title: “MBON SDG14 FKNMS Ecological Classifications” author: “Megan Hepner” date: “May 5, 2017” output: html_document —

Sustainable Development Goal

SDG14: Conserve and sustainably use the oceans, seas and marine resources + SDG14.2:VBy 2020, sustainably manage, and protect marine and coastal ecosystems to avoid significant adverse impacts, including by strengthening their resilience and take action for their restoration, to achieve healthy and productive oceans

National Marine Sanctuary Condition Report Questions

Water Quality

  1. What is the eutrophic condition of the sanctuary waters and how is it changing?
  2. Do sanctuary waters pose risks to human health and how are they changing?
  3. Have recent changes in climate alter water conditions and how are they changing?
  4. Are other stressors, individually or in combination, affecting water quality, and how are they changing?

Habitat Resources

  1. What is the integrity of major habitat types and how are they changing?
  2. What are contaminant concentrations in sanctuary habitats and how are they changing?

Living Resources

  1. What is the status and trend of keystone and foundation species and how is it changing?
  2. What is the status and trend of other focal species and how is it changing?
  3. What is the status of non-indigenous species and how is it changing?
  4. What is the status of biodiversity and how is it changing?

Maritime Archeological Resources

  1. What is the archaeological integrity of known maritime archaeological resources and how is it changing?
  2. Do known maritime archaeological resources pose an environmental hazard and how is this threat changing?

Human Demensions

  1. What are the levels of human activities that may adversely influence water quality and how are they changing?
  2. What are the levels of human activities that may adversely influence habitats and how are they changing?
  3. What are the levels of human activities that may adversely influence living resource quality and how are they changing?
  4. What are the levels of human activities that may adversely influence maritime archaeological resource quality and how are they changing?
  5. What are the states of influential human drivers and how are they changing?

FKNMS Infographic data

Classification level Icon Metric Dataset
Trophic groups Forage fish abundance, density, richness simpson, shannon RVC
Trophic groups Grouper abundance, density, richness simpson, shannon RVC
Trophic groups Grunt abundance, density, richness simpson, shannon RVC
Trophic groups Higher level reef fish abundance, density, richness simpson, shannon RVC
Trophic groups Hogfish abundance, density, richness simpson, shannon RVC
Trophic groups Lionfish abundance, density RVC
Trophic groups Opportunists abundance, density, richness simpson, shannon RVC
Trophic groups Parrotfish abundance, density, richness simpson, shannon RVC
Trophic groups Rays abundance, density, richness simpson, shannon RVC
Trophic groups Seabass and Hamlets abundance, density, richness simpson, shannon RVC
Trophic groups Sharks abundance, density, richness simpson, shannon RVC
Trophic groups Small reeffish abundance, density, richness simpson, shannon RVC
Trophic groups Snapper abundance, density, richness simpson, shannon RVC
Trophic level Trophic pyramid biomass RVC
Focal species Exploited fish abundance, density RVC
Biodiversity Reef fish biodiversity richness, simpson, shannon RVC
Foundation species Stony coral percent cover & diseased CREMP
Foundation species Sea fan percent cover & diseased CREMP
Foundation species Macroalgae percent cover & diseased CREMP
Foundation species Sponges percent cover & diseased CREMP
Keystone species Long-spinned sea urchin abundance TBD
Focal species Caribbean spiny lobster abundance TBD
Focal species Queen Conch abundance TBD
Focal species ) Sea turtles abundance TBD 
#rm(list = ls())
library(knitr)
## Warning: package 'knitr' was built under R version 3.3.2
library(tidyverse)
## Warning: package 'tidyverse' was built under R version 3.3.2
## Loading tidyverse: ggplot2
## Loading tidyverse: tibble
## Loading tidyverse: tidyr
## Loading tidyverse: readr
## Loading tidyverse: purrr
## Loading tidyverse: dplyr
## Warning: package 'ggplot2' was built under R version 3.3.2
## Warning: package 'tidyr' was built under R version 3.3.2
## Conflicts with tidy packages ----------------------------------------------
## filter(): dplyr, stats
## lag():    dplyr, stats
library(rvc)
library(vegan)
## Warning: package 'vegan' was built under R version 3.3.2
## Loading required package: permute
## Loading required package: lattice
## Warning: package 'lattice' was built under R version 3.3.2
## This is vegan 2.4-2
library(dygraphs)
## Warning: package 'dygraphs' was built under R version 3.3.2

Reef Visual Census (RVC)

In order to get the big RDS files, Megan shared her Dropbox folder big_csv, so on Mac in Terminal shell (or directly in Git pane, gear icon, Shell…), run this command to symbolically link the big_csv folder:

ln -s ~/Dropbox/big_csv big_csv
#rds files to read 
RVCdata_FK_rds = 'big_csv/RVCdata_FK.rds'
RVCdata_DT_rds = 'big_csv/RVCdata_DT.rds'
rvc94_16_csv = 'big_csv/rvc94_16.csv'

if (!all(file.exists(RVCdata_FK_rds, RVCdata_DT_rds))){
  RVCdata_FK <- getRvcData(1999:2016, "FLA KEYS", server = 'https://www.sefsc.noaa.gov/rvc_analysis20/')
  write_rds(RVCdata_FK, 'big_csv/RVCdata_FK.rds')
  RVCdata_DT <- getRvcData(1999:2016, "DRY TORT", server = 'https://www.sefsc.noaa.gov/rvc_analysis20/')
  write_rds(RVCdata_DT, 'big_csv/RVCdata_DT.rds')
} else{ #read data
RVCdata_FK = read_rds('big_csv/RVCdata_FK.rds')
RVCdata_DT = read_rds('big_csv/RVCdata_DT.rds')}

# add 1994 - 1998 RVC data and reweight by strata
if (!file.exists(rvc94_16_csv)){
  rvc98 <-read.csv("90srvc/fk1998_dat2.csv")
  rvc97 <-read.csv("90srvc/fk1997_dat2.csv")
  rvc96 <-read.csv("90srvc/fk1996_dat2.csv")
  rvc95 <-read.csv("90srvc/fk1995_dat2.csv")
  rvc94 <-read.csv("90srvc/fk1994_dat2.csv")
  rvc94_16 <- rbind(RVCdata_FK$sample_data, rvc98, rvc97, rvc96, rvc95, rvc94)
  write_csv(rvc94_16, "big_csv/rvc94_16.csv")
} else {
  rvc94_16 = read.csv("big_csv/rvc94_16.csv")
}

strat94 <- read.csv("90srvc/FKeys_NTOTS_Reweight_1994.csv")
strat <- strat94[which(strat94$YEAR<1999),]
RVCdata_FK$sample_data <- rvc94_16
RVCdata_FK$stratum_data <- rbind(strat,RVCdata_FK$stratum_data)

Trophic Groups

  1. Forage fish
  2. Grouper
  3. Grunts
  4. Higher Level Reef Fish
  5. Hogfish
  6. Lionfish
  7. Opportunists
  8. Parrotfish
  9. Rays
  10. Sea bass and Hamlets
  11. Sharks
  12. Small Reef Fish
  13. Snappers

Forage fish

Scientific name Common name RVC code
Hypoatherina harringtonensis reef silverside HYP HARR
Atherinomorus stipes hardhead silverside ATH STIP
Jenkinsia sp. herring species JEN SPE.
Harengula jaguana scaled sardine HAR JAGU
Anchoa lyolepis dusky anchovy ANC LYOL
Inermia vittata boga INE VITT
Hemiramphus brasiliensis ballyhoo HEM BRAS
Sardinella aurita spanish sardine SAR AURI
Harengula humeralis redear sardine HAR HUME
Chriodorus atherinoides hardhead halfbeak CHR ATHE 
forage_fk_abun_csv     = "trophic_groups/abundance/forage_fk_abun.csv"
forage_dt_abun_csv     = "trophic_groups/abundance/forage_dt_abun.csv"
forage_fk_den_csv      = "trophic_groups/density/forage_fk_den.csv"
forage_dt_den_csv      = "trophic_groups/density/forage_dt_den.csv"
forage_fk_diversity_csv= "trophic_groups/diversity/forage_fk_diversity.csv"
forage_dt_diversity_csv= "trophic_groups/diversity/forage_dt_diversity.csv"

if (!all(
  file.exists(
    forage_fk_abun_csv, forage_dt_abun_csv, forage_fk_den_csv, forage_dt_den_csv,
    forage_fk_diversity_csv, forage_dt_diversity_csv))){
  
  forage_fish_spp_list= c("HYP HARR", "ATH STIP", "JEN SPE.", "HAR JAGU", "ANC LYOL", "INE VITT", "HEM BRAS", "SAR AURI", "HAR HUME", "CHR ATHE")
  #abundance
  forage_fk_abun = getDomainAbundance(RVCdata_FK, forage_fish_spp_list, merge_protected = F)
  write_csv(forage_fk_abun, "big_csv/trophic_groups/abundance/forage_fk_abun.csv")
  forage_dt_abun = getDomainAbundance(RVCdata_DT, forage_fish_spp_list, merge_protected = F)
  write_csv(forage_dt_abun, "big_csv/trophic_groups/abundance/forage_dt_abun.csv")
  #density
  forage_fk_den = getDomainDensity(RVCdata_FK, forage_fish_spp_list, merge_protected = F)
  write_csv(forage_fk_den, "big_csv/trophic_groups/density/forage_fk_den.csv")
  forage_dt_den = getDomainDensity(RVCdata_DT, forage_fish_spp_list, merge_protected = F)
  write_csv(forage_dt_den, "big_csv/trophic_groups/density/forage_dt_den.csv")
  
  #fk diversity metrics 
  forage_fk_abundance = forage_fk_abun %>% 
    select(YEAR, protected_status, SPECIES_CD, abundance) %>%  
    group_by(YEAR, protected_status) %>% #48 groups 
    nest(-YEAR) %>%  
    mutate(
      data_wide = map(data, ~ spread(data=.x, SPECIES_CD, abundance, fill = 0)), 
      #species richness 
      richness = map(
        data_wide, 
        function(x) specnumber(x)),
      #simpson diversity as effective number of species 
      simpson = map( 
        data_wide,
        function(x) 1/(1 - diversity(x, index = 'simpson'))),
      #shannon diversity as effective number of species 
      shannon = map(
        data_wide,
        function(x) exp(diversity(x, index = 'shannon')))) %>%
    unnest(richness, simpson, shannon)
  
  forage_fk_diversity = forage_fk_abundance %>%
    select(YEAR, protected_status, richness, shannon, simpson) 
  write_csv(forage_fk_diversity, "big_csv/trophic_groups/diversity/forage_fk_diversity.csv")
  
  # dt diversity 
  forage_dt_abundance = forage_dt_abun %>% 
    select(YEAR, protected_status, SPECIES_CD, abundance) %>%  
    group_by(YEAR, protected_status) %>% #48 groups 
    nest(-YEAR) %>%  
    mutate(
      data_wide = map(data, ~ spread(data=.x, SPECIES_CD, abundance, fill = 0)), 
      #species richness 
      richness = map(
        data_wide, 
        function(x) specnumber(x)),
      #simpson diversity as effective number of species 
      simpson = map( 
        data_wide,
        function(x) 1/(1 - diversity(x, index = 'simpson'))),
      #shannon diversity as effective number of species 
      shannon = map(
        data_wide,
        function(x) exp(diversity(x, index = 'shannon')))) %>%
    unnest(richness, simpson, shannon)
  forage_dt_diversity = forage_dt_abundance %>%
    select(YEAR, protected_status, richness, shannon, simpson) 
  write_csv(forage_dt_diversity, "trophic_groups/diversity/forage_dt_diversity.csv")
}

