Initial code, survey data and outputs

NEFSC · May 23, 2024 · 391df7d · 391df7d
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diff --git a/R/get_thresholds_survdat_atlantis.R b/R/get_thresholds_survdat_atlantis.R
@@ -0,0 +1,53 @@
+# Use pulled survdat.rds file to get environmental thresholds for Atlantis groups
+
+
+survdat_dt <- readRDS("C:/Users/robert.gamble/Desktop/Env_Thresholds/SurvDat/surveyPull.rds")
+
+summary_table <- group_by(survdat_dt$survdat,SVSPP,SEASON)
+summary_table_SEASON <- summarise(summary_table, min_bottom_temp = min(BOTTEMP, na.rm=T), max_bottom_temp = max(BOTTEMP, na.rm=T),
+                                min_surface_temp = min(SURFTEMP,na.rm=T), max_surface_temp = max(SURFTEMP,na.rm=T),
+                                          min_bottom_sal = min(BOTSALIN,na.rm=T), max_bottom_sal = max(BOTSALIN,na.rm=T),
+                                          min_surface_sal = min(SURFSALIN,na.rm=T), max_surface_sal = max(SURFSALIN,na.rm=T))
+
+summary_table_SPECIES <- group_by(survdat_dt$survdat,SVSPP)
+summary_table_SPECIES <- summarise(summary_table_SPECIES, min_bottom_temp = min(BOTTEMP, na.rm=T), max_bottom_temp = max(BOTTEMP, na.rm=T),
+                                  min_surface_temp = min(SURFTEMP,na.rm=T), max_surface_temp = max(SURFTEMP,na.rm=T),
+                                  min_bottom_sal = min(BOTSALIN,na.rm=T), max_bottom_sal = max(BOTSALIN,na.rm=T),
+                                  min_surface_sal = min(SURFSALIN,na.rm=T), max_surface_sal = max(SURFSALIN,na.rm=T))
+
+atlantis_groups <- read.csv("C:/Users/robert.gamble/Desktop/Env_Thresholds/SurvDat/atlantis_codes_svspp_survey_thresholds.csv")
+atlantis_group_table <- group_by(atlantis_groups,Code)
+combined_table_SEASON <- full_join(summary_table_SEASON, atlantis_group_table)
+combined_table_SEASON <- filter(combined_table_SEASON, !is.na(Code))
+
+combined_table_SEASON <- group_by(combined_table_SEASON,Code,SEASON)
+summary_table_ATLANTIS_SEASON <- summarise(combined_table_SEASON,min_bottom_temp = min(min_bottom_temp), max_bottom_temp = max(max_bottom_temp),
+                                           min_surface_temp = min(min_surface_temp), max_surface_temp = max(max_surface_temp),
+                                           min_bottom_sal = min(min_bottom_sal), max_bottom_sal = max(max_bottom_sal),
+                                           min_surface_sal = min(min_surface_sal), max_surface_sal = max(max_surface_sal))
+summary_table_ATLANTIS_SEASON <- filter(summary_table_ATLANTIS_SEASON,!is.na(SEASON))
+summary_table_ATLANTIS_SEASON$min_bottom_sal[(summary_table_ATLANTIS_SEASON$min_bottom_sal == 'Inf') | (summary_table_ATLANTIS_SEASON$min_bottom_sal == '-Inf')] <- 'NA'
+summary_table_ATLANTIS_SEASON$max_bottom_sal[(summary_table_ATLANTIS_SEASON$max_bottom_sal == 'Inf') | (summary_table_ATLANTIS_SEASON$max_bottom_sal == '-Inf')] <- 'NA'
