Plotting and modeling functionsmain functions for running models and plotting its output |
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ecodata: indicator data for reporting ecosystem health |
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Coast |
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Cold pool sf index |
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Chesapeake Bay shapefiles |
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Ecological Production Units |
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A geom to fit a GLS model to a time series |
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A geom to fit a GLS model to a time series |
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A geom to fit a LM model to a short time series |
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A geom to fit a regime shifts to a time series |
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Longline survey sf index ????? |
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plot HMS species distribution |
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plot SAV |
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plot abc_acl |
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plot aggregate_biomass |
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plot chl_pp |
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plot aquaculture |
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plot Bennett indicator |
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plot blue_runner |
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plot bottom anomaly temperature time series using NEFSC survey data |
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plot bottom anomaly temperature time series |
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plot bottom anomaly temperature time series using GLORYS |
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plot bottom temperature seasonal gridded data |
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plot calanus_stage |
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plot ch_bay_sal |
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plot ch_bay_temp |
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plot ches_bay_sst |
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plot ches_bay_wq |
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plot chl_pp |
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plot cold_pool |
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plot cold_pool_sf |
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plot comdat |
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plot commercial_div |
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plots Fish Condition |
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plot energy_density |
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plot engagement |
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plot exp_n |
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plot forage anomaly |
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plot forage index |
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plot dataset name |
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plots Gulf of Maine Salmon |
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plot grayseal |
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plot gulf stream index |
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plot habitat diversity |
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plot harmful algal bloom |
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plot harborporpoise |
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plot heatwave |
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plot heatwave_peak_date |
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plot heatwave_year |
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plot hms_cpue |
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plot hms_landings |
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plot hms_stock_status |
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plot flow rate of hudson river |
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plot Larval diversity |
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plot long term sea surface temperature |
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plot mid atlantic inshore survey |
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plot massachusetts inshore data |
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plot Northern Oscillation Index |
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plot north atlantic right whale abundance |
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plot ME/NH inshore bottom trawl survey |
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plot NE observer program shark data |
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plot phytoplankton by size class |
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plot ecosystem overfishing indices |
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plot productivity_anomaly |
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plot recreational shark fishing landings |
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plot recreational data |
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plot sandlance numbers |
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plot Mid Atlantic sea bird population |
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plot New England sea bird population |
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plot Gray seal pup populations |
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plot botttom temperature anomaly |
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plot SST anomaly (OISST) |
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plot seasonal_sst_anomaly_gridded |
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Setup all plot defaults |
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plot slopewater |
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plot spawn_timing |
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plot species_dist |
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plot species groupings by SOE year |
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plot stock_Status |
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plot stomach fullness |
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plot storminess data |
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plot diversity of survey data |
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plot thermal habitat area |
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plot thermal habitat persistence |
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plot SST transition dates and timing |
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plot Warm core rings |
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plot revenue from top 10 landings |
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plot wind lease cumulative areas |
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plot probability of species occupancy in wind area |
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plot revenue by port from wind energy |
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plot wind revenue |
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plot zooplankton abundance anomaly |
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plot zoo_diversity |
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plot zoo_regime |
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plot abundance of Euphasids and Cnids |
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StatLM Stat protto based on ecodata StatGLS Need to pass arguments |
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A ggplot2 theme for faceted SOE time series figures |
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A ggplot2 theme for SOE map figures |
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A ggplot2 ggtitle formatting for SOE figure titles |
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A ggplot2 theme for SOE time series figures |
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Sea surface temperature seasonal transiition dates |
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Synthetic IndicatorsData files containing synthetic indicators used in the State of the Ecosystem Reports |
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Ecosystem Overfishing Indicators |
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Wind lease area and habitat occupancy model overlap |
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Community Port Landings and Revenue from Wind Energy Areas (WEAs) |
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Human Dimension IndicatorsData files containing human-related indicators used in the State of the Ecosystem Reports |
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ABC or ACL for Managed Stocks |
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Oyster aquaculture |
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Bennet indicator |
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Aggregated commercial fisheries data |
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Commercial fisheries diversity |
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Commercial and recreational fishery social-economic indicators |
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Highly Migratory Species Landings and Revenue |
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Highly Migratory species stock status |
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Recreational fishing indicators |
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Recreational shark fishing landings |
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Fisheries maximum and minimum landings and revenue from wind energy areas (WEAs). |
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Wind energy development speed |
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Fisheries revenue from wind lease areas |
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Megafauna IndicatorsData files containing megafauna indicators used in the State of the Ecosystem Reports |
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NEFSC survey data broken into season and aggregate group biomass |
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SAFMC managed Blue Runner presence on NES |
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Fish Condition |
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Forage fish energy density |
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Expected Number of Species per 1000 Individuals |
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Forage Index |
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Gray Seal Bycatch |
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Harbor porpoise bycatch |
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Highly Migratory Species Category |
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Highly Migratory Species Catch per Unit Effort |
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hp_density |
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longline survey |
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lps_sharks ??? |
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NEAMAP Mid-Atlantic inshore trawl survey |
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Massachusetts inshore bottom trawl survey |
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North Atlantic right whale abundance |
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New England inshore state survey data |
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New England inshore state survey data species |
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NE Observer program Shark data |
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Small fish per large fish biomass anomaly |
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Stellwagen Bank Sandlance |
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Virginia waterbird productivity |
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Common tern productivity and diet composition |
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Seal Pups counts in New England |
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Species distribution on the NES. |
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Species groupings |
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Managed species stock status |
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Stomach fullness index calculated from NEFSC fall bottom trawl surveys |
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Shannon Diversity of NEFSC Bottom Trawl Survey |
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LTL/Hab/Env IndicatorsData files containing Low Trophic Level, Habitat and Environmental indicators used in the State of the Ecosystem Reports |
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Bottom temperature |
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Bottom temperature - High Resolution |
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Bottom temperature - Seasonal Gridded Product |
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Bottom temperature - GLORYS |
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Bottom temperature anomaly |
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Calanus Stage |
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Chesapeake Bay Gridded Sea Surface Temperature |
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Chesapeake Bay salinity with historical trends for comparison |
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Chesapeake Bay temperature with historical trends for comparison |
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Chesapeake Bay Water Quality Attainment |
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Chlorophyll a and primary production |
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Cold pool index |
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Gulf Stream Index |
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Forage Anomaly |
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Habitat Diversity |
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Habitat Occupancy |
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Habitat Vulnerability |
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Harmful Algal Blooms - Alexandrium and Paralitic Shellfish Poisoning |
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Marine Heatwaves |
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Marine heatwaves within most recent year |
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Hudson River Flow |
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Ichthyoplankton diversity |
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Long-term SST |
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Phytoplankton size class |
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Chesapeake Bay Submerged Aquatic Vegetation |
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Sea-surface temperature anomaly time serries |
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Sea-surface temperature anomaly |
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Northeast Channel slopewater proportions |
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Warm core ring births |
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Zooplankton diversity |
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Zooplankton abundance anomaly |
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Zooplankton abundance anomaly used in regime shift analysis |
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Zooplankton stratified abundance for Euphausids and Cnidarians |