Grouper

Scientific name Common name RVC code
Cephalopholis cruentata graysby CEP CRUE
Cephalopholis fulva coney CEP FULV
Dermatolepis inermis marbled grouper DER INER
Epinephelus flavolimbatus yellowedge grouper EPI FLAV
Epinephelus itajara goliath grouper EPI ITAJ
Epinephelus morio red grouper EPI MORI
Epinephelus niveatus snowy grouper EPI NIVE
Epinephelus striatus nassau grouper EPI STRI
grouper-sea bass species grouper-sea bass sp SRR SPE.
Mycteroperca acutirostris western comb grouper MYC ACUT
Mycteroperca bonaci black grouper MYC BONA
Mycteroperca interstitialis yellowmouth grouper MYC INTE
Mycteroperca microlepis gag MYC MICR
Mycteroperca phenax scamp MYC PHEN
Mycteroperca tigris tiger grouper MYC TIGR
Mycteroperca venenosa yellowfin grouper MYC VENE 
grouper_fk_abun_csv     = "trophic_groups/abundance/grouper_fk_abun.csv"
grouper_dt_abun_csv     = "trophic_groups/abundance/grouper_dt_abun.csv"
grouper_fk_den_csv      = "trophic_groups/density/grouper_fk_den.csv"
grouper_dt_den_csv      = "trophic_groups/density/grouper_dt_den.csv"
grouper_fk_diversity_csv= "trophic_groups/diversity/grouper_fk_diversity.csv"
grouper_dt_diversity_csv= "trophic_groups/diversity/grouper_dt_diversity.csv"

if(!all(file.exists(grouper_fk_abun_csv,grouper_dt_abun_csv,grouper_fk_den_csv,grouper_dt_den_csv, grouper_fk_diversity_csv,grouper_dt_diversity_csv))){
  
grouper_spp_list= c("CEP CRUE", "MYC BONA", "EPI MORI", "EPI STRI", "EPI ITAJ", "CEP FULV", "MYC MICR", "MYC PHEN", "MYC VENE", "MYC INTE", "MYC TIGR", "EPI FLAV", "DER INER", "SRR SPE.", "Epi nive", "Myc acut")

#abundance
grouper_fk_abun = getDomainAbundance(RVCdata_FK, grouper_spp_list, merge_protected = F)
write_csv(grouper_fk_abun, "big_csv/trophic_groups/abundance/grouper_fk_abun.csv")

grouper_dt_abun = getDomainAbundance(RVCdata_DT, grouper_spp_list, merge_protected = F)
write_csv(grouper_dt_abun, "big_csv/trophic_groups/abundance/grouper_dt_abun.csv")

#density
grouper_fk_den = getDomainDensity(RVCdata_FK, grouper_spp_list, merge_protected = F)
write_csv(grouper_fk_den, "big_csv/trophic_groups/density/grouper_fk_den.csv")

grouper_dt_den = getDomainDensity(RVCdata_DT, grouper_spp_list, merge_protected = F)
write_csv(grouper_dt_den, "big_csv/trophic_groups/density/grouper_dt_den.csv")

#diversity metrics 
grouper_fk_abundance = grouper_fk_abun %>% 
  select(YEAR, protected_status, SPECIES_CD, abundance) %>%  
  group_by(YEAR, protected_status) %>% 
  nest(-YEAR) %>%  
  mutate(
    data_wide = map(data, ~ spread(data=.x, SPECIES_CD, abundance, fill =0)), 
     #species richness 
    richness = map(
      data_wide, 
      function(x) specnumber(x)),
    #simpson diversity as effective number of species 
    simpson = map( 
      data_wide,
      function(x) 1/(1 - diversity(x, index = 'simpson'))),
     #shannon diversity as effective number of species 
    shannon = map(
      data_wide,
      function(x) exp(diversity(x, index = 'shannon')))) %>%
  unnest(richness, simpson, shannon)

grouper_fk_diversity = grouper_fk_abundance %>%
  select(YEAR, protected_status, richness, shannon, simpson) 
write_csv(grouper_fk_diversity, "big_csv/trophic_groups/diversity/grouper_fk_diversity.csv")

#diversity metrics 
grouper_dt_abundance = grouper_dt_abun %>% 
  select(YEAR, protected_status, SPECIES_CD, abundance) %>%  
  group_by(YEAR, protected_status) %>% 
  nest(-YEAR) %>%  
  mutate(
    data_wide = map(data, ~ spread(data=.x, SPECIES_CD, abundance, fill =0)), 
     #species richness 
    richness = map(
      data_wide, 
      function(x) specnumber(x)),
    #simpson diversity as effective number of species 
    simpson = map( 
      data_wide,
      function(x) 1/(1 - diversity(x, index = 'simpson'))),
     #shannon diversity as effective number of species 
    shannon = map(
      data_wide,
      function(x) exp(diversity(x, index = 'shannon')))) %>%
  unnest(richness, simpson, shannon)

grouper_dt_diversity = grouper_dt_abundance %>%
  select(YEAR, protected_status, richness, shannon, simpson) 
write_csv(grouper_dt_diversity, "big_csv/trophic_groups/diversity/grouper_dt_diversity.csv")
}

Grunts

Scientific name Common name RVC code
Anisotremus surinamensis black margate ANI SURI
Anisotremus virginicus porkfish ANI VIRG
Haemulon album margate HAE ALBU
Haemulon aurolineatum tomtate HAE AURO
Haemulon carbonarium caesar grunt HAE CARB
Haemulon chrysargyreum smallmouth grunt HAE CHRY
Haemulon flavolineatum french grunt HAE FLAV
Haemulon macrostomum spanish grunt HAE MACR
Haemulon melanurum cottonwick HAE MELA
Haemulon parra sailors choice HAE PARR
Haemulon plumierii white grunt HAE PLUM
Haemulon sciurus bluestriped grunt HAE SCIU
Haemulon sp. grunt species HAE SPE.
Haemulon striatum striped grunt HAE STRI 
grunt_fk_abun_csv     = "trophic_groups/abundance/grunt_fk_abun.csv"
grunt_dt_abun_csv     = "trophic_groups/abundance/grunt_dt_abun.csv"
grunt_fk_den_csv      = "trophic_groups/density/grunt_fk_den.csv"
grunt_dt_den_csv      = "trophic_groups/density/grunt_dt_den.csv"
grunt_fk_diversity_csv= "trophic_groups/diversity/grunt_fk_diversity.csv"
grunt_dt_diversity_csv= "trophic_groups/diversity/grunt_dt_diversity.csv"

if(!all(file.exists(grunt_fk_abun_csv,grunt_dt_abun_csv,grunt_fk_den_csv,grunt_dt_den_csv,grunt_fk_diversity_csv,grunt_dt_diversity_csv))){
  
grunt_spp_list = c("HAE SCIU", "HAE AURO", "HAE PLUM", "HAE SPE.", "HAE FLAV", "HAE CHRY", "ANI VIRG","HAE MELA", "HAE CARB", "HAE PARR", "HAE STRI", "HAE MACR", "ANI SURI", "HAE ALBU")

#abundance
grunt_fk_abun = getDomainAbundance(RVCdata_FK, grunt_spp_list, merge_protected = F)
write_csv(grunt_fk_abun, "trophic_groups/abundance/grunt_fk_abun.csv")

grunt_dt_abun = getDomainAbundance(RVCdata_DT, grunt_spp_list, merge_protected = F)
write_csv(grunt_dt_abun, "trophic_groups/abundance/grunt_dt_abun.csv")

#density
grunt_fk_den = getDomainDensity(RVCdata_FK, grunt_spp_list, merge_protected = F)
write_csv(grunt_fk_den, "trophic_groups/density/grunt_fk_den.csv")

grunt_dt_den = getDomainDensity(RVCdata_DT, grunt_spp_list, merge_protected = F)
write_csv(grunt_dt_den, "trophic_groups/density/grunt_dt_den.csv")

#diversity metrics 
grunt_fk_abundance = grunt_fk_abun %>% 
  select(YEAR, protected_status, SPECIES_CD, abundance) %>%  
  group_by(YEAR, protected_status) %>% #48 groups 
  nest(-YEAR) %>%  
  mutate(
    data_wide = map(data, ~ spread(data=.x, SPECIES_CD, abundance, fill = 0)), 
     #species richness 
      richness = map(
      data_wide, 
      function(x) specnumber(x)),
    #simpson diversity as effective number of species 
    simpson = map( 
      data_wide,
      function(x) 1/(1 - diversity(x, index = 'simpson'))),
     #shannon diversity as effective number of species 
    shannon = map(
      data_wide,
      function(x) exp(diversity(x, index = 'shannon')))) %>%
  unnest(richness, simpson, shannon)

grunt_fk_diversity = grunt_fk_abundance %>%
  select(YEAR, protected_status, richness, simpson, shannon) 
write_csv(grunt_fk_diversity, "trophic_groups/diversity/grunt_fk_diversity.csv")

#dt diversity
grunt_dt_abundance = grunt_dt_abun %>% 
  select(YEAR, protected_status, SPECIES_CD, abundance) %>%  
  group_by(YEAR, protected_status) %>% #48 groups 
  nest(-YEAR) %>%  
  mutate(
    data_wide = map(data, ~ spread(data=.x, SPECIES_CD, abundance, fill = 0)), 
     #species richness 
      richness = map(
      data_wide, 
      function(x) specnumber(x)),
    #simpson diversity as effective number of species 
    simpson = map( 
      data_wide,
      function(x) 1/(1 - diversity(x, index = 'simpson'))),
     #shannon diversity as effective number of species 
    shannon = map(
      data_wide,
      function(x) exp(diversity(x, index = 'shannon')))) %>%
  unnest(richness, simpson, shannon)

grunt_dt_diversity = grunt_dt_abundance %>%
  select(YEAR, protected_status, richness, simpson, shannon) 
write_csv(grunt_dt_diversity, "trophic_groups/diversity/grunt_dt_diversity.csv")
}

Higher Level Reef Fish

Scientific name Common name RVC code 
higher_reef_fk_abun_csv     = "trophic_groups/abundance/higher_reef_fk_abun.csv"
higher_reef_dt_abun_csv     = "trophic_groups/abundance/higher_reef_dt_abun.csv"
higher_reef_fk_den_csv      = "trophic_groups/density/higher_reef_fk_den.csv"
higher_reef_dt_den_csv      = "trophic_groups/density/higher_reef_dt_den.csv"
higher_reef_fk_diversity_csv= "trophic_groups/diversity/higher_reef_fk_diversity.csv"
higher_reef_dt_diversity_csv= "trophic_groups/diversity/higher_reef_dt_diversity.csv"

if(!all(file.exists(higher_reef_fk_abun_csv,higher_reef_dt_abun_csv,higher_reef_fk_den_csv,higher_reef_dt_den_csv,higher_reef_fk_diversity_csv,higher_reef_dt_diversity_csv))){
  
higher_reef_spp_list = c("THA BIFA","STE PART","GYM MORI","PRI AREN","ABU SAXA","HAL BIVI","HAL GARN","HAL MACU","CHR MULT","CLE PARR","STE PLAN","CHR CYAN","MUL MART","MIC CHRY","STE ADUS","CHA CAPI","STE VARI","PEM SCHO","POM ARCU","CAN ROST","CHA OCEL","PSE MACU","HOL TRIC","CHR SCOT","HAL RADI","CAL CALA","CHA SEDE","XYR SPLE","STE LEUC","HOL CILI","POM PARU","AUL MACU","CHA STRI","OPI AURI","HAL POEY","CHR INSO","HOL ADSC","ODO DENT","STE DIEN","HOL BERM","CHA FABE","XYR MART","GER CINE","HOL RUFU","LAC TRIQ","PAR ACUM","ALU SCRI","BAL CAPR","MAL PLUM","CAN SUFF","CAN PULL","HET CRUE","OGC SPE.","XYR SPE.","ACA QUAD","CAL BAJO","MON TUCK","SPH SPEN","ARC RHOM","DIO HOLO","LAC BICA","XYR NOVA","BAL VETU","DIO HYST","HAL CYAN","GYM FUNE","DIP HOLB","APO PSEU","HOL TOWN","EQU PUNC","LAC TRIG","HAL PICT","MYR JACO","SAR VEXI","SYN INTE","HAL CAUD","AMB PINO","GYM MILI","ALU SCHO","ACA POLY","CAL PROR","CHI SCHO","HET LONG","SCO PLUM","CHR ENCH","CAL SPE.","APO MACU","CAN MACR","PAR UMBR","LAG RHOM","EQU LANC","CAL PENN","STE HISP","APO BINO","NEO MARI","ARC PROB","CHI ANTE","APO TOWN","DOR MEGA","REM REMO","OPI WHIT","CEN ARGI","SYN FOET","AST SPE.","CAR HIPP","SAR CORU","OPI MACR","GYM VICI","DIP ARGE","PAG PAGR","PAR BAIR","BOT LUNA","EUC ARGE","PRO ACUL","LAB GOBI","FIS TABA","ALU SPE.","GRA LORE","MON CILI","ECH NEUC","ALU MONO","BOT OCEL","BAL SPE.","PAR ALBI","STE SPE.","APO QUAD","ENC NIGR","GYM SAXI","OPI SPE.","ELO SAUR","MAN BIRO","APO AURO","SPH TEST","CAL NODO","DIO SPE.","SCO CARI","LAB FILA","AHL EGMO","ANT OCEL","AST GUTT","LAB SPE.","LAB SPE.","MUR RETI","AST STEL","EUC GULA","HOL SPE.","ORT CHRY","PRI OPHR","LAB BUCC","ACA SOLA","CAL LEUC","ENC CARY","GYM NIGR","MYR BREV","SAR BULL","TRA GOOD","TRA LATH","UMB CORO","EUC JONE","EUCLEFR","STY LATE","SYA MICR","SYN SCOV","APO PHEN","HIP REID","PHA XENU","AST PUNC","CHI ATIN","CHL CHRY","HIP EREC","OGC NASU","SER PHOE","SPH NEPH","MYR OCEL","PRI RUBI","RHI LENT","ALB VULP","DAC VOLI","RYP BIST","BRO BARB","HYP GUMM","OPS TAU_","EMM ATLA","UPE PARV","SYN SYNO")

