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Merge branch 'main' of https://github.com/NEFSC/READ-EDAB-enviroThres…
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jcaracappa1 committed Jul 3, 2024
2 parents de62a69 + 1b54bdb commit fc4fed1
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46 changes: 46 additions & 0 deletions get_thresholds_NRHA_atlantis.R
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# Use pulled survdat.rds file to get environmental thresholds for Atlantis groups
library(dplyr)
library(here)

# Get output data
NRHA_dt <-read.csv(here("data","NRHA_data.csv"))
atlantis_groups_dt <- read.csv(here("inputs","atlantis_codes_svspp_survey_thresholds.csv"))

# Modify data tables for ease of use
colnames(atlantis_groups_dt)[2] <- "COMNAME"
atlantis_groups_dt <- group_by(atlantis_groups_dt,Code)

atlantis_NRHA_dt <- inner_join(NRHA_dt,atlantis_groups_dt,by="COMNAME")

# The data includes a lot of 0's in the surface temperature data and some above 40 (104 F)
# for the surface temperature data. This constricts the ranges to exclude 0's and temperatures above 40.

atlantis_NRHA_dt$BottTEMP[(atlantis_NRHA_dt$BottTEMP == 0) | (atlantis_NRHA_dt$BottTEMP > 40)] <- NA
atlantis_NRHA_dt$SurfTEMP[(atlantis_NRHA_dt$SurfTEMP == 0) | (atlantis_NRHA_dt$SurfTEMP > 40)] <- NA

atlantis_NRHA_summary_table <- group_by(atlantis_NRHA_dt,Code,SEASON)
atlantis_NRHA_summary_table_SEASON <- summarise(atlantis_NRHA_summary_table, min_bottom_temp = min(BottTEMP, na.rm=T), max_bottom_temp = max(BottTEMP, na.rm=T),
min_surface_temp = min(SurfTEMP,na.rm=T), max_surface_temp = max(SurfTEMP,na.rm=T),
min_bottom_sal = min(BottSALIN,na.rm=T), max_bottom_sal = max(BottSALIN,na.rm=T),
min_surface_sal = min(SurfSALIN,na.rm=T), max_surface_sal = max(SurfSALIN,na.rm=T))


atlantis_NRHA_summary_table_SPECIES <- group_by(atlantis_NRHA_dt,Code)
atlantis_NRHA_summary_table_SPECIES <- summarise(atlantis_NRHA_summary_table_SPECIES, min_bottom_temp = min(BottTEMP, na.rm=T), max_bottom_temp = max(BottTEMP, na.rm=T),
min_surface_temp = min(SurfTEMP,na.rm=T), max_surface_temp = max(SurfTEMP,na.rm=T),
min_bottom_sal = min(BottSALIN,na.rm=T), max_bottom_sal = max(BottSALIN,na.rm=T),
min_surface_sal = min(SurfSALIN,na.rm=T), max_surface_sal = max(SurfSALIN,na.rm=T))

# Removes infinity values from the outputs and sets to NA
atlantis_NRHA_summary_table_SEASON$min_bottom_sal[(atlantis_NRHA_summary_table_SEASON$min_bottom_sal == 'Inf') | (atlantis_NRHA_summary_table_SEASON$min_bottom_sal == '-Inf')] <- 'NA'
atlantis_NRHA_summary_table_SEASON$max_bottom_sal[(atlantis_NRHA_summary_table_SEASON$max_bottom_sal == 'Inf') | (atlantis_NRHA_summary_table_SEASON$max_bottom_sal == '-Inf')] <- 'NA'
atlantis_NRHA_summary_table_SEASON$min_surface_sal[(atlantis_NRHA_summary_table_SEASON$min_surface_sal == 'Inf') | (atlantis_NRHA_summary_table_SEASON$min_surface_sal == '-Inf')] <- 'NA'
atlantis_NRHA_summary_table_SEASON$max_surface_sal[(atlantis_NRHA_summary_table_SEASON$max_surface_sal == 'Inf') | (atlantis_NRHA_summary_table_SEASON$max_surface_sal == '-Inf')] <- 'NA'

