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index 100% rename from scripts/create_plots.R rename to scripts/archive/create_plots.R diff --git a/scripts/create_plots_slides.R b/scripts/archive/create_plots_slides.R similarity index 100% rename from scripts/create_plots_slides.R rename to scripts/archive/create_plots_slides.R diff --git a/scripts/create_plots_both_reports.R b/scripts/create_plots_both_reports.R index 68350262..f110fcb4 100644 --- a/scripts/create_plots_both_reports.R +++ b/scripts/create_plots_both_reports.R @@ -9,6 +9,9 @@ # region <- "BothReports" +# source(here::here("../ecodata/R/summary_functions.R")) +# source(here::here("utils/image_functions.R")) + create_plots_both <- function(region = "BothReports") { # setup ---- @@ -17,69 +20,14 @@ create_plots_both <- function(region = "BothReports") { dir.create(out_dir) } - ## functions ---- - - # A function to create a standardized filename - create_filename <- function( - indicator, - file_region, - dir = out_dir, - extension = ".png" - ) { - file.path( - dir, - paste0( - indicator, - "_", - file_region, - "_", - Sys.Date(), - extension - ) - ) - } - - # A flexible function to generate and save a plot - save_plot <- function( - plot_expression, - indicator, - report = region, - save_dir = out_dir, - ... - ) { - # Execute the code to create the plot - p <- eval(plot_expression) - - # Check if the plot object is valid before saving - if (inherits(p, "ggplot") || inherits(p, "ggarrange")) { - message(report) - message(indicator) - message(out_dir) - fname <- create_filename( - indicator = indicator, - file_region = report, - dir = save_dir - ) - ggplot2::ggsave( - filename = fname, - plot = p, - bg = "white", - ... - ) - message("Plot saved to: ", fname) - } else { - stop("Plot object is not a valid ggplot or ggarrange object.") - } - } - # 9. Thermal Habitat Persistence Plot save_plot( plot_expression = { plt <- ecodata::plot_thermal_habitat_gridded(region) }, - indicator = "therm_hab_persist", + indicator = "therm-hab-persist-2024", width = 6.5, - height = 4 + height = 4.25 ) # 5. Energy Density Plot @@ -89,7 +37,7 @@ create_plots_both <- function(region = "BothReports") { # # plot is the same even though it takes a region parameter # ecodata::plot_energy_density(report = "NewEngland") # }, - # indicator = "energy_density", + # indicator = "energy-density", # width = 6.5, # height = 4 # ) @@ -112,7 +60,7 @@ create_plots_both <- function(region = "BothReports") { }, indicator = "harborporpoise", width = 6.5, - height = 3 + height = 3.25 ) # gray seal @@ -122,7 +70,7 @@ create_plots_both <- function(region = "BothReports") { }, indicator = "grayseal", width = 6.5, - height = 3 + height = 3.25 ) # narw-abundance @@ -132,9 +80,9 @@ create_plots_both <- function(region = "BothReports") { ggplot2::ggtitle("North Atlantic right whale abundance") + ggplot2::scale_x_continuous(limits = c(1980, 2025)) }, - indicator = "narw_abundance", + indicator = "narw-abundance", width = 6.5, - height = 2.5 + height = 2.75 ) # narw calves @@ -143,9 +91,9 @@ create_plots_both <- function(region = "BothReports") { ecodata::plot_narw(varName = "calf", n = 10) + ggplot2::ggtitle("North Atlantic right whale calf abundance") }, - indicator = "narw_calves", + indicator = "NARW-calf-abundance", width = 6.5, - height = 2.5 + height = 2.75 ) # seals @@ -155,9 +103,9 @@ create_plots_both <- function(region = "BothReports") { ecodata::plot_seal_pups(report = "NewEngland") + ggplot2::theme(legend.position = 'bottom') }, - indicator = "seal_pups", + indicator = "seals", width = 6.5, - height = 4 + height = 4.25 ) # species dist @@ -167,9 +115,9 @@ create_plots_both <- function(region = "BothReports") { b <- ecodata::plot_species_dist(varName = "depth", n = 10) ggpubr::ggarrange(a, b, ncol = 1) }, - indicator = "species_dist", + indicator = "species-dist", width = 6.5, - height = 3.5 + height = 3.75 ) # whale and dolphin dist shifts @@ -180,20 +128,20 @@ create_plots_both <- function(region = "BothReports") { ggplot2::facet_wrap(~season, nrow = 1) + ggplot2::theme(legend.position = "bottom") }, - indicator = "cetacean_dist", + indicator = "protectedspp-dist-shifts", width = 7.5, - height = 4 + height = 4.25 ) # forage shifts save_plot( plot_expression = { ecodata::plot_forage_index(varName = "cog", n = 10) + - ggplot2::coord_cartesian(xlim = c(1982, 2023)) + ggplot2::coord_cartesian(xlim = c(1982, NA)) }, - indicator = "forage_dist", + indicator = "forageshifts", width = 6.5, - height = 3.5 + height = 3.75 ) # longterm sst @@ -201,9 +149,9 @@ create_plots_both <- function(region = "BothReports") { plot_expression = { ecodata::plot_long_term_sst(n = 10) }, - indicator = "long_term_sst", + indicator = "long-term-sst", width = 6.5, - height = 2.5 + height = 2.75 ) # gsi @@ -211,9 +159,9 @@ create_plots_both <- function(region = "BothReports") { plot_expression = { ecodata::plot_gsi(varName = "westgsi", n = 10) }, - indicator = "west_gsi", + indicator = "GSI", width = 6.5, - height = 2.5 + height = 2.75 ) # cold pool size @@ -223,9 +171,9 @@ create_plots_both <- function(region = "BothReports") { b <- ecodata::plot_cold_pool(varName = "extent", n = 10) ggpubr::ggarrange(a, b, nrow = 2) }, - indicator = "cold_pool", + indicator = "cold-pool-size", width = 6.5, - height = 4 + height = 4.25 ) # cold pool timing @@ -233,9 +181,9 @@ create_plots_both <- function(region = "BothReports") { plot_expression = { ecodata::plot_cold_pool(varName = "persistence", n = 10) }, - indicator = "cold_pool_time", + indicator = "cold-pool-time", width = 6.5, - height = 2.5 + height = 2.75 ) # spawn timing @@ -243,9 +191,9 @@ create_plots_both <- function(region = "BothReports") { plot_expression = { ecodata::plot_spawn_timing(n = 10) }, - indicator = "spawn_timing", + indicator = "spawntiming", width = 6.5, - height = 4 + height = 4.25 ) # development speed @@ -254,9 +202,9 @@ create_plots_both <- function(region = "BothReports") { ecodata::plot_wind_dev_speed() + ggplot2::theme(legend.position = 'bottom') }, - indicator = "wind_dev_speed", + indicator = "wind-proposed-dev", width = 6.5, - height = 4 + height = 4.25 ) # slopewater @@ -267,7 +215,7 @@ create_plots_both <- function(region = "BothReports") { }, indicator = "slopewater", width = 6, - height = 2.5 + height = 2.75 ) # small cope center of gravity @@ -281,9 +229,9 @@ create_plots_both <- function(region = "BothReports") { ggplot2::ggtitle("Northeast U.S. Small Copepod Distribution") + ggplot2::ylab("Center of Gravity, km") }, - indicator = "smallcopeall_cog", + indicator = "smallcopeall-cog", width = 6.5, - height = 3.5 + height = 3.75 ) # large cope center of gravity @@ -297,9 +245,9 @@ create_plots_both <- function(region = "BothReports") { ggplot2::ggtitle("Northeast U.S. Large Copepod Distribution") + ggplot2::ylab("Center of Gravity, km") }, - indicator = "lgcopeall_cog", + indicator = "lgcopeall-cog", width = 6.5, - height = 3.5 + height = 3.75 ) # macrobenthos shifts @@ -319,9 +267,9 @@ create_plots_both <- function(region = "BothReports") { scales = "free_y" ) }, - indicator = "macrobenthos_dist", + indicator = "macrobenthosshifts", width = 6.5, - height = 3.5 + height = 3.75 ) # megabenthos shifts @@ -341,9 +289,9 @@ create_plots_both <- function(region = "BothReports") { ) + ggplot2::theme(legend.position = 'bottom') }, - indicator = "megabenthos_dist", + indicator = "megabenthosshifts", width = 6.5, - height = 3.5 + height = 3.75 ) # euphausiid center of gravity @@ -364,9 +312,9 @@ create_plots_both <- function(region = "BothReports") { scales = "free_y" ) }, - indicator = "euph_cog", + indicator = "euph-cog", width = 6.5, - height = 3.5 + height = 3.75 ) } diff --git a/scripts/create_plots_mab_ne.R b/scripts/create_plots_mab_ne.R index 5df1ba69..6d588247 100644 --- a/scripts/create_plots_mab_ne.R +++ b/scripts/create_plots_mab_ne.R @@ -99,9 +99,9 @@ create_plots_mab_and_ne <- function(region) { ggplot2::facet_wrap(~EPU, nrow = 2) } }, - indicator = "total_landings", + indicator = "total-landings", width = 6.5, - height = ifelse(region == "NewEngland", 5, 2.5), + height = ifelse(region == "NewEngland", 5/25, 2.75), ) # commercial landings @@ -115,9 +115,9 @@ create_plots_mab_and_ne <- function(region) { ggplot2::geom_point(size = 0.05) + ggplot2::geom_line(size = 0.05) }, - indicator = "commercial_landings", + indicator = "comm-landings", width = 6.5, - height = 7 + height = 7.25 ) # climate vulnerability landings @@ -131,9 +131,9 @@ create_plots_mab_and_ne <- function(region) { ggplot2::ylab("Total Vulnerability \n (Regional Landings)") + ggplot2::theme(legend.position = 'bottom') }, - indicator = "climatevul_land", + indicator = "climatevul-land", width = 6.5, - height = 2.5 + height = 2.75 ) # rec landings @@ -145,9 +145,9 @@ create_plots_mab_and_ne <- function(region) { n = 10 ) }, - indicator = "rec_landings", + indicator = "rec-landings", width = 6.5, - height = 2.5 + height = 2.75 ) # rec hms and sharks @@ -182,9 +182,9 @@ create_plots_mab_and_ne <- function(region) { legend = "bottom" ) }, - indicator = "rec_hms", + indicator = "rec-hms", width = 6.5, - height = 5 + height = 5.25 ) ### Implications ---- @@ -199,9 +199,9 @@ create_plots_mab_and_ne <- function(region) { stock_status_plot$p } }, - indicator = "stock_status", + indicator = "stock-status", width = 6.5, - height = 6 + height = 6.25 ) # 2. ABC/ACL Stacked Plot @@ -212,9 +212,9 @@ create_plots_mab_and_ne <- function(region) { plottype = "Stacked" ) }, - indicator = "abcacl_stacked", + indicator = "abcacl-stacked", width = 6.5, - height = 4.5 + height = 4.75 ) # 3. ABC/ACL Catch Plot @@ -225,9 +225,9 @@ create_plots_mab_and_ne <- function(region) { plottype = "Catch" ) }, - indicator = "abcacl_catch", + indicator = "abcacl-catch", width = 6.5, - height = 2.5 + height = 2.75 ) # Aggregate biomass @@ -236,9 +236,9 @@ create_plots_mab_and_ne <- function(region) { plot_expression = { ecodata::plot_aggregate_biomass(report = region, EPU = "MAB", n = 10) }, - indicator = "aggregate_biomass_mab", + indicator = "nefsc-biomass-mab", width = 6.5, - height = 7 + height = 7.25 ) } @@ -253,9 +253,9 @@ create_plots_mab_and_ne <- function(region) { ) + ggplot2::theme(panel.spacing = grid::unit(0, 'lines')) }, - indicator = "aggregate_biomass_gb", + indicator = "nefsc-biomass-gb", width = 6.5, - height = 7 + height = 7.25 ) # gulf of maine save_plot( @@ -266,15 +266,64 @@ create_plots_mab_and_ne <- function(region) { n = 10 ) }, - indicator = "aggregate_biomass_gom", + indicator = "nefsc-biomass-gom", width = 6.5, - height = 7 + height = 7.25 ) } ## Commercial profits ---- ### Indicators ---- + + # Geret's profitability indices (comdat profit) (EPU = MAB) + save_plot( + plot_expression = { + if (region == "MidAtlantic") { + ecodata::plot_comdat_profit( + report = region, + n = 30 + ) + + ggplot2::scale_color_discrete( + limits = c("cost_index", "profit_index", "revenue_index"), + labels = c("Cost Index", "Profit Index", "Revenue Index") + ) + + ggplot2::theme( + legend.position = "bottom", + legend.title = ggplot2::element_blank() + ) + } else { + gb <- ecodata::plot_comdat_profit( + report = region, + EPU = "GB", + n = 30 + ) + + ggplot2::scale_color_discrete( + limits = c("cost_index", "profit_index", "revenue_index"), + labels = c("Cost Index", "Profit Index", "Revenue Index") + ) + + ggplot2::theme(legend.position = "none") + + gom <- ecodata::plot_comdat_profit( + report = region, + EPU = "GOM", + n = 30 + ) + + ggplot2::scale_color_discrete( + limits = c("cost_index", "profit_index", "revenue_index"), + labels = c("Cost Index", "Profit Index", "Revenue Index") + ) + + ggplot2::theme( + legend.position = "bottom", + legend.title = ggplot2::element_blank() + ) + ggpubr::ggarrange(gb, gom, nrow = 2) + } + }, + indicator = "comdat-profit", + width = 6.5, + height = ifelse(region == "NewEngland", 8.25, 2.75) + ) # 1. Commercial Revenue Plot save_plot( @@ -299,9 +348,9 @@ create_plots_mab_and_ne <- function(region) { ggplot2::facet_wrap(~EPU, nrow = 2) } }, - indicator = "comm_revenue", + indicator = "comm-revenue", width = 6.5, - height = ifelse(region == "NewEngland", 5, 2.5) + height = ifelse(region == "NewEngland", 5.25, 2.75) ) # bennet @@ -347,7 +396,7 @@ create_plots_mab_and_ne <- function(region) { }, indicator = "bennet", width = 6.5, - height = ifelse(region == "NewEngland", 6, 2.5) + height = ifelse(region == "NewEngland", 6.25, 2.75) ) # bennet all @@ -389,8 +438,8 @@ create_plots_mab_and_ne <- function(region) { ) } }, - indicator = "bennet_all", - width = ifelse(region == "NewEngland", 9, 