#abundance
higher_reef_fk_abun = getDomainAbundance(RVCdata_FK, higher_reef_spp_list, merge_protected = F)
write_csv(higher_reef_fk_abun, "big_csv/trophic_groups/abundance/higher_reef_fk_abun.csv")
higher_reef_dt_abun = getDomainAbundance(RVCdata_DT, higher_reef_spp_list, merge_protected = F)
write_csv(higher_reef_dt_abun, "big_csv/trophic_groups/abundance/higher_reef_dt_abun.csv")

#density
higher_reef_fk_den = getDomainDensity(RVCdata_FK, higher_reef_spp_list, merge_protected = F)
write_csv(higher_reef_fk_den, "big_csv/trophic_groups/density/higher_reef_fk_den.csv")
higher_reef_dt_den = getDomainDensity(RVCdata_DT, higher_reef_spp_list, merge_protected = F)
write_csv(higher_reef_dt_den, "big_csv/trophic_groups/density/higher_reef_dt_den.csv")

#fk diversity
higher_reef_fk_abundance = higher_reef_fk_abun %>% 
  select(YEAR, protected_status, SPECIES_CD, abundance) %>%  
  group_by(YEAR, protected_status) %>% #48 groups 
  nest(-YEAR) %>%  
  mutate(
    data_wide = map(data, ~ spread(data=.x, SPECIES_CD, abundance, fill = 0)), 
     #species richness 
    richness = map(
      data_wide, 
      function(x) specnumber(x)),
    #simpson diversity as effective number of species 
    simpson = map( 
      data_wide,
      function(x) 1/(1 - diversity(x, index = 'simpson'))),
     #shannon diversity as effective number of species 
    shannon = map(
      data_wide,
      function(x) exp(diversity(x, index = 'shannon')))) %>%
  unnest(richness, simpson, shannon)

higher_reef_diversity = higher_reef_fk_abundance %>%
  select(YEAR, protected_status, richness, simpson, shannon) 
write_csv(higher_reef_diversity, "big_csv/trophic_groups/diversity/higher_reef_fk_diversity.csv")

#dt diversity 
higher_reef_dt_abundance = higher_reef_dt_abun %>% 
  select(YEAR, protected_status, SPECIES_CD, abundance) %>%  
  group_by(YEAR, protected_status) %>% #48 groups 
  nest(-YEAR) %>%  
  mutate(
    data_wide = map(data, ~ spread(data=.x, SPECIES_CD, abundance, fill = 0)), 
     #species richness 
    richness = map(
      data_wide, 
      function(x) specnumber(x)),
    #simpson diversity as effective number of species 
    simpson = map( 
      data_wide,
      function(x) 1/(1 - diversity(x, index = 'simpson'))),
     #shannon diversity as effective number of species 
    shannon = map(
      data_wide,
      function(x) exp(diversity(x, index = 'shannon')))) %>%
  unnest(richness, simpson, shannon)

higher_reef_diversity = higher_reef_dt_abundance %>%
  select(YEAR, protected_status, richness, simpson, shannon) 
write_csv(higher_reef_diversity, "big_csv/trophic_groups/diversity/higher_reef_dt_diversity.csv")
}

higher_reef_fk_den = read_csv("trophic_groups/density/higher_reef_fk_den.csv", 
      col_types = cols(protected_status = col_character()))

higher_reef_fk_density = higher_reef_fk_den %>%
  select(YEAR, protected_status, SPECIES_CD, density) %>% 
  group_by(YEAR, protected_status) %>%
  summarise(
  ntot = sum(density)) %>%
  filter(protected_status != "0") %>%
  filter(protected_status != "1") %>% 
  mutate(
    protected_status = recode(
      protected_status, '0'='unprotected', '1'='protected')) %>%
  spread(protected_status, ntot)

dygraph(higher_reef_fk_density, main = 'Higher Level Reef Fish Density') %>% 
    dyAxis("y", label = "Density") %>%
    dyAxis("x", label = "Year") %>%
    dyOptions(stackedGraph = T, fillAlpha = 0.6, axisLineWidth = 2)

Hogfish

Scientific name Common name RVC code
Bodianus pulchellus spotfin hogfish BOD PULC
Bodianus rufus Spanish hogfish BOD RUFU
Lachnolaimus maximus hogfish LAC MAXI 
hogfish_fk_abun_csv     = "trophic_groups/abundance/hogfish_fk_abun.csv"
hogfish_dt_abun_csv     = "trophic_groups/abundance/hogfish_dt_abun.csv"
hogfish_fk_den_csv      = "trophic_groups/density/hogfish_fk_den.csv"
hogfish_dt_den_csv      = "trophic_groups/density/hogfish_dt_den.csv"
hogfish_fk_diversity_csv= "trophic_groups/diversity/hogfish_fk_diversity.csv"
hogfish_dt_diversity_csv= "trophic_groups/diversity/hogfish_dt_diversity.csv"

if(!all(file.exists(hogfish_fk_abun_csv,hogfish_dt_abun_csv,hogfish_fk_den_csv,hogfish_dt_den_csv,hogfish_fk_diversity_csv,hogfish_dt_diversity_csv))){
                    
hogfish_spp_list = c("LAC MAXI", "BOD RUFU", "BOD PULC")

#abundance
hogfish_fk_abun = getDomainAbundance(RVCdata_FK, hogfish_spp_list, merge_protected = F)
write_csv(hogfish_fk_abun, "big_csv/trophic_groups/abundance/hogfish_fk_abun.csv")
hogfish_dt_abun = getDomainAbundance(RVCdata_DT, hogfish_spp_list, merge_protected = F)
write_csv(hogfish_dt_abun, "big_csv/trophic_groups/abundance/hogfish_dt_abun.csv")

#density
hogfish_fk_den = getDomainDensity(RVCdata_FK, hogfish_spp_list, merge_protected = F)
write_csv(hogfish_fk_den, "big_csv/trophic_groups/density/hogfish_fk_den.csv")
hogfish_dt_den = getDomainDensity(RVCdata_DT, hogfish_spp_list, merge_protected = F)
write_csv(hogfish_dt_den, "big_csv/trophic_groups/density/hogfish_dt_den.csv")

#FK diversity
hogfish_fk_abundance = hogfish_fk_abun %>% 
  select(YEAR, protected_status, SPECIES_CD, abundance) %>%  
  group_by(YEAR, protected_status) %>% #48 groups 
  nest(-YEAR) %>%  
  mutate(
    data_wide = map(data, ~ spread(data=.x, SPECIES_CD, abundance, fill = 0)), 
     #species richness 
    richness = map(
      data_wide, 
      function(x) specnumber(x)),
    #simpson diversity as effective number of species 
    simpson = map( 
      data_wide,
      function(x) 1/(1 - diversity(x, index = 'simpson'))),
     #shannon diversity as effective number of species 
    shannon = map(
      data_wide,
      function(x) exp(diversity(x, index = 'shannon')))) %>%
  unnest(richness, simpson, shannon)

hogfish_fk_diversity = hogfish_fk_abundance %>%
  select(YEAR, protected_status, richness, simpson, shannon) 
write_csv(hogfish_fk_diversity, "big_csv/trophic_groups/diversity/hogfish_fk_diversity.csv")

#DT diversity
hogfish_dt_abundance = hogfish_dt_abun %>% 
  select(YEAR, protected_status, SPECIES_CD, abundance) %>%  
  group_by(YEAR, protected_status) %>% #48 groups 
  nest(-YEAR) %>%  
  mutate(
    data_wide = map(data, ~ spread(data=.x, SPECIES_CD, abundance, fill = 0)), 
     #species richness 
    richness = map(
      data_wide, 
      function(x) specnumber(x)),
    #simpson diversity as effective number of species 
    simpson = map( 
      data_wide,
      function(x) 1/(1 - diversity(x, index = 'simpson'))),
     #shannon diversity as effective number of species 
    shannon = map(
      data_wide,
      function(x) exp(diversity(x, index = 'shannon')))) %>%
  unnest(richness, simpson, shannon)

hogfish_dt_diversity = hogfish_dt_abundance %>%
  select(YEAR, protected_status, richness, simpson, shannon) 
write_csv(hogfish_dt_diversity, "big_csv/trophic_groups/diversity/hogfish_dt_diversity.csv")
}

Lionfish

Scientific name Common name RVC code
Pterois volitans red lionfish PTE VOLI 
lionfish_fk_abun_csv     = "trophic_groups/abundance/lionfish_fk_abun.csv"
lionfish_dt_abun_csv     = "trophic_groups/abundance/lionfish_dt_abun.csv"
lionfish_fk_den_csv      = "trophic_groups/density/lionfish_fk_den.csv"
lionfish_dt_den_csv      = "trophic_groups/density/lionfish_dt_den.csv"

if(!all(file.exists(lionfish_fk_abun_csv,lionfish_dt_abun_csv,lionfish_fk_den_csv,lionfish_dt_den_csv))){
#"PTE VOLI" - lionfish

#abundance
lionfish_fk_abun = getDomainAbundance(RVCdata_FK, "PTE VOLI", merge_protected = F)
write_csv(lionfish_fk_abun, "big_csv/trophic_groups/abundance/lionfish_fk_abun.csv")
lionfish_dt_abun = getDomainAbundance(RVCdata_DT, "PTE VOLI", merge_protected = F)
write_csv(lionfish_dt_abun, "big_csv/trophic_groups/abundance/lionfish_dt_abun.csv")

#density
lionfish_fk_den = getDomainDensity(RVCdata_FK, "PTE VOLI", merge_protected = F)
write_csv(lionfish_fk_den, "big_csv/trophic_groups/density/lionfish_fk_den.csv")
lionfish_dt_den = getDomainDensity(RVCdata_DT, "PTE VOLI", merge_protected = F)
write_csv(lionfish_dt_den, "big_csv/trophic_groups/density/lionfish_dt_den.csv")
}