+summary_table_ATLANTIS_SEASON$min_surface_sal[(summary_table_ATLANTIS_SEASON$min_surface_sal == 'Inf') | (summary_table_ATLANTIS_SEASON$min_surface_sal == '-Inf')] <- 'NA'
+summary_table_ATLANTIS_SEASON$max_surface_sal[(summary_table_ATLANTIS_SEASON$max_surface_sal == 'Inf') | (summary_table_ATLANTIS_SEASON$max_surface_sal == '-Inf')] <- 'NA'
+
+combined_table_SPECIES <- full_join(summary_table_SPECIES, atlantis_group_table)
+combined_table_SPECIES <- filter(combined_table_SPECIES, !is.na(Code))
+combined_table_SPECIES <- group_by(combined_table_SPECIES,Code)
+summary_table_ATLANTIS_SPECIES <- summarise(combined_table_SPECIES,min_bottom_temp = min(min_bottom_temp), max_bottom_temp = max(max_bottom_temp),
+                                           min_surface_temp = min(min_surface_temp), max_surface_temp = max(max_surface_temp),
+                                           min_bottom_sal = min(min_bottom_sal), max_bottom_sal = max(max_bottom_sal),
+                                           min_surface_sal = min(min_surface_sal), max_surface_sal = max(max_surface_sal))
+summary_table_ATLANTIS_SPECIES <- mutate(summary_table_ATLANTIS_SPECIES, isNA_temp=min_bottom_temp+max_bottom_temp+
+                                           min_surface_temp+max_surface_temp, isNA_sal = min_bottom_sal+max_bottom_sal+
+                                           min_surface_sal+max_surface_sal)
+summary_table_ATLANTIS_SPECIES <- filter(summary_table_ATLANTIS_SPECIES,(!is.na(isNA_temp) | !is.na(isNA_sal)))
+summary_table_ATLANTIS_SPECIES <- select(summary_table_ATLANTIS_SPECIES,-isNA_temp,-isNA_sal)
+
+summary_table_ATLANTIS_SPECIES$min_bottom_sal[(summary_table_ATLANTIS_SPECIES$min_bottom_sal == 'Inf') | (summary_table_ATLANTIS_SPECIES$min_bottom_sal == '-Inf')] <- 'NA'
+summary_table_ATLANTIS_SPECIES$max_bottom_sal[(summary_table_ATLANTIS_SPECIES$max_bottom_sal == 'Inf') | (summary_table_ATLANTIS_SPECIES$max_bottom_sal == '-Inf')] <- 'NA'
+summary_table_ATLANTIS_SPECIES$min_surface_sal[(summary_table_ATLANTIS_SPECIES$min_surface_sal == 'Inf') | (summary_table_ATLANTIS_SPECIES$min_surface_sal == '-Inf')] <- 'NA'
+summary_table_ATLANTIS_SPECIES$max_surface_sal[(summary_table_ATLANTIS_SPECIES$max_surface_sal == 'Inf') | (summary_table_ATLANTIS_SPECIES$max_surface_sal == '-Inf')] <- 'NA'
+
+write.csv(summary_table_ATLANTIS_SEASON,"C:/Users/robert.gamble/Desktop/Env_Thresholds/SurvDat/atlantis_seasonal_thresholds.csv",row.names=FALSE)
+write.csv(summary_table_ATLANTIS_SPECIES,"C:/Users/robert.gamble/Desktop/Env_Thresholds/SurvDat/atlantis_group_thresholds.csv",row.names=FALSE)
diff --git a/R/surveyPull.r b/R/surveyPull.r
@@ -0,0 +1,19 @@
+#' Pull survey data for envirnomental thresholds project
+#'
+#' Require temp, depth, salinity for each species at tow level to determine
+#' observed species tolerace ranges
+#'
+#' @return survdat data pull list
