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