Opportunists

Scientific name Common name RVC code
Alectis ciliaris african pompano ALE CILI
Caranx crysos blue runner CAR CRYS
Caranx bartholomaei yellow jack CAR BART
Caranx latus horse-eye jack CAR LATU
Caranx lugubris black jack CAR LUGU
Caranx ruber bar jack CAR RUBE
Caranx sp. jack species CAR SPE.
Decapterus punctatus round scad DEC PUNC
Decapterus macarellus mackerel scad DEC MACA
Elagatis bipinnulata rainbow runner ELA BIPI
Euthynnus alletteratus little tunny EUT ALLE
Oligoplites saurus leatherjack OLI SAUR
Sphyraena barracuda great barracuda SPH BARR
Rachycentron canadum cobia RAC CANA
Scomberomorus regalis cero SCO REGA
Sphyraena picudilla southern sennet SPH PICU
Selene vomer lookdown SEL VOME
Seriola rivoliana almaco jack SER RIVO
Scomberomorus maculatus spanish mackerel SCO MACU
Seriola dumerili greater amberjack SER DUME
Scomberomorus cavalla king mackerel SCO CAVA
Sphyraena guachancho guaguanche SPH GUAC
Seriola sp. jack species SER SPE.
Seriola zonata banded rudderfish SER ZONA
Trachinotus falcatus permit TRA FALC 
opportunists_fk_abun_csv     = "trophic_groups/abundance/opportunists_fk_abun.csv"
opportunists_dt_abun_csv     = "trophic_groups/abundance/opportunists_dt_abun.csv"
opportunists_fk_den_csv      = "trophic_groups/density/opportunists_fk_den.csv"
opportunists_dt_den_csv      = "trophic_groups/density/opportunists_dt_den.csv"
opportunists_fk_diversity_csv= "trophic_groups/diversity/opportunists_fk_diversity.csv"
opportunists_dt_diversity_csv= "trophic_groups/diversity/opportunists_dt_diversity.csv"

if(!all(file.exists(opportunists_fk_abun_csv,opportunists_dt_abun_csv,opportunists_fk_den_csv,opportunists_dt_den_csv,opportunists_fk_diversity_csv,opportunists_dt_diversity_csv))){
  
opportunists_spp_list = c("CAR RUBE", "SPH BARR", "ALE CILI","DEC PUNC", "DEC MACA", "CAR CRYS", "CAR BART", "SCO REGA","SPH PICU", "CAR LATU", "SEL VOME", "ELA BIPI", "CAR SPE.", "TRA FALC", "EUT ALLE", "SER RIVO", "SCO MACU", "SER DUME", "SCO CAVA", "SPH GUAC", "CAR LUGU", "OLI SAUR", "SER SPE.", "Rac cana", "Ser zona")

#abundance
opportunists_fk_abun = getDomainAbundance(RVCdata_FK, opportunists_spp_list, merge_protected = F)
write_csv(opportunists_fk_abun, "big_csv/trophic_groups/abundance/opportunists_fk_abun.csv")

opportunists_dt_abun = getDomainAbundance(RVCdata_DT, opportunists_spp_list, merge_protected = F)
write_csv(opportunists_dt_abun, "big_csv/trophic_groups/abundance/opportunists_dt_abun.csv")

#density
opportunists_fk_den = getDomainDensity(RVCdata_FK, opportunists_spp_list, merge_protected = F)
write_csv(opportunists_fk_den, "big_csv/trophic_groups/density/opportunists_fk_den.csv")

opportunists_dt_den = getDomainDensity(RVCdata_DT, opportunists_spp_list, merge_protected = F)
write_csv(opportunists_dt_den, "big_csv/trophic_groups/density/opportunists_dt_den.csv")

#diversity
opportunists_fk_abundance = opportunists_fk_abun %>% 
  select(YEAR, protected_status, SPECIES_CD, abundance) %>%  
  group_by(YEAR, protected_status) %>% #48 groups 
  nest(-YEAR) %>%  
  mutate(
    data_wide = map(data, ~ spread(data=.x, SPECIES_CD, abundance, fill = 0)), 
     #species richness 
    richness = map(
      data_wide, 
      function(x) specnumber(x)),
    #simpson diversity as effective number of species 
    simpson = map( 
      data_wide,
      function(x) 1/(1 - diversity(x, index = 'simpson'))),
     #shannon diversity as effective number of species 
    shannon = map(
      data_wide,
      function(x) exp(diversity(x, index = 'shannon')))) %>%
  unnest(richness, simpson, shannon)

opportunists_fk_diversity = opportunists_fk_abundance %>%
  select(YEAR, protected_status, richness, simpson, shannon) 
write_csv(opportunists_fk_diversity, "big_csv/trophic_groups/diversity/opportunists_fk_diversity.csv")

#dt diversity
opportunists_dt_abundance = opportunists_dt_abun %>% 
  select(YEAR, protected_status, SPECIES_CD, abundance) %>%  
  group_by(YEAR, protected_status) %>% #48 groups 
  nest(-YEAR) %>%  
  mutate(
    data_wide = map(data, ~ spread(data=.x, SPECIES_CD, abundance, fill = 0)), 
     #species richness 
    richness = map(
      data_wide, 
      function(x) specnumber(x)),
    #simpson diversity as effective number of species 
    simpson = map( 
      data_wide,
      function(x) 1/(1 - diversity(x, index = 'simpson'))),
     #shannon diversity as effective number of species 
    shannon = map(
      data_wide,
      function(x) exp(diversity(x, index = 'shannon')))) %>%
  unnest(richness, simpson, shannon)

opportunists_dt_diversity = opportunists_dt_abundance %>%
  select(YEAR, protected_status, richness, simpson, shannon) 
write_csv(opportunists_dt_diversity, "big_csv/trophic_groups/diversity/opportunists_dt_diversity.csv")
}

Parrotfish

Scientific name Common name RVC code
Cryptotomus roseus bluelip parrotfish CRY ROSE
Nicholsina usta emerald parrotfish NIC USTA
Scarus coelestinus midnight parrotfish SCA COEL
Scarus coeruleus blue parrotfish SCA COER
Scarus guacamaia rainbow parrotfish SCA GUAC
Scarus iseri striped parrotfish SCA ISER
Scarus sp. parrotfish species SCA SPE.
Scarus taeniopterus princess parrotfish SCA TAEN
Scarus vetula queen parrotfish SCA VETU
Sparisoma atomarium greenblotch parrotfish SPA ATOM
Sparisoma aurofrenatum redband parrotfish SPA AURO
Sparisoma chrysopterum redtail parrotfish SPA CHRY
Sparisoma radians bucktooth parrotfish SPA RADI
Sparisoma rubripinne yellowtail parrotfish SPA RUBR
Sparisoma sp. parrotfish species SPA SPE.
Sparisoma viride stoplight parrotfish SPA VIRI 
parrotfish_fk_abun_csv      = "trophic_groups/abundance/parrotfish_fk_abun.csv"
parrotfish_dt_abun_csv      = "trophic_groups/abundance/parrotfish_dt_abun.csv"
parrotfish_fk_den_csv       = "trophic_groups/density/parrotfish_fk_den.csv"
parrotfish_dt_den_csv       = "trophic_groups/density/parrotfish_dt_den.csv"
parrotfish_fk_diversity_csv = "trophic_groups/diversity/parrotfish_fk_diversity.csv"
parrotfish_dt_diversity_csv = "trophic_groups/diversity/parrotfish_dt_diversity.csv"

if(!all(file.exists(parrotfish_fk_abun_csv,parrotfish_dt_abun_csv,parrotfish_fk_den_csv,parrotfish_dt_den_csv,parrotfish_fk_diversity_csv,parrotfish_dt_diversity_csv))){
  
parrotfish_spp_list = c('SCA ISER', "SCA COEL", "SPA AURO", "SPA VIRI", "SPA ATOM", "SCA TAEN", 'SPA RUBR', "SPA CHRY", "SCA VETU", "SCA COER", "SCA GUAC", "CRY ROSE", "SPA RADI", "SCA SPE.", "NIC USTA", "SPA SPE.")

#abundance
parrotfish_fk_abun = getDomainAbundance(RVCdata_FK, parrotfish_spp_list, merge_protected = F)
write_csv(parrotfish_fk_abun, "big_csv/trophic_groups/abundance/parrotfish_fk_abun.csv")

parrotfish_dt_abun = getDomainAbundance(RVCdata_DT, parrotfish_spp_list, merge_protected = F)
write_csv(parrotfish_dt_abun, "big_csv/trophic_groups/abundance/parrotfish_dt_abun.csv")

#density
parrotfish_fk_den = getDomainDensity(RVCdata_FK, parrotfish_spp_list, merge_protected = F)
write_csv(parrotfish_fk_den, "big_csv/trophic_groups/density/parrotfish_fk_den.csv")

parrotfish_dt_den = getDomainDensity(RVCdata_DT, parrotfish_spp_list, merge_protected = F)
write_csv(parrotfish_dt_den, "big_csv/trophic_groups/density/parrotfish_dt_den.csv")

#diversity
parrotfish_fk_abundance = parrotfish_fk_abun %>% 
  select(YEAR, protected_status, SPECIES_CD, abundance) %>%  
  group_by(YEAR, protected_status) %>% #48 groups 
  nest(-YEAR) %>%  
  mutate(
    data_wide = map(data, ~ spread(data=.x, SPECIES_CD, abundance, fill = 0)), 
     #species richness 
    richness = map(
      data_wide, 
      function(x) specnumber(x)),
    #simpson diversity as effective number of species 
    simpson = map( 
      data_wide,
      function(x) 1/(1 - diversity(x, index = 'simpson'))),
     #shannon diversity as effective number of species 
    shannon = map(
      data_wide,
      function(x) exp(diversity(x, index = 'shannon')))) %>%
  unnest(richness, simpson, shannon)

parrotfish_fk_diversity = parrotfish_fk_abundance %>%
  select(YEAR, protected_status, richness, simpson, shannon) 
write_csv(parrotfish_fk_diversity, "big_csv/trophic_groups/diversity/parrotfish_fk_diversity.csv")

#dt diversity
parrotfish_dt_abundance = parrotfish_dt_abun %>% 
  select(YEAR, protected_status, SPECIES_CD, abundance) %>%  
  group_by(YEAR, protected_status) %>% #48 groups 
  nest(-YEAR) %>%  
  mutate(
    data_wide = map(data, ~ spread(data=.x, SPECIES_CD, abundance, fill = 0)), 
     #species richness 
    richness = map(
      data_wide, 
      function(x) specnumber(x)),
    #simpson diversity as effective number of species 
    simpson = map( 
      data_wide,
      function(x) 1/(1 - diversity(x, index = 'simpson'))),
     #shannon diversity as effective number of species 
    shannon = map(
      data_wide,
      function(x) exp(diversity(x, index = 'shannon')))) %>%
  unnest(richness, simpson, shannon)

parrotfish_dt_diversity = parrotfish_dt_abundance %>%
  select(YEAR, protected_status, richness, simpson, shannon) 
write_csv(parrotfish_dt_diversity, "big_csv/trophic_groups/diversity/parrotfish_dt_diversity.csv")
}

parrotfish_fk_abun = read_csv('trophic_groups/abundance/parrotfish_fk_abun.csv')
## Parsed with column specification:
## cols(
##   YEAR = col_integer(),
##   REGION = col_character(),
##   SPECIES_CD = col_character(),
##   abundance = col_double(),
##   var = col_double(),
##   n = col_integer(),
##   nm = col_integer(),
##   N = col_double(),
##   NM = col_double(),
##   protected_status = col_character()
## )
parrotfish_fk_abundance = parrotfish_fk_abun %>%
  select(YEAR, protected_status, SPECIES_CD, abundance) %>% 
  group_by(YEAR, protected_status) %>%
  summarise(
  ntot = sum(abundance)) %>%
  filter(protected_status != "0") %>%
  filter(protected_status != "1") %>% 
  mutate(
    protected_status = recode(
      protected_status, '0'='unprotected', '1'='protected')) %>%
  spread(protected_status, ntot)

dygraph(parrotfish_fk_abundance, main = 'Parrotfish Abundance') %>% 
    dyAxis("y", label = "Abundance") %>%
    dyAxis("x", label = "Year") %>%
    dyOptions(stackedGraph = T)
parrotfish_fk_den = read_csv('trophic_groups/density/parrotfish_fk_den.csv')
## Parsed with column specification:
## cols(
##   YEAR = col_integer(),
##   REGION = col_character(),
##   SPECIES_CD = col_character(),
##   density = col_double(),
##   var = col_double(),
##   n = col_integer(),
##   nm = col_integer(),
##   N = col_double(),
##   NM = col_double(),
##   protected_status = col_character()
## )
parrotfish_fk_density = parrotfish_fk_den %>%
  select(YEAR, protected_status, SPECIES_CD, density) %>% 
  group_by(YEAR, protected_status) %>%
  summarise(
  ntot = sum(density)) %>%
  filter(protected_status != "0") %>%
  filter(protected_status != "1") %>% 
  mutate(
    protected_status = recode(
      protected_status, '0'='unprotected', '1'='protected')) %>%
  spread(protected_status, ntot)

dygraph(parrotfish_fk_density, main = 'Parrotfish Density') %>% 
    dyAxis("y", label = "Density") %>%
    dyAxis("x", label = "Year") %>%
    dyOptions(stackedGraph = T, fillAlpha = 0.6, axisLineWidth = 2)