+
+
+channel <- dbutils::connect_to_database("NEFSC_USERS",username)
+
+data <- survdat::get_survdat_data(channel = channel,
+                                  filterByYear = NA,
+                                  all.season = T,
+                                  shg.check = T,
+                                  conversion.factor = T,
+                                  use.SAD = F,
+                                  getBio = F,
+                                  getLengths = F,
+                                  getWeightLength = F)
diff --git a/READ-EDAB-enviroThresholds.Rproj b/READ-EDAB-enviroThresholds.Rproj
@@ -0,0 +1,13 @@
+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
diff --git a/data/surveyPull.rds b/data/surveyPull.rds
diff --git a/inputs/atlantis_codes_svspp_survey_thresholds.csv b/inputs/atlantis_codes_svspp_survey_thresholds.csv
@@ -0,0 +1,191 @@
+Code,Name,SVSPP
+PSH,Dusky shark,3
+SK,Roughtail stingray,4
+SSH,Sandbar shark,9
+DSH,Sand tiger,12
+SMO,Smooth dogfish,13
+DSH,Chain dogfish,14
+DOG,Spiny dogfish,15
+DSH,Atlantic angel shark,16
+BLS,Blue shark,17
+SK,Bluntnose stingray,18
+SK,Bullnose ray,19
+SK,Atlantic torpedo,21
+SK,Barndoor skate,22
+WSK,Winter skate,23
+SK,Clearnose skate,24
+SK,Rosette skate,25
+LSK,Little skate,26
+SK,Smooth skate,27
+SK,Thorny skate,28
+BPF,Round herring,31
+HER,Atlantic herring,32
+FDE,Alewife,33
+FDE,Blueback herring,34
+FDE,American shad,35
+MEN,Menhaden,36
+FDE,Hickory shad,37
+ANC,Bay anchovy,43
+ANC,Striped anchovy,44
+BPF,Argentine,46
+MPF,Lanternfish,56
+FDF,Eel unclassified,60
+FDF,Conger eel,63
+OHK,Offshore hake,69
+SHK,Silver hake,72
+COD,Atlantic cod,73
+HAD,Haddock,74
+POL,Pollock,75
+WHK,White hake,76
+RHK,Red hake,77
+FDF,Spotted hake,78
+FDF,Fourbeard rockling,83
+FDF,Cusk,84
+FDF,Threebeard rockling,85
+FDF,Grenadier unclassified,90
+FDF,Roughhead grenadier,92
+HAL,Atlantic halibut,101
+PLA,American plaice,102
+SUF,Summer flounder,103
+FOU,Fourspot flounder,104
+YTF,Yellowtail flounder,105
+WIF,Winter flounder,106
+WTF,Witch flounder,107
+WPF,Windowpane flounder,108
+FLA,Gulfstream flounder,109
+FDF,Longspine snipefish,111
+FDF,John Dory,112
+BPF,Atlantic silverside,113
+FDF,Threespine stickleback,115
+FDF,Northern pipefish,116
+FLA,Hogchoker,118
+FDF,Trumpetfish,119
+MAK,Atlantic mackerel,121
+BPF,Chub mackerel,124
+BUT,Butterfish,131
+FDF,Atlantic moonfish,132
+FDF,Lookdown,133
+BLF,Bluefish,135
+DRM,Atlantic croaker,136
+STB,Striped Bass,139
+BSB,Black sea bass,141
+SCU,Scup,143
+DRM,Weakfish,145
+DRM,Northern kingfish,146
+DRM,Black drum,147
+DRM,Silver perch,148
+DRM,Spot,149
+TYL,Tilefish,151
+FDF,Longspine scorpionfish,154
+RED,Acadian redfish,155
+FDF,Blackbelly rosefish,156
+FDF,Sculpins unclassified,160
+FDF,Moustache sculpin,161
+FDF,Shorthorn sculpin,162
+FDF,Longhorn sculpin,163
+FDF,Sea raven,164
+FDF,Lumpfish,168
+FDF,Northern searobin,171
