Reference

Plotting and modeling functions main functions for running models and plotting its output
ecodata	ecodata: indicator data for reporting ecosystem health
coast	Coast
cold_pool_sf	Cold pool sf index
ches_bay_sf	Chesapeake Bay shapefiles
epu_sf	Ecological Production Units
geom_gls()	A geom to fit a GLS model to a time series
geom_lm()	A geom to fit a LM model to a short time series
geom_regime()	A geom to fit a regime shifts to a time series
longlinesurvey_sf	Longline survey sf index ?????
StatLM	StatLM Stat protto based on ecodata StatGLS Need to pass arguments
theme_facet()	A ggplot2 theme for faceted SOE time series figures
theme_map()	A ggplot2 theme for SOE map figures
theme_title()	A ggplot2 ggtitle formatting for SOE figure titles
theme_ts()	A ggplot2 theme for SOE time series figures
trans_dates	Sea surface temperature seasonal transiition dates
plot_bottom_temp_anomaly_glorys()	plot bottom anomaly temperature time series using Glorys data
plot_bottom_temp_anomaly_space()	plot botttom temperature anomaly
plot_bottom_temp_anomaly_survey()	plot bottom anomaly temperature time series using NEFSC survey data
plot_bottom_temp_anomaly_time()	plot bottom anomaly temperature time series
plot_forage_index()	plot forage index
plot_sst()	plot SST
plot_sst_anomaly()	plot SST anomaly
plot_sst_transition_dates()	plot SST transition_dates
plot_sst_transition_dates_length()	plot SST transition_dates
Synthetic Indicators Data files containing synthetic indicators used in the State of the Ecosystem Reports
ppr	Ecosystem Overfishing Indicators
wind_occupancy	Wind lease area and habitat occupancy model overlap
wind_port	Community Port Landings and Revenue from Wind Energy Areas (WEAs)
Human Dimension Indicators Data files containing human-related indicators used in the State of the Ecosystem Reports
abc.acl	ABC or ACL for Managed Stocks
aquaculture	Oyster aquaculture
bennet	Bennet indicator
comdat	Aggregated commercial fisheries data
commercial_div	Commercial fisheries diversity
engagement	Commercial and recreational fishery social-economic indicators
hms_landings	Highly Migratory Species Landings and Revenue
hms_stock_status	Highly Migratory species stock status
recdat	Recreational fishing indicators
rec_hms	Recreational shark fishing landings
wea_landings_rev	Fisheries maximum and minimum landings and revenue from wind energy areas (WEAs).
wind_dev_speed	Wind energy development speed
wind_revenue	Fisheries revenue from wind lease areas
Megafauna Indicators Data files containing megafauna indicators used in the State of the Ecosystem Reports
aggregate_biomass	NEFSC survey data broken into season and aggregate group biomass
blue_runner	SAFMC managed Blue Runner presence on NES
condition	Fish Condition
energy_density	Forage fish energy density
exp_n	Expected Number of Species per 1000 Individuals
forage_index	Forage Index
grayseal	Gray Seal Bycatch
harborporpoise	Harbor porpoise bycatch
hms_category	Highly Migratory Species Category
hms_cpue	Highly Migratory Species Catch per Unit Effort
hp_density	hp_density
long_line_survey	longline survey
lps_sharks	lps_sharks ???
mab_inshore_survey	NEAMAP Mid-Atlantic inshore trawl survey
mass_inshore_survey	Massachusetts inshore bottom trawl survey
narw	North Atlantic right whale abundance
ne_inshore_survey	New England inshore state survey data
ne_inshore_survey_species	New England inshore state survey data species
observed_sharks	NE Observer program Shark data
productivity_anomaly	Small fish per large fish biomass anomaly
sandlance	Stellwagen Bank Sandlance
seabird_mab	Virginia waterbird productivity
seabird_ne	Common tern productivity and diet composition
seal_pups	Seal Pups counts in New England
species_dist	Species distribution on the NES.
species_groupings	Species groupings
stock_status	Managed species stock status
stom_fullness	Stomach fullness index calculated from NEFSC fall bottom trawl surveys
survey_shannon	Shannon Diversity of NEFSC Bottom Trawl Survey
LTL/Hab/Env Indicators Data files containing Low Trophic Level, Habitat and Environmental indicators used in the State of the Ecosystem Reports
bottom_temp	Bottom temperature
bottom_temp_comp	Bottom temperature - High Resolution
bottom_temp_seasonal_gridded	Bottom temperature - Seasonal Gridded Product
bottom_temp_glorys	Bottom temperature - GLORYS
seasonal_bt_anomaly_gridded	Bottom temperature anomaly
calanus_stage	Calanus Stage
ches_bay_sst	Chesapeake Bay Gridded Sea Surface Temperature
ch_bay_sal	Chesapeake Bay salinity with historical trends for comparison
ch_bay_temp	Chesapeake Bay temperature with historical trends for comparison
ches_bay_wq	Chesapeake Bay Water Quality Attainment
chl_pp	Chlorophyll a and primary production
cold_pool	Cold pool index
gsi	Gulf Stream Index
forage_anomaly	Forage Anomaly
habitat_diversity	Habitat Diversity
habitat_occupancy	Habitat Occupancy
habitat_vulnerability	Habitat Vulnerability
habs	Harmful Algal Blooms - Alexandrium and Paralitic Shellfish Poisoning
heatwave	Marine Heatwaves
heatwave_year	Marine heatwaves within most recent year
hudson_river_flow	Hudson River Flow
ichthyo_diversity	Ichthyoplankton diversity
long_term_sst	Long-term SST
phyto_size	Phytoplankton size class
SAV	Chesapeake Bay Submerged Aquatic Vegetation
seasonal_oisst_anom	Sea-surface temperature anomaly time serries
seasonal_sst_anomaly_gridded	Sea-surface temperature anomaly
slopewater	Northeast Channel slopewater proportions
wcr	Warm core ring births
zoo_diversity	Zooplankton diversity
zoo_abundance_anom	Zooplankton abundance anomaly
zoo_regime	Zooplankton abundance anomaly used in regime shift analysis
zoo_strat_abun	Zooplankton stratified abundance for Euphausids and Cnidarians