atlantis_NRHA_summary_table_SPECIES$min_bottom_sal[(atlantis_NRHA_summary_table_SPECIES$min_bottom_sal == 'Inf') | (atlantis_NRHA_summary_table_SPECIES$min_bottom_sal == '-Inf')] <- 'NA'
atlantis_NRHA_summary_table_SPECIES$max_bottom_sal[(atlantis_NRHA_summary_table_SPECIES$max_bottom_sal == 'Inf') | (atlantis_NRHA_summary_table_SPECIES$max_bottom_sal == '-Inf')] <- 'NA'
atlantis_NRHA_summary_table_SPECIES$min_surface_sal[(atlantis_NRHA_summary_table_SPECIES$min_surface_sal == 'Inf') | (atlantis_NRHA_summary_table_SPECIES$min_surface_sal == '-Inf')] <- 'NA'
atlantis_NRHA_summary_table_SPECIES$max_surface_sal[(atlantis_NRHA_summary_table_SPECIES$max_surface_sal == 'Inf') | (atlantis_NRHA_summary_table_SPECIES$max_surface_sal == '-Inf')] <- 'NA'

write.csv(atlantis_NRHA_summary_table_SEASON,here("thresholds","atlantis_seasonal_thresholds_NRHA.csv"),row.names=FALSE)
write.csv(atlantis_NRHA_summary_table_SPECIES,here("thresholds","atlantis_group_thresholds_NRHA.csv"),row.names=FALSE)
52 changes: 0 additions & 52 deletions thresholds/atlantis_group_thresholds.csv
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This file was deleted.