Rays

Scientific name Common name RVC code
Aetobatus narinari spotted eagle ray AET NARI
Dasyatis americana southern stingray DAS AMER
Echeneis naucrates sharksucker ECH NAUC
Narcine bancroftii lesser electric ray NAR BANC
Rhinoptera bonasus cownosed ray RHI BONA
Urobatis jamaicensis yellow stingray URO JAMA 
rays_fk_abun_csv     = "trophic_groups/abundance/rays_fk_abun.csv"
rays_dt_abun_csv     = "trophic_groups/abundance/rays_dt_abun.csv"
rays_fk_den_csv      = "trophic_groups/density/rays_fk_den.csv"
rays_dt_den_csv      = "trophic_groups/density/rays_dt_den.csv"
rays_fk_diversity_csv= "trophic_groups/diversity/rays_fk_diversity.csv"
rays_dt_diversity_csv= "trophic_groups/diversity/rays_dt_diversity.csv"

if(!all(file.exists(rays_fk_abun_csv,rays_dt_abun_csv,rays_fk_den_csv,rays_dt_den_csv,rays_fk_diversity_csv,rays_dt_diversity_csv))){
  
rays_spp_list = c("URO JAMA", "ECH NAUC", "DAS AMER", "AET NARI", "NAR BANC", "Rhi bona")

#abundance
rays_fk_abun = getDomainAbundance(RVCdata_FK, rays_spp_list, merge_protected = F)
write_csv(rays_fk_abun, "big_csv/trophic_groups/abundance/rays_fk_abun.csv")

rays_dt_abun = getDomainAbundance(RVCdata_DT, rays_spp_list, merge_protected = F)
write_csv(rays_dt_abun, "big_csv/trophic_groups/abundance/rays_dt_abun.csv")

#density
rays_fk_den = getDomainDensity(RVCdata_FK, rays_spp_list, merge_protected = F)
write_csv(rays_fk_den, "big_csv/trophic_groups/density/rays_fk_den.csv")

rays_dt_den = getDomainDensity(RVCdata_DT, rays_spp_list, merge_protected = F)
write_csv(rays_dt_den, "big_csv/trophic_groups/density/rays_dt_den.csv")

#diversity
rays_fk_abundance = rays_fk_abun %>% 
  select(YEAR, protected_status, SPECIES_CD, abundance) %>%  
  group_by(YEAR, protected_status) %>% #48 groups 
  nest(-YEAR) %>%  
  mutate(
    data_wide = map(data, ~ spread(data=.x, SPECIES_CD, abundance, fill = 0)), 
     #species richness 
    richness = map(
      data_wide, 
      function(x) specnumber(x)),
    #simpson diversity as effective number of species 
    simpson = map( 
      data_wide,
      function(x) 1/(1 - diversity(x, index = 'simpson'))),
     #shannon diversity as effective number of species 
    shannon = map(
      data_wide,
      function(x) exp(diversity(x, index = 'shannon')))) %>%
  unnest(richness, simpson, shannon)

rays_fk_diversity = rays_fk_abundance %>%
  select(YEAR, protected_status, richness, simpson, shannon) 
write_csv(rays_fk_diversity, "big_csv/trophic_groups/diversity/rays_fk_diversity.csv")

#dt diversity
rays_dt_abundance = rays_dt_abun %>% 
  select(YEAR, protected_status, SPECIES_CD, abundance) %>%  
  group_by(YEAR, protected_status) %>% #48 groups 
  nest(-YEAR) %>%  
  mutate(
    data_wide = map(data, ~ spread(data=.x, SPECIES_CD, abundance, fill = 0)), 
     #species richness 
    richness = map(
      data_wide, 
      function(x) specnumber(x)),
    #simpson diversity as effective number of species 
    simpson = map( 
      data_wide,
      function(x) 1/(1 - diversity(x, index = 'simpson'))),
     #shannon diversity as effective number of species 
    shannon = map(
      data_wide,
      function(x) exp(diversity(x, index = 'shannon')))) %>%
  unnest(richness, simpson, shannon)

rays_dt_diversity = rays_dt_abundance %>%
  select(YEAR, protected_status, richness, simpson, shannon) 
write_csv(rays_dt_diversity, "big_csv/trophic_groups/diversity/rays_dt_diversity.csv")
}

Sea bass and Hamlets

Scientific name Common name RVC code
Alphestes afer mutton hamlet ALP AFER
Centropristis ocyurus bank sea bass CEN OCYU
Centropristis striata black sea bass CEN STRI
Diplectrum formosum sand perch DIP FORM
Epinephelus adscensionis rock hind EPI ADSC
Epinephelus drummondhayi speckled hind EPI DRUM
Epinephelus guttatus red hind EPI GUTT
Hypoplectrus chlorurus yellowtail hamlet HYP CHLO
Hypoplectrus gemma blue hamlet HYP GEMM
Hypoplectrus guttavarius shy hamlet HYP GUTT
Hypoplectrus hybrid hybrid hamlet HYP HYBR
Hypoplectrus indigo indigo hamlet HYP INDI
Hypoplectrus nigricans black hamlet HYP NIGR
Hypoplectrus puella barred hamlet HYP PUEL
Hypoplectrus sp. hamlet species HYP SPE.
Hypoplectrus tann tan hamlet HYP TANN
Hypoplectrus unicolor butter hamlet HYP UNIC
Liopropoma eukrines wrasse basslet LIO EUKR
Liopropoma mowbrayi cave basslet LIO MOWB
Liopropoma rubre peppermint basslet LIO RUBE
Paranthias furcifer atlantic creolefish PAR FURC
Pristipomoides aquilonaris wenchman PRI AQUI
Rypticus maculatus whitespotted soapfish RYP MACU
Rypticus saponaceus greater soapfish RYP SAPO
Schultzea beta school bass SCH BETA
Serranus annularis orangeback bass SER ANNU
Serranus baldwini lantern bass SER BALD
Serranus subligarius belted sandfish SER SUBL
Serranus tabacarius tobaccofish SER TABA
Serranus tigrinus harlequin bass SER TIGR
Serranus tortugarum chalk bass SER TORT 
seabass_fk_abun_csv     = "trophic_groups/abundance/seabass_fk_abun.csv"
seabass_dt_abun_csv     = "trophic_groups/abundance/seabass_dt_abun.csv"
seabass_fk_den_csv      = "trophic_groups/density/seabass_fk_den.csv"
seabass_dt_den_csv      = "trophic_groups/density/seabass_dt_den.csv"
seabass_fk_diversity_csv= "trophic_groups/diversity/seabass_fk_diversity.csv"
seabass_dt_diversity_csv= "trophic_groups/diversity/seabass_dt_diversity.csv"

if(!all(file.exists(seabass_fk_abun_csv,seabass_dt_abun_csv,seabass_fk_den_csv,seabass_dt_den_csv,seabass_fk_diversity_csv,seabass_dt_diversity_csv))){
  
sea_bass_hamlet_spp_list = c("SER TIGR","HYP GEMM","HYP UNIC","SER TABA","SER BALD","HYP PUEL","EPI ADSC","SER TORT","EPI GUTT","HYP NIGR","DIP FORM","HYP SPE.","SCH BETA","HYP TANN", "RYP SAPO","PAR FURC","HYP INDI","HYP GUTT","ALP AFER","LIO EUKR","SER ANNU","LIO RUBE","HYP HYBR","HYP CHLO","PRI AQUI","RYP MACU","SER SUBL","CEN OCYU","CEN STRI","Epi drum","Lio mowb")

#abundance
seabass_fk_abun = getDomainAbundance(RVCdata_FK, sea_bass_hamlet_spp_list, merge_protected = F)
write_csv(seabass_fk_abun, "big_csv/trophic_groups/abundance/seabass_fk_abun.csv")
seabass_dt_abun = getDomainAbundance(RVCdata_DT, sea_bass_hamlet_spp_list, merge_protected = F)
write_csv(seabass_dt_abun, "big_csv/trophic_groups/abundance/seabass_dt_abun.csv")

#density
seabass_fk_den = getDomainDensity(RVCdata_FK, sea_bass_hamlet_spp_list, merge_protected = F)
write_csv(seabass_fk_den, "big_csv/trophic_groups/density/seabass_fk_den.csv")
seabass_dt_den = getDomainDensity(RVCdata_DT, sea_bass_hamlet_spp_list, merge_protected = F)
write_csv(seabass_dt_den, "big_csv/trophic_groups/density/seabass_dt_den.csv")

#diversity
seabass_fk_abundance = seabass_fk_abun %>% 
  select(YEAR, protected_status, SPECIES_CD, abundance) %>%  
  group_by(YEAR, protected_status) %>% #48 groups 
  nest(-YEAR) %>%  
  mutate(
    data_wide = map(data, ~ spread(data=.x, SPECIES_CD, abundance, fill = 0)), 
     #species richness 
    richness = map(
      data_wide, 
      function(x) specnumber(x)),
    #simpson diversity as effective number of species 
    simpson = map( 
      data_wide,
      function(x) 1/(1 - diversity(x, index = 'simpson'))),
     #shannon diversity as effective number of species 
    shannon = map(
      data_wide,
      function(x) exp(diversity(x, index = 'shannon')))) %>%
  unnest(richness, simpson, shannon)

seabass_fk_diversity = seabass_fk_abundance %>%
  select(YEAR, protected_status, richness, simpson, shannon) 
write_csv(seabass_fk_diversity, "big_csv/trophic_groups/diversity/seabass_fk_diversity.csv")

#dt diversity
seabass_dt_abundance = seabass_dt_abun %>% 
  select(YEAR, protected_status, SPECIES_CD, abundance) %>%  
  group_by(YEAR, protected_status) %>% #48 groups 
  nest(-YEAR) %>%  
  mutate(
    data_wide = map(data, ~ spread(data=.x, SPECIES_CD, abundance, fill = 0)), 
     #species richness 
    richness = map(
      data_wide, 
      function(x) specnumber(x)),
    #simpson diversity as effective number of species 
    simpson = map( 
      data_wide,
      function(x) 1/(1 - diversity(x, index = 'simpson'))),
     #shannon diversity as effective number of species 
    shannon = map(
      data_wide,
      function(x) exp(diversity(x, index = 'shannon')))) %>%
  unnest(richness, simpson, shannon)

seabass_dt_diversity = seabass_dt_abundance %>%
  select(YEAR, protected_status, richness, simpson, shannon) 
write_csv(seabass_dt_diversity, "big_csv/trophic_groups/diversity/seabass_dt_diversity.csv")
}