+FDF,Striped searobin,172
+FDF,Armored searobin,173
+FDF,Searobin uncl,174
+FDF,Cunner,176
+TAU,Tautog,177
+FDF,Oyster toadfish,185
+FDF,Wrymouth,191
+OPT,Ocean pout,193
+FDF,Northern puffer,196
+GOO,Goosefish,197
+MPF,Weitzmans pearlsides,229
+SK,Cownose ray,270
+SK,Spotted eagle ray,271
+NSH,Bristled longbeak,296
+NSH,Aesop shrimp,297
+LOB,Lobster,301
+NSH,Northern shrimp other pandalids,306
+OSH,Other penaeids,307
+RCB,Red deep-sea crab,310
+BMS,Cancer crab,311
+BMS,Jonah crab,312
+BMS,Atantic rock crab,313
+BMS,Blue crab,314
+BMS,Spider crab,317
+BMS,Horseshoe crab,318
+BMS,Lady crab,322
+BMS,Snow crab,325
+BMS,Green crab,327
+BG,Benthic grazer,331
+BMS,Knobbed whelk,337
+BFF,Iceland scallop,340
+DSH,Nurse shark,350
+PSH,White shark,351
+PSH,Shortfin mako,352
+POR,Porbeagle shark,353
+PSH,Silky shark,355
+DSH,Bull shark,356
+PSH,Blacktip shark,357
+PSH,Tiger shark,358
+DSH,Lemon shark,359
+DSH,Sharpnose shark,360
+DSH,Scalloped hammerhead,362
+PSH,Great hammerhead,363
+SK,Atlantic stingray,373
+SK,Yellow stingray,377
+FDF,Shortnose sturgeon,379
+FDF,Atlantic sturgeon,380
+SDF,American eel,384
+SCA,Sea scallop,401
+BFF,Bay scallop,402
+CLA,Atlantic surf clam,403
+BFF,Atlantic calico scallop,404
+BFF,Arctic surfclam,407
+QHG,Ocean quahog,409
+FDF,Pipefish unclassified,421
+FDE,Gizzard shad,426
+FDF,Largescale lizardfish,433
+FDF,Shortjaw lizardfish,434
+FDF,Inshore lizardfish,435
+FDF,Offshore lizardfish,437
+FDF,Red lizardfish,438
+FDF,Tomcod,453
+FDF,Atlantic needlefish,471
+FDF,Fourspine stickleback,488
+FDF,Whitenose pipefish,491
+FDF,Dusky pipefish,494
+FDF,Chain pipefish,495
+ISQ,Illex squid,502
+LSQ,Loligo squid,503
+BC,Octopus unclassified,510
+BC,Common octopus,511
+BC,Spoonarm octopus,512
+BC,Unicorn octopus,513
+FDF,Sand perch,530
+TYL,Blueline tilefish,621
+FDF,Sheepshead,631
+FDF,Hogfish,682
+BIL,Swordfish,700
+TUN,Albacore,703
+TUN,Blackfin tuna,705
+TUN,Bigeye tuna,706
+BIL,Blue marlin,707
+BIL,White marlin,708
+BPF,American sandlance,734
+TUN,Little tunny,743
+BFT,Atlantic bluefin tuna,747
+BPF,Harvest fish,749
+FDF,Lizardfish unclassified,852
+SAL,Atlantic salmon,894
+FDF,Blackspotted stickleback,901
+FDF,Ninespine stickleback,902
+OSH,Brown shrimp,913
+OSH,Pink shrimp,914
+OSH,White shrimp,915
+DSH,Thresher shark,925
+PSH,Finetooth shark,928
+PSH,Blacknose shark,929
+PSH,Bignose shark,929
+REP,Loggerhead seaturtle,950
+REP,Green seaturtle,951
+REP,Leatherback seaturtle,952
+REP,Hawksbill seaturtle,953
+REP,Kemp's Ridley seaturtle,954
diff --git a/thresholds/atlantis_group_thresholds.csv b/thresholds/atlantis_group_thresholds.csv
@@ -0,0 +1,52 @@
+"Code","min_bottom_temp","max_bottom_temp","min_surface_temp","max_surface_temp","min_bottom_sal","max_bottom_sal","min_surface_sal","max_surface_sal"
+"ANC",2,29.4,0,29.9,"22.1","36.487","20.286","36.493"
+"BG",6.2,24.7,9.2,28.1,"NA","NA","NA","NA"