4), + indicator = "bennet-all", + width = ifelse(region == "NewEngland", 9.25, 4.25), height = 6.5 ) @@ -408,58 +457,9 @@ create_plots_mab_and_ne <- function(region) { ) + ggplot2::ylab("Total Vulnerability \n (Regional Revenue)") }, - indicator = "climatevul_rev", + indicator = "climatevul-rev", width = 6.5, - height = 2.5 - ) - - # Geret's profitability indices (comdat profit) (EPU = MAB) - save_plot( - plot_expression = { - if (region == "MidAtlantic") { - ecodata::plot_comdat_profit( - report = region, - n = 30 - ) + - ggplot2::scale_color_discrete( - limits = c("cost_index", "profit_index", "revenue_index"), - labels = c("Cost Index", "Profit Index", "Revenue Index") - ) + - ggplot2::theme( - legend.position = "bottom", - legend.title = ggplot2::element_blank() - ) - } else { - gb <- ecodata::plot_comdat_profit( - report = region, - EPU = "GB", - n = 30 - ) + - ggplot2::scale_color_discrete( - limits = c("cost_index", "profit_index", "revenue_index"), - labels = c("Cost Index", "Profit Index", "Revenue Index") - ) + - ggplot2::theme(legend.position = "none") - - gom <- ecodata::plot_comdat_profit( - report = region, - EPU = "GOM", - n = 30 - ) + - ggplot2::scale_color_discrete( - limits = c("cost_index", "profit_index", "revenue_index"), - labels = c("Cost Index", "Profit Index", "Revenue Index") - ) + - ggplot2::theme( - legend.position = "bottom", - legend.title = ggplot2::element_blank() - ) - ggpubr::ggarrange(gb, gom, nrow = 2) - } - }, - indicator = "comdat_profit", - width = 6.5, - height = ifelse(region == "NewEngland", 8, 2.5) + height = 2.75 ) ## Recreational opportunities ---- @@ -475,9 +475,9 @@ create_plots_mab_and_ne <- function(region) { n = 10 ) }, - indicator = "rec_op", + indicator = "rec-op", width = 6.5, - height = 2.5 + height = 2.75 ) # 2. Recreational Diversity Plot @@ -495,9 +495,9 @@ create_plots_mab_and_ne <- function(region) { ggplot2::ylab('Effective Shannon Index') } }, - indicator = "rec_div", + indicator = "rec-div", width = 6.5, - height = 2.5 + height = 2.75 ) ## Stability ---- @@ -536,9 +536,9 @@ create_plots_mab_and_ne <- function(region) { ggpubr::ggarrange(a, b, nrow = 2) } }, - indicator = "comm_div_fleet", + indicator = "comm-div-fleet", width = 6.5, - height = ifelse(region == "NewEngland", 5, 2.5) + height = ifelse(region == "NewEngland", 5.25, 2.75) ) # 2. Commercial Diversity Species Diversity Plot @@ -555,9 +555,9 @@ create_plots_mab_and_ne <- function(region) { plt + ggplot2::ylab('Effective Shannon Index') } }, - indicator = "commercial_div_species_div", + indicator = "commercial-div-species-div", width = 6.5, - height = 2.5 + height = 2.75 ) # 3. Recreational Diversity Catch Plot @@ -565,9 +565,9 @@ create_plots_mab_and_ne <- function(region) { plot_expression = { ecodata::plot_recdat(report = region, varName = "catchdiversity", n = 10) }, - indicator = "recdat_div_catch", + indicator = "recdat-div-catch", width = 6.5, - height = 2.5 + height = 2.75 ) # total primary production @@ -609,7 +609,7 @@ create_plots_mab_and_ne <- function(region) { }, indicator = "totpp", width = 6.5, - height = ifelse(region == "NewEngland", 5, 2.5) + height = ifelse(region == "NewEngland", 5.25, 2.75) ) # 4. Zooplankton Diversity Plot @@ -627,9 +627,9 @@ create_plots_mab_and_ne <- function(region) { ggplot2::facet_wrap(~EPU, nrow = 1, scales = "free_y") } }, - indicator = "zoo_diversity", + indicator = "zoo-diversity", width = 6.5, - height = ifelse(region == "NewEngland", 4, 2.5) + height = ifelse(region == "NewEngland", 4.25, 2.75) ) # 5. Expected N Plot @@ -665,9 +665,9 @@ create_plots_mab_and_ne <- function(region) { ggplot2::facet_wrap(~EPU, nrow = 2) } }, - indicator = "exp_n", + indicator = "exp-n", width = 6.5, - height = ifelse(region == "NewEngland", 5, 2.5) + height = ifelse(region == "NewEngland", 5.25, 2.75) ) #zooplankton community PCA @@ -684,9 +684,9 @@ create_plots_mab_and_ne <- function(region) { ggplot2::facet_wrap(~EPU, nrow = 2) } }, - indicator = "zoo_community", + indicator = "zoo-community", width = 6.5, - height = ifelse(region == "NewEngland", 5, 2.5) + height = ifelse(region == "NewEngland", 5.25, 2.75) ) # finfish traits @@ -713,7 +713,7 @@ create_plots_mab_and_ne <- function(region) { }, indicator = "traits", width = 6.5, - height = ifelse(region == "NewEngland", 5, 2.5) + height = ifelse(region == "NewEngland", 5.25, 2.75) ) #finfish traits - trophic level @@ -739,9 +739,9 @@ create_plots_mab_and_ne <- function(region) { ggplot2::facet_wrap(~EPU, nrow = 2) } }, - indicator = "traits_tl", + indicator = "traits-tl", width = 6.5, - height = ifelse(region == "NewEngland", 4.5, 2.5) + height = ifelse(region == "NewEngland", 4.75, 2.75) ) #finfish traits - growth rate @@ -759,9 +759,9 @@ create_plots_mab_and_ne <- function(region) { ggplot2::facet_wrap(~EPU, nrow = 2) } }, - indicator = "traits_k", + indicator = "traits-k", width = 6.5, - height = ifelse(region == "NewEngland", 4.5, 2.5) + height = ifelse(region == "NewEngland", 4.75, 2.75) ) ## Community social and climate vulnerability ---- @@ -778,9 +778,9 @@ create_plots_mab_and_ne <- function(region) { legend.title = ggplot2::element_blank() ) }, - indicator = "commercial_engagement", + indicator = "commercial-engagement", width = 7, - height = 5 + height = 5.25 ) # 2. Recreational Engagement Plot @@ -792,9 +792,9 @@ create_plots_mab_and_ne <- function(region) { ) + ggplot2::theme(plot.title = ggplot2::element_text(vjust = 0)) }, - indicator = "recreational_engagement", + indicator = "recreational-engagement", width = 6.5, - height = 4 + height = 4.25 ) # 3. Community Climate Vulnerability Exposure Plot @@ -808,7 +808,7 @@ create_plots_mab_and_ne <- function(region) { }, indicator = "commvulex", width = 6.5, - height = 3 + height = 3.25 ) ### Risks to managing seasonally ---- @@ -818,23 +818,46 @@ create_plots_mab_and_ne <- function(region) { plot_expression = { ecodata::plot_trans_dates(report = region, varName = "length", n = 10) }, - indicator = "transition_date", + indicator = "transition", width = 6.5, - height = ifelse(region == "NewEngland", 4, 2.5) + height = ifelse(region == "NewEngland", 4.25, 2.75) ) # Monthly Chlorophyll Plot save_plot( plot_expression = { - ecodata::plot_chl_pp( - report = region, - plottype = "monthly", - n = 30 - ) + if (region == "MidAtlantic") { + ecodata::plot_chl_pp( + report = region, + plottype = "monthly", + EPU = "MAB", + n = 30 + ) + } else { + gb <- ecodata::plot_chl_pp( + report = region, + plottype = "monthly", + EPU = "GB", + n = 30 + ) + gom <- ecodata::plot_chl_pp( + report = region, + plottype = "monthly", + EPU = "GOM", + n = 30 + ) + ggpubr::ggarrange( + gb, + gom, + ncol = 1, + common.legend = TRUE, + legend = "bottom" + ) + } }, - indicator = "monthly_chl", + indicator = "chl-month", width = 6.5, - height = ifelse(region == "NewEngland", 7, 3.5) + height = ifelse(region == "NewEngland", 7.25, 3.75) ) ### Risks to setting catch limits ---- @@ -876,9 +899,9 @@ create_plots_mab_and_ne <- function(region) { ) } }, - indicator = "productivity_anomaly", + indicator = "productivity-anomaly", width = 6.5, - height = ifelse(region == "NewEngland", 8.5, 7.5) + height = ifelse(region == "NewEngland", 8.75, 7.75) ) # condition factor @@ -916,21 +939,21 @@ create_plots_mab_and_ne <- function(region) { ) } }, - indicator = "condition", + indicator = ifelse(region == "NewEngland", "ne-cf", "mab-cf"), width = 6.5, - height = ifelse(region == "NewEngland", 7, 6) + height = ifelse(region == "NewEngland", 7.25, 6.25) ) - # 5. Energy Density Plot - save_plot( - plot_expression = { - ecodata::plot_energy_density(report = region) + - ggplot2::theme(legend.position = 'bottom') - }, - indicator = "energy_density", - width = 6.5, - height = 4 - ) + # # 5. Energy Density Plot + # save_plot( + # plot_expression = { + # ecodata::plot_energy_density(report = region) + + # ggplot2::theme(legend.position = 'bottom') + # }, + # indicator = "energy-density", + # width = 6.5, + # height = 4 + # ) # 6. Forage Index Plot save_plot( @@ -944,7 +967,7 @@ create_plots_mab_and_ne <- function(region) { }, indicator = "foragebio", width = 6.5, - height = ifelse(region == "NewEngland", 5, 2.5) + height = ifelse(region == "NewEngland", 5.25, 2.75) ) # 7. Benthos Plot @@ -971,7 +994,7 @@ create_plots_mab_and_ne <- function(region) { }, indicator = "benthos", width = 6.5, - height = 5 + height = 5.25 ) # 8. Zooplankton Anomaly Plot @@ -1013,9 +1036,9 @@ create_plots_mab_and_ne <- function(region) { legend = "bottom" ) }, - indicator = "zooplankton_anomaly", + indicator = "zoopanom", width = 6.5, - height = 7.5 + height = 7.75 ) # Advection Index @@ -1024,9 +1047,9 @@ create_plots_mab_and_ne <- function(region) { ecodata::plot_advection(report = region, n = 10, varName = 6) + ggplot2::theme(legend.position = 'bottom') }, - indicator = "advection_index", + indicator = "advection-index", width = 6.5, - height = 3 + height = 3.25 ) # Seasonal OISST Anomaly - MAB ONLY @@ -1035,9 +1058,9 @@ create_plots_mab_and_ne <- function(region) { plot_expression = { ecodata::plot_seasonal_oisst_anom(report = region, n = 10) }, - indicator = "seasonal_oisst_anom", + indicator = "seasonal-oisst-anom", width = 6.5, - height = 4.5 + height = 4.75 ) } @@ -1054,9 +1077,9 @@ create_plots_mab_and_ne <- function(region) { ) + ggplot2::theme(legend.position = 'bottom') }, - indicator = "bottom_temp_anom", + indicator = "bottom-temp-anom", width = 6.5, - height = 4.5 + height = 4.75 ) } @@ -1073,9 +1096,9 @@ create_plots_mab_and_ne <- function(region) { ggplot2::facet_wrap(~EPU, nrow = 2) } }, - indicator = "bottom_temp_insitu", + indicator = "bottom-temp-insitu", width = 6.5, - height = ifelse(region == "NewEngland", 5, 2.5) + height = ifelse(region == "NewEngland", 5.25, 2.75) ) # Other ocean uses: offshore wind ---- @@ -1097,8 +1120,8 @@ create_plots_mab_and_ne <- function(region) { ggplot2::ggtitle("New England: Fishery Revenue in Active Projects") } }, - indicator = "wind_revenue", + indicator = "wea-spp-rev", width = 6.5, - height = 2.5 + height = 2.75 ) } diff --git a/scripts/create_plots_ne_only.R b/scripts/create_plots_ne_only.R index dd9a0fab..40875d9b 100644 --- a/scripts/create_plots_ne_only.R +++ b/scripts/create_plots_ne_only.R @@ -78,6 +78,21 @@ create_plots_ne <- function(region = "NewEngland") } } + #NE only - rec_hms from LPS only, no MRIP + save_plot( + plot_expression = { + rec_lps_sharks_plot <- ecodata::plot_lps_sharks( + report = region, + n = 10 + ) + + ggplot2::ggtitle(paste(region2, "Large Pelagics Survey Rec. Shark Landings")) + + ggplot2::theme(legend.background = ggplot2::element_rect(fill = "white")) + }, + indicator = "rec-hms", + width = 6.5, + height = 3.25 + ) + # calfin center of gravity -- NE only save_plot( plot_expression = { @@ -89,9 +104,9 @@ create_plots_ne <- function(region = "NewEngland") )+ ggplot2::theme(legend.position = 'bottom') }, - indicator = "calfin_cog", + indicator = "calfin-cog", width = 6.5, - height = 4 + height = 4.25 ) # mass inshore survey -- NE only @@ -101,9 +116,9 @@ create_plots_ne <- function(region = "NewEngland") ggplot2::geom_point()+ ggplot2::geom_line() }, - indicator = "mass_inshore", + indicator = "mass-biomass", width = 6, - height = 6 + height = 6.25 ) # seabird productivity -- NE only @@ -113,9 +128,9 @@ create_plots_ne <- function(region = "NewEngland") ecodata::plot_seabird_ne(varName = "productivity", n = 10) + ggplot2::coord_cartesian(xlim = c(1991, 2025)) }, - indicator = "seabird_productivity", + indicator = "seabird-ne-productivity", width = 6.5, - height = 2.5 + height = 2.75 ) } @@ -130,24 +145,7 @@ create_plots_ne <- function(region = "NewEngland") }, indicator = "salmon", width = 6.5, - height = 4 + height = 4.25 ) } - - #NE only - rec_hms from LPS only, no MRIP - save_plot( - plot_expression = { - rec_lps_sharks_plot <- ecodata::plot_lps_sharks( - report = region, - n = 10 - ) + - ggplot2::ggtitle(paste(region2, "Large Pelagics Survey Rec. Shark Landings")) + - ggplot2::theme(legend.background = ggplot2::element_rect(fill = "white")) - }, - indicator = "rec_hms_NE", - width = 6.5, - height = 4.5 - ) - } -# create_plots_ne(region = "NewEngland") \ No newline at end of file diff --git a/scripts/create_plots_slides_both_reports.R b/scripts/create_plots_slides_both_reports.R index 2954cf93..311dc6bf 100644 --- a/scripts/create_plots_slides_both_reports.R +++ b/scripts/create_plots_slides_both_reports.R @@ -77,21 +77,21 @@ create_plots_slides_both <- function(region = "BothReports") { plot_expression = { plt <- ecodata::plot_thermal_habitat_gridded(region) }, - indicator = "therm_hab_persist", + indicator = "therm-hab-persist-2024", width = 6.5, - height = 4 + height = 4.25 ) - # 5. Energy Density Plot - save_plot( - plot_expression = { - # plot is the same even though it takes a region parameter - ecodata::plot_energy_density(report = "NewEngland") - }, - indicator = "energy_density", - width = 6.5, - height = 4 - ) + # # 5. Energy Density Plot + # save_plot( + # plot_expression = { + # # plot is the same even though it takes a region parameter + # ecodata::plot_energy_density(report = "NewEngland") + # }, + # indicator = "energy-density", + # width = 6.5, + # height = 4 + # ) # GOM ocean acidification GOMoa_image <- "https://github.com/NOAA-EDAB/ecodata/raw/dev/data-raw/workshop/images/Hunt_WBD_2024_pCO2_OMa_Weekly_Climatology-ChrisH_2025.pdf" @@ -111,7 +111,7 @@ create_plots_slides_both <- function(region = "BothReports") { }, indicator = "harborporpoise", width = 6.5, - height = 3 + height = 3.25 ) # gray seal @@ -121,7 +121,7 @@ create_plots_slides_both <- function(region = "BothReports") { }, indicator = "grayseal", width = 6.5, - height = 3 + height = 3.25 ) # narw-abundance @@ -131,9 +131,9 @@ create_plots_slides_both <- function(region = "BothReports") { ggplot2::ggtitle("North Atlantic right whale abundance") + ggplot2::scale_x_continuous(limits = c(1980, 2025)) }, - indicator = "narw_abundance", + indicator = "narw-abundance", width = 6.5, - height = 2.5 + height = 2.75 ) # narw calves @@ -142,9 +142,9 @@ create_plots_slides_both <- function(region = "BothReports") { ecodata::plot_narw(varName = "calf", n = 10) + ggplot2::ggtitle("North Atlantic right whale calf abundance") }, - indicator = "narw_calves", + indicator = "NARW-calf-abundance", width = 6.5, - height = 2.5 + height = 2.75 ) # seals @@ -154,9 +154,9 @@ create_plots_slides_both <- function(region = "BothReports") { ecodata::plot_seal_pups(report = "NewEngland") + ggplot2::theme(legend.position = 'bottom') }, - indicator = "seal_pups", + indicator = "seals", width = 6.5, - height = 4 + height = 4.25 ) # species dist @@ -166,9 +166,9 @@ create_plots_slides_both <- function(region = "BothReports") { b <- ecodata::plot_species_dist(varName = "depth", n = 10) ggpubr::ggarrange(a, b, ncol = 1) }, - indicator = "species_dist", + indicator = "species-dist", width = 6.5, - height = 3.5 + height = 3.75 ) # whale and dolphin dist shifts @@ -179,9 +179,9 @@ create_plots_slides_both <- function(region = "BothReports") { ggplot2::facet_wrap(~season, nrow = 1) + ggplot2::theme(legend.position = "bottom") }, - indicator = "cetacean_dist", + indicator = "protectedspp-dist-shifts", width = 7.5, - height = 4 + height = 4.25 ) # forage shifts @@ -189,9 +189,9 @@ create_plots_slides_both <- function(region = "BothReports") { plot_expression = { ecodata::plot_forage_index(varName = "cog", n = 10) }, - indicator = "forage_dist", + indicator = "forageshifts", width = 6.5, - height = 3.5 + height = 3.75 ) # longterm sst @@ -199,9 +199,9 @@ create_plots_slides_both <- function(region = "BothReports") { plot_expression = { ecodata::plot_long_term_sst(n = 10) }, - indicator = "long_term_sst", + indicator = "long-term-sst", width = 6.5, - height = 2.5 + height = 2.75 ) # gsi @@ -209,9 +209,9 @@ create_plots_slides_both <- function(region = "BothReports") { plot_expression = { ecodata::plot_gsi(varName = "westgsi", n = 10) }, - indicator = "west_gsi", + indicator = "GSI", width = 6.5, - height = 2.5 + height = 2.75 ) # cold pool size @@ -221,9 +221,9 @@ create_plots_slides_both <- function(region = "BothReports") { b <- ecodata::plot_cold_pool(varName = "extent", n = 10) ggpubr::ggarrange(a, b, nrow = 2) }, - indicator = "cold_pool", + indicator = "cold-pool-size", width = 6.5, - height = 5 + height = 5.25 ) # cold pool timing @@ -231,9 +231,9 @@ create_plots_slides_both <- function(region = "BothReports") { plot_expression = { ecodata::plot_cold_pool(varName = "persistence", n = 10) }, - indicator = "cold_pool_time", + indicator = "cold-pool-time", width = 6.5, - height = 2.5 + height = 2.75 ) # spawn timing @@ -241,9 +241,9 @@ create_plots_slides_both <- function(region = "BothReports") { plot_expression = { ecodata::plot_spawn_timing(n = 10) }, - indicator = "spawn_timing", + indicator = "spawntiming", width = 6.5, - height = 4 + height = 4.25 ) @@ -253,9 +253,9 @@ create_plots_slides_both <- function(region = "BothReports") { ecodata::plot_wind_dev_speed() + ggplot2::theme(legend.position = 'bottom') }, - indicator = "wind_dev_speed", + indicator = "wind-proposed-dev", width = 6.5, - height = 4 + height = 4.25 ) # slopewater @@ -266,7 +266,7 @@ create_plots_slides_both <- function(region = "BothReports") { }, indicator = "slopewater", width = 6, - height = 4 + height = 4.25 ) # small cope center of gravity @@ -280,9 +280,9 @@ create_plots_slides_both <- function(region = "BothReports") { ggplot2::ggtitle("Northeast U.S. Small Copepod Distribution") + ggplot2::ylab("Center of Gravity, km") }, - indicator = "smallcopeall_cog", + indicator = "smallcopeall-cog", width = 6.5, - height = 3.5 + height = 3.75 ) # large cope center of gravity @@ -296,9 +296,9 @@ create_plots_slides_both <- function(region = "BothReports") { ggplot2::ggtitle("Northeast U.S. Large Copepod Distribution") + ggplot2::ylab("Center of Gravity, km") }, - indicator = "lgcopeall_cog", + indicator = "lgcopeall-cog", width = 6.5, - height = 3.5 + height = 3.75 ) # macrobenthos shifts @@ -318,9 +318,9 @@ create_plots_slides_both <- function(region = "BothReports") { scales = "free_y" ) }, - indicator = "macrobenthos_dist", + indicator = "macrobenthosshifts", width = 6.5, - height = 3.5 + height = 3.75 ) # megabenthos shifts @@ -339,9 +339,9 @@ create_plots_slides_both <- function(region = "BothReports") { scales = "free_y") + ggplot2::theme(legend.position = 'bottom') }, - indicator = "megabenthos_dist", + indicator = "megabenthosshifts", width = 6.5, - height = 3.5 + height = 3.75 ) # euphausiid center of gravity @@ -362,9 +362,9 @@ create_plots_slides_both <- function(region = "BothReports") { scales = "free_y" ) }, - indicator = "euph_cog", + indicator = "euph-cog", width = 6.5, - height = 3.5 + height = 3.75 ) } \ No newline at end of file diff --git a/scripts/create_plots_slides_mab_ne.R b/scripts/create_plots_slides_mab_ne.R