Function reference • ecodata

Plotting and modeling functions main functions for running models and plotting its output
`ecodata` `ecodata-package`	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_gls_gauss()`	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 ?????
`plot_HMS_species_distribution()`	plot HMS species distribution
`plot_SAV()`	plot SAV
`plot_abc_acl()`	plot abc_acl
`plot_aggregate_biomass()`	plot aggregate_biomass
`plot_annual_chl_pp()`	plot chl_pp
`plot_aquaculture()`	plot aquaculture
`plot_bennet()`	plot Bennett indicator
`plot_blue_runner()`	plot blue_runner
`plot_bottom_temp()`	plot bottom anomaly temperature time series using NEFSC survey data
`plot_bottom_temp_comp()`	plot bottom anomaly temperature time series
`plot_bottom_temp_glorys()`	plot bottom anomaly temperature time series using GLORYS
`plot_bottom_temp_seasonal_gridded()`	plot bottom temperature seasonal gridded data
`plot_calanus_stage()`	plot calanus_stage
`plot_ch_bay_sal()`	plot ch_bay_sal
`plot_ch_bay_temp()`	plot ch_bay_temp
`plot_ches_bay_sst()`	plot ches_bay_sst
`plot_ches_bay_wq()`	plot ches_bay_wq
`plot_chl_pp()`	plot chl_pp
`plot_cold_pool()`	plot cold_pool
`plot_cold_pool_sf()`	plot cold_pool_sf
`plot_comdat()`	plot comdat
`plot_commercial_div()`	plot commercial_div
`plot_condition()`	plots Fish Condition
`plot_energy_density()`	plot energy_density
`plot_engagement()`	plot engagement
`plot_exp_n()`	plot exp_n
`plot_forage_anomaly()`	plot forage anomaly
`plot_forage_index()`	plot forage index
`plot_function_template()`	plot dataset name
`plot_gom_salmon()`	plots Gulf of Maine Salmon
`plot_grayseal()`	plot grayseal
`plot_gsi()`	plot gulf stream index
`plot_habitat_diversity()`	plot habitat diversity
`plot_habs()`	plot harmful algal bloom
`plot_harborporpoise()`	plot harborporpoise
`plot_heatwave()`	plot heatwave
`plot_heatwave_peak_date()`	plot heatwave_peak_date
`plot_heatwave_year()`	plot heatwave_year
`plot_hms_cpue()`	plot hms_cpue
`plot_hms_landings()`	plot hms_landings
`plot_hms_stock_status()`	plot hms_stock_status
`plot_hudson_river_flow()`	plot flow rate of hudson river
`plot_ichthyo_diversity()`	plot Larval diversity
`plot_long_term_sst()`	plot long term sea surface temperature
`plot_mab_inshore_survey()`	plot mid atlantic inshore survey
`plot_mass_inshore_survey()`	plot massachusetts inshore data
`plot_nao()`	plot Northern Oscillation Index
`plot_narw()`	plot north atlantic right whale abundance
`plot_ne_inshore_survey()`	plot ME/NH inshore bottom trawl survey
`plot_observed_sharks()`	plot NE observer program shark data
`plot_phyto_size()`	plot phytoplankton by size class
`plot_ppr()`	plot ecosystem overfishing indices
`plot_productivity_anomaly()`	plot productivity_anomaly
`plot_rec_hms()`	plot recreational shark fishing landings
`plot_recdat()`	plot recreational data
`plot_sandlance()`	plot sandlance numbers
`plot_seabird_mab()`	plot Mid Atlantic sea bird population
`plot_seabird_ne()`	plot New England sea bird population
`plot_seal_pups()`	plot Gray seal pup populations
`plot_seasonal_bt_anomaly_gridded()`	plot botttom temperature anomaly
`plot_seasonal_oisst_anom()`	plot SST anomaly (OISST)
`plot_seasonal_sst_anomaly_gridded()`	plot seasonal_sst_anomaly_gridded
`plot_setup()`	Setup all plot defaults
`plot_slopewater()`	plot slopewater
`plot_spawn_timing()`	plot spawn_timing
`plot_species_dist()`	plot species_dist
`plot_species_groupings()`	plot species groupings by SOE year
`plot_stock_status()`	plot stock_Status
`plot_stom_fullness()`	plot stomach fullness
`plot_storminess()`	plot storminess data
`plot_survey_shannon()`	plot diversity of survey data
`plot_thermal_habitat_area()`	plot thermal habitat area
`plot_thermal_habitat_persistence()`	plot thermal habitat persistence
`plot_trans_dates()`	plot SST transition dates and timing
`plot_wcr()`	plot Warm core rings
`plot_wea_landings_rev()`	plot revenue from top 10 landings
`plot_wind_dev_speed()`	plot wind lease cumulative areas
`plot_wind_occupancy()`	plot probability of species occupancy in wind area
`plot_wind_port()`	plot revenue by port from wind energy
`plot_wind_revenue()`	plot wind revenue
`plot_zoo_abundance_anom()`	plot zooplankton abundance anomaly
`plot_zoo_diversity()`	plot zoo_diversity
`plot_zoo_regime()`	plot zoo_regime
`plot_zoo_strat_abun()`	plot abundance of Euphasids and Cnids
`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
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

Reference

Plotting and modeling functions

Synthetic Indicators

Human Dimension Indicators

Megafauna Indicators

LTL/Hab/Env Indicators