappa1]: https://github.com/jcaracappa1
-[gambler1650]: https://github.com/gambler1650
+| [jcaracappa1](https://github.com/jcaracappa1)                                                      | [gambler1650](https://github.com/gambler1650)                                                     |
+| -------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------- |
+| [![](https://avatars1.githubusercontent.com/u/57966543?s=100&v=4)](https://github.com/jcaracappa1) | [![](https://avatars1.githubusercontent.com/u/5949383?s=100&v=4)](https://github.com/gambler1650) |
 
 ### Team members
 
 Members of the Atlantis team other than the core development team:
 
-In alphabetical order:
-
-| [andybeet] | [sgaichas] | [ScottLarge-NOAA] |  [slucey] | [RMORSEcode] |
-|---|---|---|---|---|
-| [![][andybeet-img]][andybeet] | [![][sgaichas-img]][sgaichas] | [![][ScottLarge-NOAA-img]][ScottLarge-NOAA] | [![][slucey-img]][slucey] | [![][RMORSEcode-img]][RMORSEcode] | 
-
-[andybeet-img]: https://avatars1.githubusercontent.com/u/22455149?s=100&v=4
-[sgaichas-img]: https://avatars1.githubusercontent.com/u/8172302?s=100&v=4
-[ScottLarge-NOAA-img]: https://avatars1.githubusercontent.com/u/62562436?s=100&v=4
-[slucey-img]: https://avatars1.githubusercontent.com/u/5578254?s=100&v=4
-[RMORSEcode-img]: https://avatars1.githubusercontent.com/u/10620840?s=100&v=4
-[andybeet]: https://github.com/andybeet
-[sgaichas]: https://github.com/sgaichas
-[ScottLarge-NOAA]: https://github.com/ScottLarge-NOAA
-[slucey]: https://github.com/slucey
-[RMORSEcode]: https://github.com/RMORSEcode
+In alphabetical
+order:
 
+| [andybeet](https://github.com/andybeet)                                                         | [sgaichas](https://github.com/sgaichas)                                                        | [slarge](https://github.com/slarge)                                                  | [slucey](https://github.com/slucey)                                                          | [RMORSEcode](https://github.com/RMORSEcode)                                                       |
+| ----------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------ | -------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------- |
+| [![](https://avatars1.githubusercontent.com/u/22455149?s=100&v=4)](https://github.com/andybeet) | [![](https://avatars1.githubusercontent.com/u/8172302?s=100&v=4)](https://github.com/sgaichas) | [![](https://avatars1.githubusercontent.com/u/5000131?s=100&v=4)](https://github.com/slarge) | [![](https://avatars1.githubusercontent.com/u/5578254?s=100&v=4)](https://github.com/slucey) | [![](https://avatars1.githubusercontent.com/u/10620840?s=100&v=4)](https://github.com/RMORSEcode) |
 
 #### Legal disclaimer
 

README.md

@@ -21,8 +21,7 @@ trends in the NEUS from 1964 to the mid
 
 ### Development team
 
-In alphabetical
-order:
+In alphabetical order:
 
 | [jcaracappa1](https://github.com/jcaracappa1)                                                      | [gambler1650](https://github.com/gambler1650)                                                     |
 | -------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------- |
@@ -32,11 +31,10 @@ order:
 
 Members of the Atlantis team other than the core development team:
 
-In alphabetical
-order:
+In alphabetical order:
 
-| [andybeet](https://github.com/andybeet)                                                         | [sgaichas](https://github.com/sgaichas)                                                        | [slarge](https://github.com/slarge)                                                  | [slucey](https://github.com/slucey)                                                          | [RMORSEcode](https://github.com/RMORSEcode)                                                       |
-| ----------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------ | -------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------- |
+| [andybeet](https://github.com/andybeet)                                                         | [sgaichas](https://github.com/sgaichas)                                                        | [slarge](https://github.com/slarge)                                                          | [slucey](https://github.com/slucey)                                                          | [RMORSEcode](https://github.com/RMORSEcode)                                                       |
+| ----------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------- |
 | [![](https://avatars1.githubusercontent.com/u/22455149?s=100&v=4)](https://github.com/andybeet) | [![](https://avatars1.githubusercontent.com/u/8172302?s=100&v=4)](https://github.com/sgaichas) | [![](https://avatars1.githubusercontent.com/u/5000131?s=100&v=4)](https://github.com/slarge) | [![](https://avatars1.githubusercontent.com/u/5578254?s=100&v=4)](https://github.com/slucey) | [![](https://avatars1.githubusercontent.com/u/10620840?s=100&v=4)](https://github.com/RMORSEcode) |
 