index 33d4f5d8..e83ce625 100644 --- a/scripts/create_plots_slides_mab_ne.R +++ b/scripts/create_plots_slides_mab_ne.R @@ -47,9 +47,9 @@ create_plots_slides_mab_and_ne <- function(region) { ggplot2::facet_wrap(~EPU, nrow = 2) } }, - indicator = "total_landings", + indicator = "total-landings", width = 6.5, - height = ifelse(region == "NewEngland", 5, 4), + height = ifelse(region == "NewEngland", 5.25, 4.25), ) # commercial landings @@ -63,9 +63,9 @@ create_plots_slides_mab_and_ne <- function(region) { ggplot2::geom_point(size = 0.05) + ggplot2::geom_line(size = 0.05) }, - indicator = "commercial_landings", + indicator = "comm-landings", width = 6.5, - height = ifelse(region == "NewEngland", 6, 5) + height = ifelse(region == "NewEngland", 6.25, 5.25) ) # climate vulnerability landings @@ -79,9 +79,9 @@ create_plots_slides_mab_and_ne <- function(region) { ggplot2::ylab("Total Vulnerability \n (Regional Landings)") + ggplot2::theme(legend.position = 'bottom') }, - indicator = "climatevul_land", + indicator = "climatevul-land", width = 6.5, - height = 2.5 + height = 2.75 ) # rec landings @@ -93,9 +93,9 @@ create_plots_slides_mab_and_ne <- function(region) { n = 10 ) }, - indicator = "rec_landings", + indicator = "rec-landings", width = 6.5, - height = 2 + height = 2.25 ) # rec hms and sharks - MAB ONLY @@ -134,9 +134,9 @@ create_plots_slides_mab_and_ne <- function(region) { rec_lps_sharks_plot } }, - indicator = "rec_hms", + indicator = "rec-hms", width = 6.5, - height = ifelse(region == 'MidAtlantic', 5, 2) + height = ifelse(region == 'MidAtlantic', 5.25, 2.25) ) ### Implications ---- @@ -154,9 +154,9 @@ create_plots_slides_mab_and_ne <- function(region) { p } }, - indicator = "stock_status", + indicator = "stock-status", width = 6.5, - height = ifelse(region == "NewEngland", 6, 5) + height = ifelse(region == "NewEngland", 6.25, 5.25) ) # 2. ABC/ACL Stacked Plot @@ -167,9 +167,9 @@ create_plots_slides_mab_and_ne <- function(region) { plottype = "Stacked" ) }, - indicator = "abcacl_stacked", + indicator = "abcacl-stacked", width = 6.5, - height = 4 + height = 4.25 ) # 3. ABC/ACL Catch Plot @@ -180,9 +180,9 @@ create_plots_slides_mab_and_ne <- function(region) { plottype = "Catch" ) }, - indicator = "abcacl_catch", + indicator = "abcacl-catch", width = 6.5, - height = 2.5 + height = 2.75 ) # Aggregate biomass @@ -207,9 +207,9 @@ create_plots_slides_mab_and_ne <- function(region) { ) ) }, - indicator = "aggregate_biomass_mab", + indicator = "nefsc-biomass-mab", width = 6.5, - height = 7 + height = 7.25 ) } @@ -224,9 +224,9 @@ create_plots_slides_mab_and_ne <- function(region) { ) + ggplot2::theme(panel.spacing = grid::unit(0, 'lines')) }, - indicator = "aggregate_biomass_gb", + indicator = "nefsc-biomass-gb", width = 6, - height = 7 + height = 7.25 ) # gulf of maine save_plot( @@ -237,9 +237,9 @@ create_plots_slides_mab_and_ne <- function(region) { n = 10 ) }, - indicator = "aggregate_biomass_gom", + indicator = "nefsc-biomass-gom", width = 6, - height = 7 + height = 7.25 ) } @@ -281,9 +281,9 @@ create_plots_slides_mab_and_ne <- function(region) { ggpubr::ggarrange(gb, gom, nrow = 2) } }, - indicator = "comdat_profit", + indicator = "comdat-profit", width = 6.5, - height = ifelse(region == "NewEngland", 5.5, 4) + height = ifelse(region == "NewEngland", 5.75, 4.25) ) ## Commercial profits ---- @@ -312,9 +312,9 @@ create_plots_slides_mab_and_ne <- function(region) { ggplot2::facet_wrap(~EPU, nrow = 2) } }, - indicator = "comm_revenue", + indicator = "comm-revenue", width = 6.5, - height = ifelse(region == "NewEngland", 4.5, 4.5) + height = ifelse(region == "NewEngland", 4.75, 4.75) ) # bennet @@ -360,7 +360,7 @@ create_plots_slides_mab_and_ne <- function(region) { }, indicator = "bennet", width = 6.5, - height = ifelse(region == "NewEngland", 8, 6) + height = ifelse(region == "NewEngland", 8.25, 6.25) ) # bennet all @@ -402,9 +402,9 @@ create_plots_slides_mab_and_ne <- function(region) { ) } }, - indicator = "bennet_all", + indicator = "bennet-all", width = 9, - height = ifelse(region == "NewEngland", 6.5, 9) + height = ifelse(region == "NewEngland", 6.75, 9.25) ) # 4. Climate Vulnerability Revenue Plot @@ -418,53 +418,11 @@ create_plots_slides_mab_and_ne <- function(region) { ggplot2::theme(legend.position = "bottom") + ggplot2::ylab("Total Vulnerability \n (Regional Revenue)") }, - indicator = "climatevul_rev", + indicator = "climatevul-rev", width = 6.5, - height = 2.5 + height = 2.75 ) - # Geret's profitability indices (comdat profit) (EPU = MAB) - save_plot( - plot_expression = { - if (region == "MidAtlantic") { - ecodata::plot_comdat_profit( - report = region, - n = 23 - ) + - ggplot2::scale_color_discrete( - limits = c("cost_index", "profit_index", "revenue_index"), - labels = c("Cost Index", "Profit Index", "Revenue Index") - ) + - ggplot2::theme(legend.position = "bottom") - } else { - gb <- ecodata::plot_comdat_profit( - report = region, - EPU = "GB", - n = 23 - ) + - ggplot2::scale_color_discrete( - limits = c("cost_index", "profit_index", "revenue_index"), - labels = c("Cost Index", "Profit Index", "Revenue Index") - ) + - ggplot2::theme(legend.position = "none") - - gom <- ecodata::plot_comdat_profit( - report = region, - EPU = "GOM", - n = 23 - ) + - ggplot2::scale_color_discrete( - limits = c("cost_index", "profit_index", "revenue_index"), - labels = c("Cost Index", "Profit Index", "Revenue Index") - ) + - ggplot2::theme(legend.position = "bottom") - ggpubr::ggarrange(gb, gom, nrow = 2) - } - }, - indicator = "comdat_profit", - width = 6.5, - height = ifelse(region == "NewEngland", 8, 4.5) - ) ## Recreational opportunities ---- @@ -479,9 +437,9 @@ create_plots_slides_mab_and_ne <- function(region) { n = 10 ) }, - indicator = "rec_op", + indicator = "rec-op", width = 6.5, - height = 2.5 + height = 2.75 ) # 2. Recreational Diversity Plot @@ -499,9 +457,9 @@ create_plots_slides_mab_and_ne <- function(region) { ggplot2::ylab('Effective Shannon Index') } }, - indicator = "rec_div", + indicator = "rec-div", width = 6.5, - height = 2.5 + height = 2.75 ) ## Stability ---- @@ -540,9 +498,9 @@ create_plots_slides_mab_and_ne <- function(region) { ggpubr::ggarrange(a, b, nrow = 2) } }, - indicator = "comm_div_fleet", + indicator = "comm-div-fleet", width = 6.5, - height = 4 + height = 4.25 ) # 2. Commercial Diversity Species Diversity Plot @@ -559,9 +517,9 @@ create_plots_slides_mab_and_ne <- function(region) { plt + ggplot2::ylab('Effective Shannon Index') } }, - indicator = "commercial_div_species_div", + indicator = "commercial-div-species-div", width = 6.5, - height = 2.5 + height = 2.75 ) # 3. Recreational Diversity Catch Plot @@ -569,9 +527,9 @@ create_plots_slides_mab_and_ne <- function(region) { plot_expression = { ecodata::plot_recdat(report = region, varName = "catchdiversity", n = 10) }, - indicator = "recdat_div_catch", + indicator = "recdat-div-catch", width = 6.5, - height = 2.5 + height = 2.75 ) # total primary production @@ -616,7 +574,7 @@ create_plots_slides_mab_and_ne <- function(region) { }, indicator = "totpp", width = 6.5, - height = ifelse(region == "NewEngland", 4, 2.5) + height = ifelse(region == "NewEngland", 4.25, 2.75) ) # 4. Zooplankton Diversity Plot @@ -634,9 +592,9 @@ create_plots_slides_mab_and_ne <- function(region) { ggplot2::facet_wrap(~EPU, nrow = 1, scales = "free_y") } }, - indicator = "zoo_diversity", + indicator = "zoo-diversity", width = 6.5, - height = ifelse(region == "NewEngland", 4, 2.5) + height = ifelse(region == "NewEngland", 4.25, 2.75) ) # 5. Expected N Plot @@ -672,9 +630,9 @@ create_plots_slides_mab_and_ne <- function(region) { ggplot2::facet_wrap(~EPU, nrow = 2) } }, - indicator = "exp_n", + indicator = "exp-n", width = 6.5, - height = ifelse(region == "NewEngland", 3.5, 4) + height = ifelse(region == "NewEngland", 3.75, 4.25) ) #zooplankton community PCA @@ -691,9 +649,9 @@ create_plots_slides_mab_and_ne <- function(region) { ggplot2::facet_wrap(~EPU, nrow = 2) } }, - indicator = "zoo_community", + indicator = "zoo-community", width = 6.5, - height = ifelse(region == "NewEngland", 5, 3.5) + height = ifelse(region == "NewEngland", 5.25, 3.75) ) # finfish traits -- original for pdfs @@ -719,7 +677,7 @@ create_plots_slides_mab_and_ne <- function(region) { }, indicator = "traits", width = 6.5, - height = ifelse(region == "NewEngland", 3.5, 4) + height = ifelse(region == "NewEngland", 3.75, 4.25) ) #finfish traits - growth rate @@ -736,9 +694,9 @@ create_plots_slides_mab_and_ne <- function(region) { ggplot2::facet_wrap(~EPU, nrow = 2) } }, - indicator = "traits_k", + indicator = "traits-k", width = 6.5, - height = ifelse(region == "NewEngland", 4.5, 4) + height = ifelse(region == "NewEngland", 4.75, 4.25) ) # finfish traits -- trophic level @@ -763,9 +721,9 @@ create_plots_slides_mab_and_ne <- function(region) { ggplot2::facet_wrap(~EPU, nrow = 2) } }, - indicator = "traits_tl", + indicator = "traits-tl", width = 6.5, - height = ifelse(region == "NewEngland", 4.5, 4) + height = ifelse(region == "NewEngland", 4.75, 4.25) ) ## Community social and climate vulnerability ---- @@ -782,9 +740,9 @@ create_plots_slides_mab_and_ne <- function(region) { legend.title = ggplot2::element_blank() ) }, - indicator = "commercial_engagement", + indicator = "commercial-engagement", width = 7, - height = 5 + height = 5.25 ) # 2. Recreational Engagement Plot @@ -796,9 +754,9 @@ create_plots_slides_mab_and_ne <- function(region) { ) + ggplot2::theme(plot.title = ggplot2::element_text(vjust = 0)) }, - indicator = "recreational_engagement", + indicator = "recreational-engagement", width = 6.5, - height = 3.5 + height = 3.75 ) # 3. Community Climate Vulnerability Exposure Plot @@ -812,7 +770,7 @@ create_plots_slides_mab_and_ne <- function(region) { }, indicator = "commvulex", width = 6.5, - height = 4 + height = 4.25 ) ### Risks to managing seasonally ---- @@ -822,23 +780,46 @@ create_plots_slides_mab_and_ne <- function(region) { plot_expression = { ecodata::plot_trans_dates(report = region, varName = "length", n = 10) }, - indicator = "transition_date", + indicator = "transition", width = 6.5, - height = ifelse(region == "NewEngland", 5, 2.5) + height = ifelse(region == "NewEngland", 5.25, 2.75) ) # Monthly Chlorophyll Plot save_plot( plot_expression = { - ecodata::plot_chl_pp( - report = region, - plottype = "monthly", - n = 30 - ) + if (region == "MidAtlantic") { + ecodata::plot_chl_pp( + report = region, + plottype = "monthly", + EPU = "MAB", + n = 30 + ) + } else { + gb <- ecodata::plot_chl_pp( + report = region, + plottype = "monthly", + EPU = "GB", + n = 30 + ) + gom <- ecodata::plot_chl_pp( + report = region, + plottype = "monthly", + EPU = "GOM", + n = 30 + ) + ggpubr::ggarrange( + gb, + gom, + ncol = 1, + common.legend = TRUE, + legend = "bottom" + ) + } }, - indicator = "monthly_chl", + indicator = "chl-month", width = 6.5, - height = ifelse(region == "NewEngland", 5.5, 4) + height = ifelse(region == "NewEngland", 5.75, 4.25) ) ### Risks to setting catch limits ---- @@ -880,9 +861,9 @@ create_plots_slides_mab_and_ne <- function(region) { ) } }, - indicator = "productivity_anomaly", + indicator = "productivity-anomaly", width = 6.5, - height = ifelse(region == "NewEngland", 9.5, 8.5) + height = ifelse(region == "NewEngland", 9.75, 8.75) ) # condition factor @@ -920,23 +901,23 @@ create_plots_slides_mab_and_ne <- function(region) { ) } }, - indicator = "condition", + indicator = ifelse(region == "NewEngland", "ne-cf", "mab-cf"), width = ifelse(region == "NewEngland", 13, 6.5), # width = 6.5, - height = 7 + height = 7.25 # height = ifelse(region == "NewEngland", 7, 6) ) - # 5. Energy Density Plot - save_plot( - plot_expression = { - ecodata::plot_energy_density(report = region) + - ggplot2::theme(legend.position = 'bottom') - }, - indicator = "energy_density", - width = 6.5, - height = 4 - ) + # # 5. Energy Density Plot + # save_plot( + # plot_expression = { + # ecodata::plot_energy_density(report = region) + + # ggplot2::theme(legend.position = 'bottom') + # }, + # indicator = "energy-density", + # width = 6.5, + # height = 4 + # ) # 6. Forage Index Plot save_plot( @@ -950,7 +931,7 @@ create_plots_slides_mab_and_ne <- function(region) { }, indicator = "foragebio", width = 6.5, - height = ifelse(region == "NewEngland", 5, 2.5) + height = ifelse(region == "NewEngland", 5.25, 2.75) ) # 7. Benthos Plot @@ -977,7 +958,7 @@ create_plots_slides_mab_and_ne <- function(region) { }, indicator = "benthos", width = 6.5, - height = ifelse(region == "NewEngland", 8, 6) + height = ifelse(region == "NewEngland", 8.25, 