Sharks

Scientific name Common name RVC code
Carcharhinus falciformis silky shark CAR FALC
Carcharhinus leucas bull shark CAR LEUC
Carcharhinus limbatus blacktip shark CAR LIMB
Carcharhinus obscurus dusky shark CAR OBSC
Carcharhinus plumbeus sandbar shark CAR PLUM
Carcharhinus perezii reef shark CAR PERE
Galeocerdo cuvieri tiger shark GAL CUVI
Ginglymostoma cirratum nurse shark GIN CIRR
Negaprion brevirostris lemon shark Neg BREV
Sphyrna mokarran great hammerhead SPH MOKA
Sphyrna tiburo bonnethead SPH TIBU
Sphyrna lewini scalloped hammerhead SPH LEWI 
sharks_fk_abun_csv      = "trophic_groups/abundance/sharks_fk_abun.csv"
sharks_dt_abun_csv      = "trophic_groups/abundance/sharks_dt_abun.csv"
sharks_fk_den_csv       = "trophic_groups/density/sharks_fk_den.csv"
sharks_dt_den_csv       = "trophic_groups/density/sharks_dt_den.csv"
sharks_fk_diversity_csv = "trophic_groups/diversity/sharks_fk_diversity.csv"
sharks_dt_diversity_csv = "trophic_groups/diversity/sharks_dt_diversity.csv"

if(!all(file.exists(sharks_fk_abun_csv,sharks_dt_abun_csv,sharks_fk_den_csv,sharks_dt_den_csv,sharks_fk_diversity_csv,sharks_dt_diversity_csv))){
  
sharks_spp_list = c("GIN CIRR", "CAR PERE", "CAR LEUC", "CAR LIMB", "SPH MOKA", "SPH TIBU", "CAR FALC", "SPH LEWI", "CAR OBSC", "Neg brev", "CAR PLUM", 'Gal cuvi')

#abundance
sharks_fk_abun = getDomainAbundance(RVCdata_FK, sharks_spp_list, merge_protected = F)
write_csv(sharks_fk_abun, "big_csv/trophic_groups/abundance/sharks_fk_abun.csv")
sharks_dt_abun = getDomainAbundance(RVCdata_DT, sharks_spp_list, merge_protected = F)
write_csv(sharks_dt_abun, "big_csv/trophic_groups/abundance/sharks_dt_abun.csv")

#density
sharks_fk_den = getDomainDensity(RVCdata_FK, sharks_spp_list, merge_protected = F)
write_csv(sharks_fk_den, "big_csv/trophic_groups/density/sharks_fk_den.csv")
sharks_dt_den = getDomainDensity(RVCdata_DT, sharks_spp_list, merge_protected = F)
write_csv(sharks_dt_den, "big_csv/trophic_groups/density/sharks_dt_den.csv")

#diversity
sharks_fk_abundance = sharks_fk_abun %>% 
  select(YEAR, protected_status, SPECIES_CD, abundance) %>%  
  group_by(YEAR, protected_status) %>% #48 groups 
  nest(-YEAR) %>%  
  mutate(
    data_wide = map(data, ~ spread(data=.x, SPECIES_CD, abundance, fill = 0)), 
     #species richness 
    richness = map(
      data_wide, 
      function(x) specnumber(x)),
    #simpson diversity as effective number of species 
    simpson = map( 
      data_wide,
      function(x) 1/(1 - diversity(x, index = 'simpson'))),
     #shannon diversity as effective number of species 
    shannon = map(
      data_wide,
      function(x) exp(diversity(x, index = 'shannon')))) %>%
  unnest(richness, simpson, shannon)

sharks_fk_diversity = sharks_fk_abundance %>%
  select(YEAR, protected_status, richness, simpson, shannon) 
write_csv(sharks_fk_diversity, "big_csv/trophic_groups/diversity/sharks_fk_diversity.csv")

#dt diversity
sharks_dt_abundance = sharks_dt_abun %>% 
  select(YEAR, protected_status, SPECIES_CD, abundance) %>%  
  group_by(YEAR, protected_status) %>% #48 groups 
  nest(-YEAR) %>%  
  mutate(
    data_wide = map(data, ~ spread(data=.x, SPECIES_CD, abundance, fill = 0)), 
     #species richness 
    richness = map(
      data_wide, 
      function(x) specnumber(x)),
    #simpson diversity as effective number of species 
    simpson = map( 
      data_wide,
      function(x) 1/(1 - diversity(x, index = 'simpson'))),
     #shannon diversity as effective number of species 
    shannon = map(
      data_wide,
      function(x) exp(diversity(x, index = 'shannon')))) %>%
  unnest(richness, simpson, shannon)

sharks_dt_diversity = sharks_dt_abundance %>%
  select(YEAR, protected_status, richness, simpson, shannon) 
write_csv(sharks_dt_diversity, "big_csv/trophic_groups/diversity/sharks_dt_diversity.csv")
}

sharks_fk_den= read_csv('trophic_groups/density/sharks_fk_den.csv')
## Parsed with column specification:
## cols(
##   YEAR = col_integer(),
##   REGION = col_character(),
##   SPECIES_CD = col_character(),
##   density = col_double(),
##   var = col_double(),
##   n = col_integer(),
##   nm = col_integer(),
##   N = col_double(),
##   NM = col_double(),
##   protected_status = col_character()
## )
sharks_fk_density = sharks_fk_den %>%
  select(YEAR, protected_status, SPECIES_CD, density) %>% 
  group_by(YEAR, protected_status) %>%
  summarise(
  ntot = sum(density)) %>%
  filter(protected_status != "0") %>%
  filter(protected_status != "1") %>%
  spread(protected_status, ntot)

dygraph(sharks_fk_density, main = 'Sharks Density') %>% 
    dyAxis("y", label = "Density") %>%
    dyAxis("x", label = "Year") %>%
    dyOptions(stackedGraph = T, fillAlpha = 0.6, axisLineWidth = 2)

Small Reef Fish

Scientific name Common name RVC code 
small_reef_fk_abun_csv      = "trophic_groups/abundance/small_reef_fk_abun.csv"
small_reef_dt_abun_csv      = "trophic_groups/abundance/small_reef_dt_abun.csv"
small_reef_fk_den_csv       = "trophic_groups/density/small_reef_fk_den.csv"
small_reef_dt_den_csv       = "trophic_groups/density/small_reef_dt_den.csv"
small_reef_fk_diversity_csv = "trophic_groups/diversity/small_reef_fk_diversity.csv"
small_reef_dt_diversity_csv = "trophic_groups/diversity/small_reef_dt_diversity.csv"

if(!all(file.exists(small_reef_fk_abun_csv,small_reef_dt_abun_csv,small_reef_fk_den_csv,small_reef_dt_den_csv,small_reef_fk_diversity_csv,small_reef_dt_diversity_csv))){ 

small_reef_fish_spp_list = c("COR PERS","ACA COER","KYP SECT","ACA BAHI","ACA CHIR","COR GLAU","ELA OCEA","GNA THOM","PTE CALL","ACA SPE.","MAL TRIA","COR DICR","PAR MARM","MAL MACR","OPH MACC","CTE SAEP","MIC CARR","PTE HELE","HEM SIMU","SCA CRIS","COR EIDO","GOB SPE.","TYL CROC","MIC MICR","ACA ASPE","COR SPE.","BLE SPE.","STR NOTA","MEL NIGE","HYP BERM","EMB PAND","ELA EVEL","ACA CHAP","EMB BAHA","COR LIPE","NES LONG","ENN BOEH","ACA MARI","LAB NUCH","MAL VERS","MAL GILL","ELA MACR","PRI HIPO","GOB DILE","ELA SAUC","ELA XANT","STR TIMU","MAL AURO","PAR MARN","CHA LIMB","OXY STIG","ELA HORS","PAR NIGR","COR PUNC","ACA SPIN","BOL BOQU","ElA RAND","LAB KALI","LAB NIGR","ENN ALTI")

#abundance
small_reef_fk_abun = getDomainAbundance(RVCdata_FK, small_reef_fish_spp_list, merge_protected = F)
write_csv(small_reef_fk_abun, "big_csv/trophic_groups/abundance/small_reef_fk_abun.csv")

small_reef_dt_abun = getDomainAbundance(RVCdata_DT, small_reef_fish_spp_list, merge_protected = F)
write_csv(small_reef_dt_abun, "big_csv/trophic_groups/abundance/small_reef_dt_abun.csv")

#density
small_reef_fk_den = getDomainDensity(RVCdata_FK, small_reef_fish_spp_list, merge_protected = F)
write_csv(small_reef_fk_den, "big_csv/trophic_groups/density/small_reef_fk_den.csv")

small_reef_dt_den = getDomainDensity(RVCdata_DT, small_reef_fish_spp_list, merge_protected = F)
write_csv(small_reef_dt_den, "big_csv/trophic_groups/density/small_reef_dt_den.csv")

#fk diversity
small_reef_fk_abundance = small_reef_fk_abun %>% 
  select(YEAR, protected_status, SPECIES_CD, abundance) %>%  
  group_by(YEAR, protected_status) %>% #48 groups 
  nest(-YEAR) %>%  
  mutate(
    data_wide = map(data, ~ spread(data=.x, SPECIES_CD, abundance, fill = 0)), 
     #species richness 
    richness = map(
      data_wide, 
      function(x) specnumber(x)),
    #simpson diversity as effective number of species 
    simpson = map( 
      data_wide,
      function(x) 1/(1 - diversity(x, index = 'simpson'))),
     #shannon diversity as effective number of species 
    shannon = map(
      data_wide,
      function(x) exp(diversity(x, index = 'shannon')))) %>%
  unnest(richness, simpson, shannon)

small_reef_fk_diversity = small_reef_fk_abundance %>%
  select(YEAR, protected_status, richness, simpson, shannon) 
write_csv(small_reef_fk_diversity, "big_csv/trophic_groups/diversity/small_reef_fk_diversity.csv")

#dt diversity
small_reef_dt_abundance = small_reef_dt_abun %>% 
  select(YEAR, protected_status, SPECIES_CD, abundance) %>%  
  group_by(YEAR, protected_status) %>% #48 groups 
  nest(-YEAR) %>%  
  mutate(
    data_wide = map(data, ~ spread(data=.x, SPECIES_CD, abundance, fill = 0)), 
     #species richness 
    richness = map(
      data_wide, 
      function(x) specnumber(x)),
    #simpson diversity as effective number of species 
    simpson = map( 
      data_wide,
      function(x) 1/(1 - diversity(x, index = 'simpson'))),
     #shannon diversity as effective number of species 
    shannon = map(
      data_wide,
      function(x) exp(diversity(x, index = 'shannon')))) %>%
  unnest(richness, simpson, shannon)

small_reef_dt_diversity = small_reef_dt_abundance %>%
  select(YEAR, protected_status, richness, simpson, shannon) 
write_csv(small_reef_dt_diversity, "big_csv/trophic_groups/diversity/small_reef_dt_diversity.csv")
}

Snappers

Scientific name Common name RVC code
Lutjanus analis mutton snapper LUT ANAL
Lutjanus apodus schoolmaster LUT APOD
Lutjanus buccanella blackfin snapper LUT BUCC
Lutjanus campechanus red snapper Lut CAMP
Lutjanus cyanopterus cubera snapper LUT CYAN
Lutjanus griseus gray snapper LUT GRIS
Lutjanus jocu dog snapper LUT JOCU
Lutjanus mahogoni mahogany snapper LUT MAHO
Lutjanus synagris lane snapper LUT SYNA
Ocyurus chrysurus yellowtail snapper OCY CHRY
Rhomboplites aurorubens vermilion snapper RHO AURO
snapper species snapper species LUT SPE. 
snapper_fk_abun_csv      = "trophic_groups/abundance/snapper_fk_abun.csv"
snapper_dt_abun_csv      = "trophic_groups/abundance/snapper_dt_abun.csv"
snapper_fk_den_csv       = "trophic_groups/density/snapper_fk_den.csv"
snapper_dt_den_csv       = "trophic_groups/density/snapper_dt_den.csv"
snapper_fk_diversity_csv = "trophic_groups/diversity/snapper_fk_diversity.csv"
snapper_dt_diversity_csv = "trophic_groups/diversity/snapper_dt_diversity.csv"

if(!all(file.exists(snapper_fk_abun_csv,snapper_dt_abun_csv,snapper_fk_den_csv,snapper_dt_den_csv,snapper_fk_diversity_csv,snapper_dt_diversity_csv))){
  
snapper_spp_list = c("OCY CHRY", "LUT GRIS", "LUT ANAL", "LUT APOD", "LUT SYNA", "LUT MAHO", "LUT JOCU", "LUT BUCC", 'LUT SPE.', "LUT CYAN", "RHO AURO", "Lut camp")