 #### Legal disclaimer

data-raw/Atlantis_1_5_groups_svspp_nespp3.csv

@@ -0,0 +1,234 @@
+Code,Name,SVSPP,NESPP3
+MAK,Atlantic mackerel,121,212
+HER,Atlantic herring,32,168
+WHK,White hake,76,153
+WHK,White hake,76,154
+BLF,Bluefish,135,23
+WPF,Windowpane flounder,108,125
+SUF,Summer flounder,103,121
+WIF,Winter flounder,106,119
+WIF,Winter flounder,106,120
+WTF,Witch flounder,107,122
+FOU,Fourspot flounder,104,127
+HAL,Atlantic halibut,101,159
+PLA,American plaice,102,124
+FLA,Gulfstream flounder,109,129
+FLA,Hogchoker,118,128
+BFT,Atlantic bluefin tuna,747,467
+TUN,Albacore,703,470
+TUN,Bigeye tuna,706,469
+TUN,Blackfin tuna,705,464
+TUN,Little tunny,743,468
+BIL,Blue marlin,707,217
+BIL,White marlin,708,216
+BIL,Swordfish,700,432
+MPF,Lanternfish,56,655
+MPF,Weitzmans pearlsides,229,NA
+BUT,Butterfish,131,51
+BPF,Argentine,46,NA
+BPF,American sandlance,734,206
+BPF,Harvest fish,749,165
+BPF,Atlantic silverside,113,362
+BPF,Round herring,31,166
+BPF,Chub mackerel,124,215
+BPF,Halfbeak,NA,164
+ANC,Bay anchovy,43,6
+ANC,Striped anchovy,44,NA
+GOO,Goosefish,197,11
+GOO,Goosefish,197,12
+MEN,Menhaden,36,221
+FDE,Alewife,33,1
+FDE,Gizzard shad,426,134
+FDE,Blueback herring,34,112
+FDE,Hickory shad,37,173
+FDE,American shad,35,347
+FDE,Smelt,NA,371
+COD,Atlantic cod,73,81
+COD,Atlantic cod,73,82
+SHK,Silver hake,72,509
+OHK,Offshore hake,69,508
+POL,Pollock,75,269
+POL,Pollock,75,270
+RHK,Red hake,77,152
+BSB,Black sea bass,141,335
+SCU,Scup,143,329
+TYL,Blueline tilefish,621,444
+TYL,Tilefish,151,446
+TYL,Tilefish unclassified,NA,447
+RED,Acadian redfish,155,240
+OPT,Ocean pout,193,250
+SAL,Atlantic salmon,894,305
+DRM,Atlantic croaker,136,90
+DRM,Weakfish,145,344
+DRM,Northern kingfish,146,196
+DRM,Black drum,147,106
+DRM,Silver perch,148,NA
+DRM,Spot,149,406
+STB,Striped Bass,139,418
+TAU,Tautog,177,438
+WOL,Northern wolffish,NA,668
+WOL,Spotted wolffish,NA,510
+SDF,American eel,384,115
+FDF,Spotted hake,78,662
+FDF,Fourbeard rockling,83,526
+FDF,Threebeard rockling,85,NA
+FDF,Cusk,84,96
+FDF,Roughhead grenadier,92,137
+FDF,Grenadier unclassified,90,138
+FDF,Longspine snipefish,111,NA
+FDF,John Dory,112,188
+FDF,Threespine stickleback,115,NA
+FDF,Fourspine stickleback,488,NA
+FDF,Ninespine stickleback,902,522
+FDF,Blackspotted stickleback,901,NA
+FDF,Pipefish unclassified,421,NA
+FDF,Chain pipefish,495,NA
+FDF,Dusky pipefish,494,NA
+FDF,Northern pipefish,116,526
+FDF,Whitenose pipefish,491,NA
+FDF,Trumpetfish,119,NA
+FDF,Atlantic moonfish,132,NA
+FDF,Lookdown,133,526
+FDF,Longspine scorpionfish,154,NA
+FDF,Blackbelly rosefish,156,242
+FDF,Longhorn sculpin,163,326
+FDF,Moustache sculpin,161,NA
+FDF,Shorthorn sculpin,162,NA
+FDF,Sculpins unclassified,160,326
+FDF,Sea raven,164,327
+FDF,Armored searobin,173,343
+FDF,Northern searobin,171,340
+FDF,Striped searobin,172,342
+FDF,Searobin uncl,174,341
+FDF,Cunner,176,93
+FDF,Conger eel,63,116
+FDF,Eel unclassified,60,117
+FDF,Northern puffer,196,429
+FDF,Wrymouth,191,NA
+FDF,Garfish,NA,133
+FDF,Hagfish,NA,150
+FDF,Hogfish,682,179
+FDF,Lumpfish,168,210
+FDF,Oyster toadfish,185,451
+FDF,Sand perch,530,311
+FDF,Atlantic needlefish,471,19
+FDF,Sheepshead,631,356
+FDF,Atlantic sturgeon,380,420
+FDF,Shortnose sturgeon,379,422
