Package index • 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_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_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_benthos_index(): plot benthos index

plot_blue_runner(): plot blue_runner

plot_bottom_temp_glorys(): plot bottom anomaly temperature time series using GLORYS

plot_bottom_temp_insitu(): plot bottom anomaly temperature time series using NEFSC survey data

plot_bottom_temp_model_anom(): plot bottom anomaly temperature time series

plot_bottom_temp_model_gridded(): plot bottom temperature seasonal gridded data

plot_calanus_stage(): plot calanus_stage

plot_cetacean_dist(): plot HMS species distribution

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_community_climate_vulnerability(): plot community climate vulnerability

plot_condition(): plots Fish Condition

plot_demo(): plot demo for SOE report

plot_energy_density(): plot energy_density

plot_engagement(): plot fishery engagement and community social vulnerability

plot_exp_n(): plot exp_n

plot_finfish_traits(): plot finfish traits

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_lps_sharks(): plot shark fishing landings from large pelagics survey

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_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_oisst_anom_gridded(): plot seasonal_oisst_anom_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_gridded(): 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

plot_zooplankton_index(): plot zooplankton 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

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

community_climate_vulnerability: Community climate vulnerability indicators

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

benthos_index: Benthos Index

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

zooplankton_index: Zooplankton Index

LTL/Hab/Env Indicators

Data files containing Low Trophic Level, Habitat and Environmental indicators used in the State of the Ecosystem Reports

bottom_temp_insitu: Bottom temperature

bottom_temp_model_anom: Bottom temperature - High Resolution

bottom_temp_model_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 and phytoplankton size class

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

SAV: Chesapeake Bay Submerged Aquatic Vegetation

seasonal_oisst_anom: Sea-surface temperature anomaly time serries

seasonal_oisst_anom_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