#abundance
snapper_fk_abun = getDomainAbundance(RVCdata_FK, snapper_spp_list, merge_protected = F)
write_csv(snapper_fk_abun, "big_csv/trophic_groups/abundance/snapper_fk_abun.csv")
snapper_dt_abun = getDomainAbundance(RVCdata_DT, snapper_spp_list, merge_protected = F)
write_csv(snapper_dt_abun, "big_csv/trophic_groups/abundance/snapper_dt_abun.csv")

#density
snapper_fk_den = getDomainDensity(RVCdata_FK, snapper_spp_list, merge_protected = F)
write_csv(snapper_fk_den, "big_csv/trophic_groups/density/snapper_fk_den.csv")
snapper_dt_den = getDomainDensity(RVCdata_DT, snapper_spp_list, merge_protected = F)
write_csv(snapper_dt_den, "big_csv/trophic_groups/density/snapper_dt_den.csv")

#diversity
snapper_fk_abundance = snapper_fk_abun %>% 
  select(YEAR, protected_status, SPECIES_CD, abundance) %>%  
  group_by(YEAR, protected_status) %>% #48 groups 
  nest(-YEAR) %>%  
  mutate(
    data_wide = map(data, ~ spread(data=.x, SPECIES_CD, abundance, fill = 0)), 
     #species richness 
    richness = map(
      data_wide, 
      function(x) specnumber(x)),
    #simpson diversity as effective number of species 
    simpson = map( 
      data_wide,
      function(x) 1/(1 - diversity(x, index = 'simpson'))),
     #shannon diversity as effective number of species 
    shannon = map(
      data_wide,
      function(x) exp(diversity(x, index = 'shannon')))) %>%
  unnest(richness, simpson, shannon)

snapper_fk_diversity = snapper_fk_abundance %>%
  select(YEAR, protected_status, richness, simpson, shannon) 
write_csv(snapper_fk_diversity, "big_csv/trophic_groups/diversity/snapper_fk_diversity.csv")

#dt diversity
snapper_dt_abundance = snapper_dt_abun %>% 
  select(YEAR, protected_status, SPECIES_CD, abundance) %>%  
  group_by(YEAR, protected_status) %>% #48 groups 
  nest(-YEAR) %>%  
  mutate(
    data_wide = map(data, ~ spread(data=.x, SPECIES_CD, abundance, fill = 0)), 
     #species richness 
    richness = map(
      data_wide, 
      function(x) specnumber(x)),
    #simpson diversity as effective number of species 
    simpson = map( 
      data_wide,
      function(x) 1/(1 - diversity(x, index = 'simpson'))),
     #shannon diversity as effective number of species 
    shannon = map(
      data_wide,
      function(x) exp(diversity(x, index = 'shannon')))) %>%
  unnest(richness, simpson, shannon)

snapper_dt_diversity = snapper_dt_abundance %>%
  select(YEAR, protected_status, richness, simpson, shannon) 
write_csv(snapper_dt_diversity, "big_csv/trophic_groups/diversity/snapper_dt_diversity.csv") 
}

snapper_fk_den = read_csv("trophic_groups/density/snapper_fk_den.csv", 
      col_types = cols(protected_status = col_character()))

snapper_fk_density = snapper_fk_den %>%
  select(YEAR, protected_status, SPECIES_CD, density) %>% 
  group_by(YEAR, protected_status) %>%
  summarise(
  ntot = sum(density)) %>%
  filter(protected_status != "0") %>%
  filter(protected_status != "1") %>% 
  mutate(
    protected_status = recode(
      protected_status, '0'='unprotected', '1'='protected')) %>%
  spread(protected_status, ntot)

dygraph(snapper_fk_density, main = 'Snapper Density') %>% 
    dyAxis("y", label = "Density") %>%
    dyAxis("x", label = "Year") %>%
    dyOptions(stackedGraph = T, fillAlpha = 0.6, axisLineWidth = 2)

Read in abundance, density, and diversity csv files for trophic groups

# read in all abundance csv files for trophic groups 
path = "trophic_groups/abundance/"
files = list.files(path=path, pattern = "*.csv")
for(file in files){
  perpos <- which(strsplit(file, "")[[1]]==".")
  assign(
    gsub(" ","",substr(file, 1, perpos-1)), 
    read.csv(paste(path, file, sep= "")))  
}

# read in all density csv files for trophic groups
path = "trophic_groups/density/"
files = list.files(path=path, pattern = "*.csv")
for(file in files){
  perpos <- which(strsplit(file, "")[[1]]==".")
  assign(
    gsub(" ","",substr(file, 1, perpos-1)), 
    read.csv(paste(path, file, sep= "")))  
}

# read in all diversity csv files for trophic groups
path = "trophic_groups/diversity/"
files = list.files(path=path, pattern = "*.csv")
for(file in files){
  perpos <- which(strsplit(file, "")[[1]]==".")
  assign(
    gsub(" ","",substr(file, 1, perpos-1)), 
    read.csv(paste(path, file, sep= "")))  
}

Grouper Test w/ BB

Metrics: - abundance - density - richness - Simpson - Shannon

  • Q: Have multiple groups, so how to look at single metric across groups? A: TrelliscopeJS to the rescue!

  • Protected areas: in/out

For big_csv/trophic_groups/abundance/*_*_abun.csv: - YEAR - REGION: FLA KEYS, or Dry Tortugas - SPECIES_CD: species code - abundance: units? - var: Variance in average density per secondary sampling unit - n: Number of primary sampling units sampled - nm: Number of secondary sampling units sampled - N: Number of possible primary sample units - NM: Number of possible secondary sampling units - protected_status: The protected status. Only present if merge_protected is FALSE

So far, per species. Then when summing to # of individuals across species, lose biomass idea.

TODO: - get weighted biomass as density! - sum abundance across species

Plotting with htmlwidgets: leaflet: - dygraphs for R

#csv = "big_csv/trophic_groups/abundance/grouper_fk_abun.csv"
grouper = read_csv("trophic_groups/diversity/grouper_fk_diversity.csv")
grouper_abun = read_csv("trophic_groups/abundance/grouper_fk_abun.csv")

grouper_abundance = grouper_abun %>%
  select(YEAR,protected_status, SPECIES_CD,abundance) %>% 
  group_by(YEAR, protected_status) %>%
  summarise(
  ntot = sum(abundance)) %>%
  filter(protected_status != "all") %>%
  mutate(
    protected_status = recode(
      protected_status, '0'='unprotected', '1'='protected')) %>%
  spread(protected_status, ntot)

dygraph(grouper_abundance, main = 'Grouper Abundance') %>% 
    dyAxis("y", label = "Abundance") %>%
    dyAxis("x", label = "Year") %>%
    dyOptions(stackedGraph = T)
  

source('~/github/cr-metrics/functions.R')

plot_timeseries(
  title   = 'Grouper Richness',
  y_label = 'Richness',
  x_label = 'Year',
  csv_tv  = csv,
  col_t   = 'YEAR',
  filter  = 'protected_status == "all"',
  col_y   = 'grouper_richness',
  skip    = 0)

grouper = grouper %>%
  filter(protected_status != 'all') %>%
  select(YEAR, protected_status, shannon) %>%
  mutate(
    protected_status = recode(
      protected_status, '0'='unprotected', '1'='protected')) %>%
  spread(protected_status, shannon)

dygraph(grouper, main = 'Grouper Shannon Diversity') %>% 
    dyAxis("y", label = "Effective Number of Species") %>%
    dyAxis("x", label = "Year") %>%
     dyOptions(stackedGraph = T)%>% 
    dyRangeSelector(height = 20)

Trophic Level

#potential visualize as a stacked chart 
trophic_levels = read_csv('big_csv/FKNMS_infographic_list.csv')
# Parsed with column specification:
# cols(
#   Ecological_classification = col_character(),
#   Sanctuary_Classifcation_level = col_character(),
#   Icons = col_character(),
#   Latin_Name = col_character(),
#   Common_Name = col_character(),
#   RVC_CODE = col_character(),
#   Trophic_Level = col_integer(),
#   Representative_Species = col_character(),
#   Dataset = col_character(),
#   Metric = col_character(),
#   Lead = col_character()
# )

trophic_levels = trophic_levels %>%
  select(RVC_CODE, Trophic_Level) %>% 
  group_by(Trophic_Level) #4 trophic levels, #421 species 
trophic_levels

tax<-RVCdata_FK$taxonomic_data
names(tax)
trophic_levels$SPECIES_CD<-trophic_levels$RVC_CODE

taxgroup<-merge(tax,trophic_levels,by='SPECIES_CD')

RVCdata_FK$taxonomic_data<-taxgroup
names(lookup1)

#
lookup1

lookup1=subset(RVCdata_FK$taxonomic_data,Trophic_Level %in% c("1"),select =c("RVC_CODE","Trophic_Level"))
lookup2=subset(RVCdata_FK$taxonomic_data,Trophic_Level %in% c("2"),select =c("RVC_CODE","Trophic_Level"))
lookup3=subset(RVCdata_FK$taxonomic_data,Trophic_Level %in% c("3"),select =c("RVC_CODE","Trophic_Level"))


Biom1 = getDomainTotalBiomass(RVCdata_FK, species = lookup1$RVC_CODE, growth_parameters=RVCdata_FK$taxonomic_data, group = lookup1)

Exploited reef fish

Scientific name Common name RVC code Comment
Cephalopholis cruentata Graysby CEP CRUE exploited
Epinephelus itajara Goliath grouper EPI ITAJ moritorium
Epinephelus striatus Nassau grouper EPI STRI moritorium
Epinephelus Morio Red grouper EPI MORI exploited
Lachnolaimus maximus Hogfish LAC MAXI exploited
Lutjanus analis Mutton snapper LUT ANAL exploited
Lutjanus griseus Grey snapper LUT GRIS exploited
Mycteroperca bonaci Black grouper MYC BONA exploited
Ocyurus chrysurus Yellowtail snapper OCY CHRY exploited 
exploited_fk_abun_csv = "exploited_species/exploited_fk_abun.csv"
exploited_dt_abun_csv = "exploited_species/exploited_dt_abun.csv"
exploited_fk_den_csv  = "exploited_species/exploited_fk_den.csv"
exploited_dt_den_csv  = "exploited_species/exploited_dt_den.csv"

if(!all(file.exists(exploited_fk_abun_csv, exploited_dt_abun_csv, exploited_fk_den_csv, exploited_dt_den_csv))){
  
exploited_spp_list= c(
    "CEP CRUE", #Graysby
    "EPI ITAJ", #Goliath Grouper 
    "EPI MORI", #Red Grouper
    "EPI STRI", #Nassau Grouper 
    "LAC MAXI", #Hogfish
    "LUT ANAL", #Mutton Snapper
    "LUT GRIS", #Grey Snapper    
    "MYC BONA", #Black Grouper
    "OCY CHRY" #Yellowtail Snapper 
    )
#abundance
exploited_fk_abun <- getDomainAbundance(RVCdata_FK, species = exploited_spp_list, merge_protected = F)
write_csv(exploited_fk_abun,"big_csv/exploited/exploited_fk_abun.csv")
exploited_dt_abun <- getDomainAbundance(RVCdata_DT, species = exploited_spp_list, merge_protected = F)
write_csv(exploited_dt_abun,"big_csv/exploited/exploited_dt_abun.csv")
#density 
exploited_fk_den <- getDomainDensity(RVCdata_FK, species = exploited_spp_list, merge_protected = F)
write_csv(exploited_fk_den,"big_csv/exploited/exploited_fk_den.csv")
exploited_dt_den <- getDomainDensity(RVCdata_DT, species = exploited_spp_list, merge_protected = F)
write_csv(exploited_dt_den,"big_csv/exploited/exploited_dt_den.csv")