+FDF,Sturgeon unclassified,NA,421
+FDF,Tomcod,453,453
+FDF,Inshore lizardfish,435,526
+FDF,Largescale lizardfish,433,NA
+FDF,Lizardfish unclassified,852,NA
+FDF,Offshore lizardfish,437,NA
+FDF,Red lizardfish,438,NA
+FDF,Shortjaw lizardfish,434,NA
+HAD,Haddock,74,147
+HAD,Haddock,74,148
+YTF,Yellowtail flounder,105,123
+DOG,Spiny dogfish,15,352
+SMO,Smooth dogfish,13,351
+SSH,Sandbar shark,9,482
+DSH,Chain dogfish,14,346
+DSH,Atlantic angel shark,16,477
+DSH,Nurse shark,350,348
+DSH,Sand tiger,12,349
+DSH,Bull shark,356,489
+DSH,Lemon shark,359,492
+DSH,Sharpnose shark,360,494
+DSH,Scalloped hammerhead,362,478
+DSH,Thresher shark,925,353
+BLS,Blue shark,17,493
+POR,Porbeagle shark,353,481
+PSH,Dusky shark,3,484
+PSH,Great hammerhead,363,386
+PSH,Shortfin mako,352,355
+PSH,White shark,351,480
+PSH,Blacknose shark,354,503
+PSH,Silky shark,355,485
+PSH,Blacktip shark,357,487
+PSH,Tiger shark,358,491
+PSH,Finetooth shark,928,499
+PSH,Bignose shark,929,483
+WSK,Winter skate,23,367
+LSK,Little skate,26,366
+SK,Barndoor skate,22,368
+SK,Clearnose skate,24,372
+SK,Rosette skate,25,364
+SK,Smooth skate,27,369
+SK,Thorny skate,28,370
+SK,Atlantic torpedo,21,526
+SK,Bullnose ray,19,NA
+SK,Cownose ray,270,285
+SK,Spotted eagle ray,271,NA
+SK,Bluntnose stingray,18,NA
+SK,Roughtail stingray,4,NA
+SK,Atlantic stingray,373,286
+SK,Yellow stingray,377,NA
+SB,Seabirds,NA,NA
+PIN,Pinnipeds,NA,NA
+REP,Green seaturtle,951,809
+REP,Hawksbill seaturtle,953,814
+REP,Kemp’s Ridley seaturtle,954,810
+REP,Leatherback seaturtle,952,812
+REP,Loggerhead seaturtle,950,813
+REP,Olive Ridley seaturtle,NA,818
+REP,Turtles unclassified,NA,816
+RWH,Right whales,NA,NA
+BWH,Baleen whales,NA,NA
+SWH,Small toothed whales,NA,NA
+TWH,Toothed whales ,NA,NA
+INV,Invasive vertebrate species,NA,NA
+LSQ,Loligo squid,503,801
+ISQ,Illex squid,502,802
+SCA,Sea scallop,401,800
+QHG,Ocean quahog,409,754
+CLA,Atlantic surf clam,403,769
+BFF,Bay scallop,402,799
+BFF,Atlantic calico scallop,404,797
+BFF,Iceland scallop,340,795
+BFF,Scallop unclassified,NA,796
+BFF,Arctic surfclam,407,765
+BG,Benthic grazer,331,NA
+LOB,Lobster,301,727
+RCB,Red deep-sea crab,310,710
+BMS,Atantic rock crab,313,712
+BMS,Blue crab,314,700
+BMS,Cancer crab,311,714
+BMS,Green crab,327,708
+BMS,Hermit crab,NA,702
+BMS,Horseshoe crab,318,724
+BMS,Jonah crab,312,711
+BMS,Lady crab,322,701
+BMS,Snow crab,325,718
+BMS,Spider crab,317,715
+BMS,Knobbed whelk,337,777
+NSH,Northern shrimp other pandalids,306,736
+NSH,Aesop shrimp,297,NA
+NSH,Bristled longbeak,296,NA
+OSH,Pink shrimp,914,NA
+OSH,Brown shrimp,913,NA
+OSH,White shrimp,915,NA
+OSH,Other penaeids,307,NA
+ZL,Carnivorous zooplankton,NA,NA
+BD,Deposit Feeder,NA,NA
+MA,Macroalgae,NA,NA
+MB,Microphtybenthos,NA,NA
+SG,Seagrass,NA,NA
+BC,Starfish,NA,828
+BC,Common octopus,511,NA
+BC,Octopus unclassified,510,786
+BC,Spoonarm octopus,512,NA
+BC,Unicorn octopus,513,NA
+ZG,Gelatinous zooplankton,NA,NA
+PL,Diatom,NA,NA
+DF,Dinoflagellates,NA,NA
+PS,Pico-phytoplankton,NA,NA
+ZM,Mesozooplankton,NA,NA
+ZS,Microzooplankton,NA,NA
+PB,Pelagic Bacteria,NA,NA
+BB,Sediment Bacteria,NA,NA
+BO,Meiobenthos,NA,NA
+DL,Labile detritus,NA,NA
+DR,Refractory detritus,NA,NA
+DC,Carrion3,NA,NA