34 changes: 34 additions & 0 deletions thresholds/atlantis_group_thresholds_NRHA.csv
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"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"
"BLF",5.4,34,5.4,34,"0","39.5","0","39.4"
"BSB",2.3,30.42,2.76,31.3,"3.6","36.7","3","37.07"
"BUT",3.36,34.3,0.6,34.4,"0","39.5","0.7","39.4"
"COD",-1,24.78000069,-0.6,27,"11.58998","35.535","0.05","34.957"
"DOG",0.6,22.91,-0.5,28.58,"2.5","37.77","10.2","36.478"
"DRM",0.2,39.8,-0.4,38.5,"0","41.5","0","39.4"
"FDE",0.1,38.1,-0.09,34.7,"0","38.78","0","39"
"HAD",1.6,20.1,0.6,27.03,"22.19","35.742","0.05","35.891"
"HAL",2,14.1,1.21,20.82,"25.98","34.96","11.5","33.95"
"HER",-0.5,26.6,-0.75,29.7,"0.4","38.78","0","37"
"LSK",-1.4,24.3,-1.4,28.36,"3.6","36.19844","6.3","36.363"
"MAK",2.48,24.54000092,1.21,27.4,"20.5","36.18","7.64","36.25"
"OHK",3.2,17.64,2.2,29.76,"32.234","36.344","29.884","36.624"
"OPT",0.1,20.2,0.4,27.03,"22.7","36.19844","11.3","36.187"
"PLA",1.3,21.9,0.7,25.2,"20.25","38.78","9.8","35.691"
"POL",1.6,21.3,0.6,25.2,"22.19","35.512","0.05","35.445"
"QHG",3,20.7,4.6,25.3,"29.33","34.185","11","33.95"
"RED",1.5,24.82999992,1.17,26.1,"20.25","38.78","9.8","35.968"
"RHK",0.1,25,-0.4,30.8,"2","38.78","0","36.407"
"SAL",3.5,8.7,3.7,8.4,"25.8","25.8","25.3","25.3"
"SCU",3.35,28.51,3.14,30.2,"3.6","39.5","6.9","39.4"
"SDF",0.5,36.4,2.75,36.4,"0","35.726","0","35.7"
"SHK",1,24.46,0.4,29.76,"6.8","38.78","0.05","36.606"
"SK",1.7,28.8,0.7,29.8,"3.6","37.77","2","36.93"
"SUF",1.74,38.1,0.9,34,"0","41.5","0","37"
"TAU",-0.5,30.6,-0.35688,32,"9.1","35.31","6.6","36.6"
"TYL",7.95,17.95,6.64,28.8,"33.118","36.359","32.057","36.43"
"WHK",1.3,25.3,0.6,29.13,"20.25","38.78","0.05","36.389"
"WIF",-1.4,28.15999985,-1.4,32.3,"5.7","38.78","0","36"
"WPF",-1.2,38.1,-0.9,32,"0.5","41.5","0","36.94"
"WSK",-1.4,23.6,-1.4,24.41538,"11.58998","36.431","11","36.43"
"WTF",1.5,26.1,1.5,26.73,"20.25","35.894","11","36.478"
"YTF",-1,19.6,-0.6,27,"20.25","35.786","11.2","35.764"
52 changes: 52 additions & 0 deletions thresholds/atlantis_group_thresholds_survdat.csv
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"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",2,29.4,1.9,29.9,"22.1","36.487","20.286","36.493"
"BG",6.2,24.7,9.2,28.1,"NA","NA","NA","NA"
"BLF",6.3,29.4,5.58,29.9,"22.1","36.389","20.356","36.574"
"BPF",1.1,28.2,0.6,29.76,"24.138","36.554","20.286","36.574"
"BSB",2.99,29.85,2.76,29.9,"27.345","36.404","23.547","36.414"
"BUT",2.5,29.85,0.6,29.76,"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",1.1,22.91,0.6,28.58,"23.52","36.255","20.286","36.478"
"DRM",2.8,29.4,1.5,29.9,"22.1","36.62","20.356","36.613"
"FDE",1,26.78,0.9,27.25,"23.267","36.168","15.925","36.111"
"FLA",1.1,28.51,1.41,29.76,"24.655","36.846","23.231","36.613"
"FOU",0.9,26.75,1,29.76,"26.547","36.44","23.547","36.613"
"GOO",0.9,23.63,0.8,29.21,"29.705","36.342","24.249","36.478"
"HAD",1.1,18.96,0.4,27.03,"30.613","35.742","24.249","35.891"
"HAL",1.8,13.9,1,20.82,"31.056","34.96","27.148","33.873"
"HER",1.23,26.6,0.7,27,"23.267","36.418","15.925","36.38"
"ISQ",1.1,29.85,0.6,29.76,"27.643","36.512","23.547","36.624"
"LOB",1.1,24.3,0.6,27.4,"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",2.41,29.85,0.6,29.76,"22.1","36.875","20.615","36.624"
"MAK",2.48,22.53,1,27.4,"26.032","35.932","24.729","36.111"
"MEN",3.5,26.2,2.38,26.42,"23.52","35.344","21.177","35.325"
"MPF",2.6,27.55,1.9,29.76,"31.697","36.489","25.318","36.624"
"NSH",1.35,18.6,1.2,26.3,"30.895","35.853","24.249","36.17"
"OHK",1.1,17.64,2.1,29.76,"32.234","36.344","29.884","36.624"
"OPT",0.1,19.12,0.4,27.03,"26.547","35.772","15.925","36.187"
"PLA",1,16.9,0.4,25.2,"26.547","35.588","24.249","35.691"
"POL",1.3,18.56,0.6,24.3,"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",3,14.8,3.18,26.67,"32.286","35.672","30.185","35.789"
"RED",1,18.53,0.4,26.1,"31.251","35.754","25.318","35.968"
"RHK",1.36,22.49,0.88,27.4,"25.809","36.361","15.925","36.407"
"SAL",8.7,8.7,8.4,8.4,"NA","NA","NA","NA"
"SCA",1.44,22.59,1.41,28.58,"29.986","36.312","24.754","36.355"
"SCU",3.35,28.51,1,29.31,"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",1.74,24.46,0.6,29.76,"23.52","36.383","15.925","36.606"
"SMO",5.32,27.7,3.48,29.02,"26.938","36.489","20.356","36.592"
"SSH",8.1,25.67,8.01,28,"22.1","36.418","22.1","36.578"
"STB",1.96,20.97,1.88,22.54,"23.267","35.244","18.355","34.42"
"SUF",1.74,29.4,1,29.9,"22.1","36.741","20.356","36.556"
"TAU",1.7,27.7,1,28.4,"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",1.6,25.3,0.6,29.13,"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",1,18.53,1,26.73,"30.691","35.894","24.249","36.478"
"YTF",-1,19.39,-0.6,27,"26.547","35.786","15.925","35.764"
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