}

exploited_den = read_csv("exploited_species/exploited_fk_den.csv")
## Parsed with column specification:
## cols(
##   YEAR = col_integer(),
##   REGION = col_character(),
##   SPECIES_CD = col_character(),
##   density = col_double(),
##   var = col_double(),
##   n = col_integer(),
##   nm = col_integer(),
##   N = col_double(),
##   NM = col_double(),
##   protected_status = col_character()
## )
exploited_density = exploited_den %>%
  mutate(
    protected_status = recode(
      protected_status, '0'='unprotected', '1'='protected'), 
    common_name = recode(
      SPECIES_CD,
      'CEP CRUE' = 'Graysby',
      'EPI ITAJ' = 'Goliath_Grouper',
      'EPI MORI' = 'Red_Grouper',
      'EPI STRI' = 'Nassau_Grouper',
      'LAC MAXI' = 'Hogfish',
      'LUT ANAL' = 'Mutton_Snapper',
      'LUT GRIS' = 'Grey_Snapper',
      'MYC BONA' = 'Black_Grouper',
      'OCY CHRY' = 'Yellowtail_Snapper')) %>% 
  select(YEAR, common_name, protected_status, density) %>%
  group_by(YEAR, common_name, protected_status) %>%
  filter(protected_status != "all") %>%
  summarise(
    ntot = sum(density)) %>%
  spread(common_name, ntot)
 
#Graysby density    
Graysby = exploited_density %>%
  select(YEAR, protected_status, Graysby) %>%
  spread(protected_status, Graysby)

dygraph(Graysby, main = 'Graysby Density') %>% 
    dyAxis("y", label = "Density") %>%
    dyAxis("x", label = "Year") %>%
    dyOptions(stackedGraph = T)
#Grey_Snapper density    
Grey_Snapper = exploited_density %>%
  select(YEAR, protected_status, Grey_Snapper) %>%
  spread(protected_status, Grey_Snapper)

dygraph(Grey_Snapper, main = 'Grey Snapper Density') %>% 
    dyAxis("y", label = "Density") %>%
    dyAxis("x", label = "Year") %>%
    dyOptions(stackedGraph = T, fillAlpha = 0.6, axisLineWidth = 2)
#Hogfish density    
Hogfish = exploited_density %>%
  select(YEAR, protected_status, Hogfish) %>%
  spread(protected_status, Hogfish)

dygraph(Hogfish, main = 'Hogfish Density') %>% 
    dyAxis("y", label = "Density") %>%
    dyAxis("x", label = "Year") %>%
    dyOptions(stackedGraph = T, fillAlpha = 0.6, axisLineWidth = 2)
#Goliath grouper density 
Goliath_Grouper = exploited_density %>%
  select(YEAR, protected_status, Goliath_Grouper) %>%
  spread(protected_status, Goliath_Grouper)

dygraph(Goliath_Grouper, main = 'Goliath Grouper Density') %>% 
    dyAxis("y", label = "Density") %>%
    dyAxis("x", label = "Year") %>%
    dyOptions(stackedGraph = T, fillAlpha = 0.6, axisLineWidth = 2)
##Nassau Grouper
Nassau_Grouper = exploited_density %>%
  select(YEAR, protected_status, Nassau_Grouper) %>%
  spread(protected_status, Nassau_Grouper)

dygraph(Nassau_Grouper, main = 'Nassau Grouper Density') %>% 
    dyAxis("y", label = "Density") %>%
    dyAxis("x", label = "Year") %>%
    dyOptions(stackedGraph = T, fillAlpha = 0.6, axisLineWidth = )
##Yellowtail Snapper 
yellowtail_snapper = exploited_density %>%
  select(YEAR, protected_status, Yellowtail_Snapper) %>%
  spread(protected_status, Yellowtail_Snapper)

dygraph(yellowtail_snapper, main = 'Yellowtail Snapper Density') %>% 
    dyAxis("y", label = "Density") %>%
    dyAxis("x", label = "Year") %>%
    dyOptions(stackedGraph = T, fillAlpha = 0.6, axisLineWidth = 2)
#exploited reef fish density in protected areas 
exploited_density_protected = exploited_density %>%
  filter(protected_status == 'protected') %>% 
  select(YEAR, Black_Grouper, Goliath_Grouper, Graysby, Grey_Snapper, Hogfish, Mutton_Snapper, Nassau_Grouper,Red_Grouper, Yellowtail_Snapper)

dygraph(exploited_density_protected, main = "Exploited Reef Fish Density in Protected Areas") %>% 
    dyAxis("y", label = "Density") %>%
    dyAxis("x", label = "Year") %>%
    dyOptions(stackedGraph = T, fillAlpha = 0.6, axisLineWidth = 2, colors = rainbow(9))

Reef Fish Biodiversity

domain_fk_abun_diversity = read_csv('big_csv/abundance_domain/domain_fk_abun_diversity.csv')
## Parsed with column specification:
## cols(
##   YEAR = col_integer(),
##   protected_status = col_character(),
##   dom_richness = col_integer(),
##   dom_simpson = col_double(),
##   dom_shannon = col_double()
## )
domain_dt_abun_diversity = read_csv("big_csv/abundance_domain/domain_dt_abun_diversity.csv")
## Parsed with column specification:
## cols(
##   YEAR = col_integer(),
##   protected_status = col_character(),
##   dom_richness = col_integer(),
##   dom_simpson = col_double(),
##   dom_shannon = col_double()
## )
strata_fk_abun_diversity = read_csv("big_csv/abundance_strata/strata_fk_abun_diversity.csv")
## Parsed with column specification:
## cols(
##   YEAR = col_integer(),
##   STRAT = col_character(),
##   protected_status = col_character(),
##   strata_richness = col_integer(),
##   strata_simpson = col_double(),
##   strata_shannon = col_double()
## )
strata_dt_abun_diversity = read_csv("big_csv/abundance_strata/strata_dt_abun_diversity.csv")
## Parsed with column specification:
## cols(
##   YEAR = col_integer(),
##   STRAT = col_character(),
##   PROT = col_integer(),
##   strata_richness = col_integer(),
##   strata_simpson = col_double(),
##   strata_shannon = col_double()
## )
psu_fk_abun_diversity = read_csv("big_csv/abundance_psu/psu_fk_abun_diversity.csv", 
          col_types = cols(protected_status = col_character())) 
psu_dt_abun_diversity = read_csv("big_csv/abundance_psu/psu_dt_abun_diversity.csv")
## Parsed with column specification:
## cols(
##   YEAR = col_integer(),
##   PRIMARY_SAMPLE_UNIT = col_character(),
##   psu_richness = col_integer(),
##   psu_simpson = col_double(),
##   psu_shannon = col_double()
## )
domain_fk_abun_diversity = read_csv('big_csv/abundance_domain/domain_fk_abun_diversity.csv')
## Parsed with column specification:
## cols(
##   YEAR = col_integer(),
##   protected_status = col_character(),
##   dom_richness = col_integer(),
##   dom_simpson = col_double(),
##   dom_shannon = col_double()
## )
## Simpson for protected and unprotected stacked 
fk_simpson = domain_fk_abun_diversity %>% 
  filter(protected_status != 'all') %>%
  select(YEAR, protected_status, dom_simpson) %>%
  mutate(
    protected_status = recode(
      protected_status, '0'='Unprotected', '1'='Protected')) %>%
  spread(protected_status, dom_simpson)

dygraph(fk_simpson, main = "Simpson Reef Fish Diversity") %>% 
  dyAxis("y", label = "Effective Number of Species", valueRange = c(0, 50)) %>%
  dyAxis("x", label = "Year") %>%
  dySeries("Protected", strokeWidth = 2, strokePattern = "dashed") %>% 
  dySeries("Unprotected", strokeWidth = 2) %>%
  dyOptions(stackedGraph = T, fillAlpha = 0.8, axisLineWidth = 2)
  #dyRangeSelector(height = 20) 

## Shannon for protected and unprotected stacked 
fk_shannon = domain_fk_abun_diversity %>% 
  filter(protected_status != 'all') %>%
  select(YEAR, protected_status, dom_shannon) %>%
  mutate(
    protected_status = recode(
      protected_status, '0'='Unprotected', '1'='Protected')) %>%
  spread(protected_status, dom_shannon)

dygraph(fk_shannon, main = "Shannon Reef Fish Diversity") %>% 
  dyAxis("y", label = "Effective Number of Species", valueRange = c(0, 75)) %>%
  dyAxis("x", label = "Year") %>%
  dySeries("Protected", strokeWidth = 2, strokePattern = "dashed") %>% 
  dySeries("Unprotected", strokeWidth = 2) %>%
  dyOptions(stackedGraph = T, fillAlpha = 0.8, axisLineWidth = 2)
  #dyRangeSelector(height = 20) 

d = domain_fk_abun_diversity %>% 
  filter(protected_status != 0) %>% 
  filter(protected_status != 1)

#Simpson for "all" filled 
dygraph_simp = d %>%
  select(YEAR, dom_simpson)

dygraph(dygraph_simp, main = "Simpson Diversity of Reef Fish in FKNMS") %>%
  dyOptions(fillGraph = T, fillAlpha = 0.4, drawPoints = T, pointSize = 2) %>%
  dySeries("dom_simpson", label = "Simpson Diversity", color = "red") %>% 
  dyAxis("y", label = "Effective Number of Species") %>% 
  dyAxis("x", label = "Year") %>%
  dyOptions(stackedGraph = T, fillAlpha = 0.6, axisLineWidth = 2)
#Shannon for "all" filled 
dygraph_shannon = d %>%
  select(YEAR, dom_shannon)

dygraph(dygraph_shannon, main = "Shannon Diversity of Reef Fish in FKNMS") %>%
  dyOptions(fillGraph = T, fillAlpha = 0.4, drawPoints = T, pointSize = 2) %>%
  dySeries("dom_shannon", label = "Shannon Diversity", color = "blue") %>% 
  dyAxis("y", label = "Effective Number of Species") %>% 
  dyAxis("x", label = "Year") %>% 
  dyOptions(stackedGraph = T, fillAlpha = 0.6, axisLineWidth = 2)
#Richness for "all" filled 
dygraph_richness = d %>%
  select(YEAR, dom_richness)

dygraph(dygraph_richness, main = "Species Richness of Reef Fish in FKNMS") %>%
  dyOptions(fillGraph = T, fillAlpha = 0.4, drawPoints = T, pointSize = 2) %>%
  dySeries("dom_richness", label = "Species Richness", color = "purple") %>% 
  dyAxis("y", label = "Number of Species") %>% 
  dyAxis("x", label = "Year") %>% 
  dyOptions(stackedGraph = T, fillAlpha = 0.6, axisLineWidth = 2)
## Simpson and Shannon stacked for "all"
dygraph_simp_shannon = d %>%
  select(YEAR, dom_simpson, dom_shannon)

dygraph(dygraph_simp_shannon, main = "Florida Keys Reef Fish Biodiversity") %>% 
  dyAxis("y", label = "Effective Number of Species", valueRange = c(0, 70)) %>%
  dyAxis("x", label = "Year") %>%
  dySeries("dom_shannon", label = "Shannon Diversity", color = "blue") %>% 
  dySeries("dom_simpson", label = "Simpson Diversity", color = "red") %>% 
  dyOptions(stackedGraph = T, fillAlpha = 0.6, axisLineWidth = 1.5) %>% #drawGrid = F
  dyLegend(width = 400)
#Richness, Shannon, Simpson stacked for "all"
dygraph_rich_simp_shannon = d %>%
  select(YEAR, dom_simpson, dom_shannon, dom_richness)

dygraph(dygraph_rich_simp_shannon, main = "Florida Keys Reef Fish Biodiversity") %>% 
  dyAxis("y", label = "Effective Number of Species") %>% 
  dyAxis("x", label = "Year") %>%
  dySeries("dom_richness", label = "Richness", color = "purple") %>%
  dySeries("dom_shannon", label = "Shannon",  color = "blue") %>% 
  dySeries("dom_simpson", label = "Simpson", color = "red") %>% 
  dyOptions(stackedGraph = T, fillAlpha = 0.6, axisLineWidth = 2) %>% #drawGrid = F
  dyLegend(width = 400)

Coreal Reef Evaluation and Monitoring Project (CREMP)

Stony Corals

Sea turtles

Queen conch

Caribbean spiny lobster

Long-spinned sea urchin