+"BLF",6.3,29.4,0,29.9,"22.1","36.389","20.356","36.574"
+"BPF",1.1,28.2,0,29.76,"24.138","36.554","20.286","36.574"
+"BSB",2.99,29.85,0,29.9,"27.345","36.404","23.547","36.414"
+"BUT",0,29.85,0,29.76,"22.1","36.846","20.356","36.613"
+"CLA",3.9,24.24,3.3,26.77,"30.189","34.754","29.387","34.624"
+"COD",-1,19.2,-0.6,26.7,"26.547","35.535","24.249","34.957"
+"DOG",1.1,22.91,0,28.58,"23.52","36.255","20.286","36.478"
+"DRM",2.8,29.4,0,29.9,"22.1","36.62","20.356","36.613"
+"FDE",0,26.78,0,27.25,"23.267","36.168","15.925","36.111"
+"FLA",1.1,28.51,0,29.76,"24.655","36.846","23.231","36.613"
+"FOU",0.9,26.75,0,29.76,"26.547","36.44","23.547","36.613"
+"GOO",0,23.63,0,29.21,"29.705","36.342","24.249","36.478"
+"HAD",0,18.96,0,27.03,"30.613","35.742","24.249","35.891"
+"HAL",1.8,13.9,0,20.82,"31.056","34.96","27.148","33.873"
+"HER",1.23,26.6,0,27,"23.267","36.418","15.925","36.38"
+"ISQ",0,29.85,0,29.76,"27.643","36.512","23.547","36.624"
+"LOB",0,24.3,0,27.4,"26.547","36.107","15.925","36.466"
+"LSK",-1.4,23.45,-1.4,28.36,"23.52","35.995","15.925","36.363"
+"LSQ",2.41,29.85,0,29.76,"22.1","36.875","20.615","36.624"
+"MAK",0,22.53,0,27.4,"26.032","35.932","24.729","36.111"
+"MEN",3.5,26.2,0,26.42,"23.52","35.344","21.177","35.325"
+"MPF",2.6,27.55,0,29.76,"31.697","36.489","25.318","36.624"
+"NSH",1.35,18.6,0,26.3,"30.895","35.853","24.249","36.17"
+"OHK",0,17.64,0,29.76,"32.234","36.344","29.884","36.624"
+"OPT",0.1,19.12,0,27.03,"26.547","35.772","15.925","36.187"
+"PLA",1,16.9,0,25.2,"26.547","35.588","24.249","35.691"
+"POL",1.3,18.56,0,24.3,"30.577","35.63","27.021","35.445"
+"POR",11.34,11.34,12.59,12.59,"34.476","34.476","32.746","32.746"
+"QHG",4.91,17.51,5.51,19.22,"32.453","34.52","31.746","33.927"
+"RCB",3,14.8,0,26.67,"32.286","35.672","30.185","35.789"
+"RED",1,18.53,0,26.1,"31.251","35.754","25.318","35.968"
+"RHK",0,22.49,0,27.4,"25.809","36.361","15.925","36.407"
+"SAL",8.7,8.7,8.4,8.4,"NA","NA","NA","NA"
+"SCA",1.44,22.59,0,28.58,"29.986","36.312","24.754","36.355"
+"SCU",3.35,28.51,0,29.31,"22.1","36.741","22.1","36.578"
+"SDF",5.33,20.1,5.35,23.34,"26.995","35.726","25.031","34.708"
+"SHK",0,24.46,0,29.76,"23.52","36.383","15.925","36.606"
+"SMO",5.32,27.7,0,29.02,"26.938","36.489","20.356","36.592"
+"SSH",8.1,25.67,0,28,"22.1","36.418","22.1","36.578"
+"STB",1.96,20.97,0,22.54,"23.267","35.244","18.355","34.42"
+"SUF",1.74,29.4,0,29.9,"22.1","36.741","20.356","36.556"
+"TAU",1.7,27.7,0,28.4,"27.732","34.355","24.94","34.225"
+"TYL",3.25,19.66,2,28.8,"31.032","36.359","31.017","36.43"
+"WHK",1.6,25.3,0,29.13,"29.029","35.835","24.249","36.389"
+"WIF",-1.4,23.12,-1.4,27,"26.547","35.459","15.925","35.679"
+"WPF",-1.2,27.7,-0.9,28.7,"23.267","36.341","15.925","36.354"
+"WSK",-1.4,21.88,-1.4,25.2,"24.138","36.431","15.925","36.43"
+"WTF",0,18.53,0,26.73,"30.691","35.894","24.249","36.478"
+"YTF",-1,19.39,-0.6,27,"26.547","35.786","15.925","35.764"