6.25) ) # 8. Zooplankton Anomaly Plot @@ -1019,9 +1000,9 @@ create_plots_slides_mab_and_ne <- function(region) { legend = "bottom" ) }, - indicator = "zooplankton_anomaly", + indicator = "zoopanom", width = 6.5, - height = 7.5 + height = 7.75 ) # Advection Index @@ -1030,9 +1011,9 @@ create_plots_slides_mab_and_ne <- function(region) { ecodata::plot_advection(report = region, n = 10, varName = 6) + ggplot2::theme(legend.position = 'bottom') }, - indicator = "advection_index", + indicator = "advection-index", width = 6.5, - height = 3 + height = 3.25 ) # Seasonal OISST Anomaly - MAB ONLY @@ -1041,9 +1022,9 @@ create_plots_slides_mab_and_ne <- function(region) { plot_expression = { ecodata::plot_seasonal_oisst_anom(report = region, n = 10) }, - indicator = "seasonal_oisst_anom", + indicator = "seasonal-oisst-anom", width = 6.5, - height = 4.5 + height = 4.75 ) } @@ -1060,9 +1041,9 @@ create_plots_slides_mab_and_ne <- function(region) { ) + ggplot2::theme(legend.position = 'bottom') }, - indicator = "bottom_temp_anom", + indicator = "bottom-temp-anom", width = 6.5, - height = 4.5 + height = 4.75 ) } @@ -1079,9 +1060,9 @@ create_plots_slides_mab_and_ne <- function(region) { ggplot2::facet_wrap(~EPU, nrow = 2) } }, - indicator = "bottom_temp_insitu", + indicator = "bottom-temp-insitu", width = 6.5, - height = ifelse(region == "NewEngland", 5, 2.5) + height = ifelse(region == "NewEngland", 5.25, 2.75) ) # Other ocean uses: offshore wind ---- @@ -1102,8 +1083,8 @@ create_plots_slides_mab_and_ne <- function(region) { ggplot2::ggtitle("New England: Fishery Revenue in Active Projects") } }, - indicator = "wind_revenue", + indicator = "wea-spp-rev", width = 6.5, - height = 4 + height = 4.25 ) } diff --git a/scripts/create_plots_slides_ne_only.R b/scripts/create_plots_slides_ne_only.R index c9229562..27ca6bdf 100644 --- a/scripts/create_plots_slides_ne_only.R +++ b/scripts/create_plots_slides_ne_only.R @@ -89,9 +89,9 @@ create_plots_slides_ne <- function(region = "NewEngland") ggplot2::ggtitle(paste(region2, "Large Pelagics Survey Rec. Shark Landings")) + ggplot2::theme(legend.background = ggplot2::element_rect(fill = "white")) }, - indicator = "rec_hms", + indicator = "rec-hms", width = 6.5, - height = 3 + height = 3.25 ) # calfin center of gravity -- NE only @@ -105,9 +105,9 @@ create_plots_slides_ne <- function(region = "NewEngland") )+ ggplot2::theme(legend.position = 'bottom') }, - indicator = "calfin_cog", + indicator = "calfin-cog", width = 6.5, - height = 4 + height = 4.25 ) # mass inshore survey -- NE only @@ -117,9 +117,9 @@ create_plots_slides_ne <- function(region = "NewEngland") ggplot2::geom_point() + ggplot2::geom_line() }, - indicator = "mass_inshore", + indicator = "mass-biomass", width = 6, - height = 6 + height = 6.25 ) # seabird productivity -- NE only @@ -129,9 +129,9 @@ create_plots_slides_ne <- function(region = "NewEngland") ecodata::plot_seabird_ne(varName = "productivity", n = 10) + ggplot2::coord_cartesian(xlim = c(1991, 2025)) }, - indicator = "seabird_productivity", + indicator = "seabird-ne-productivity", width = 6.5, - height = 2.5 + height = 2.75 ) } @@ -146,7 +146,7 @@ create_plots_slides_ne <- function(region = "NewEngland") }, indicator = "salmon", width = 6.5, - height = 4 + height = 4.25 ) } } \ No newline at end of file diff --git a/utils/figure_captions_summary.csv b/utils/figure_captions_summary.csv index 620dc1c1..70ae55a6 100644 --- a/utils/figure_captions_summary.csv +++ b/utils/figure_captions_summary.csv @@ -1,88 +1,88 @@ chunkName,ecodata_object,plain.language.figure.description,fig_cap_ne,fig_cap_ma,fig_cap_both,fig_path_ne,fig_path_ma,fig_path_both,slide_fig_path_ma,slide_fig_path_ne,slide_fig_path_both,alt_text_ma,alt_text_ne,alt_text_both -abcacl-catch,abc_acl,dot plot showing catch per ABC or ACL by year,NA,Total catch divided by ABC/ACL for Mid-Atlantic Fishery Management Council managed fisheries. High points are recreational black sea bass (2021) and scup (2022). Red line indicates the median ratio across all fisheries.,NA,NA,images\MidAtlantic\abcacl_catch_MidAtlantic,NA,images\MidAtlantic\slide_abcacl_catch_MidAtlantic,NA,NA,NA,NA,NA -abcacl-stacked,abc_acl,"bar plot showing ABC or ACL, colored by species",NA,Sum of catch limits (in metric tons) across all Mid-Atlantic Fishery Management Council managed commercial (C) and recreational (R) fsheries.,NA,NA,images\MidAtlantic\abcacl_stacked_MidAtlantic,NA,images\MidAtlantic\slide_abcacl_stacked_MidAtlantic,NA,NA,NA,NA,NA +abcacl-catch,abc_acl,dot plot showing catch per ABC or ACL by year,NA,Total catch divided by ABC/ACL for Mid-Atlantic Fishery Management Council managed fisheries. High points are recreational black sea bass (2021) and scup (2022). Red line indicates the median ratio across all fisheries.,NA,NA,images\MidAtlantic\abcacl-catch_MidAtlantic,NA,images\MidAtlantic\slide_abcacl-catch_MidAtlantic,NA,NA,NA,NA,NA +abcacl-stacked,abc_acl,"bar plot showing ABC or ACL, colored by species",NA,Sum of catch limits (in metric tons) across all Mid-Atlantic Fishery Management Council managed commercial (C) and recreational (R) fsheries.,NA,NA,images\MidAtlantic\abcacl-stacked_MidAtlantic,NA,images\MidAtlantic\slide_abcacl-stacked_MidAtlantic,NA,NA,NA,NA,NA bennet,bennet,bar plot colored by price and volume,"Revenue change from 1982 values in 2024 dollars (black); Price (blue), and Volume Indicators (green) for total commercial landings in Georges Bank (GB: top) and the Gulf of Maine (GOM: bottom).","Revenue change from 1982 values in 2024 dollars (black); Price (blue), and Volume Indicators (green) for total commercial landings in the Mid-Atlantic Bight.",NA,images\NewEngland\bennet_NewEngland,images\MidAtlantic\bennet_MidAtlantic,NA,images\MidAtlantic\slide_bennet_MidAtlantic,images\NewEngland\slide_bennet_NewEngland,NA,NA,NA,NA -bennet-all,bennet,bar plot colored by guild,"Total price and volume indicators in 2024 dollars (black) for commercial landings, and individual guild contributions to each indicator from Georges Bank (GB: top panels) and the Gulf of Maine (GOM: bottom panels).","Total price (top) and volume (bottom) indicators in 2024 dollars (black) for commercial landings, and individual guild contributions to each indicator, in the Mid-Atlantic Bight.",NA,images\NewEngland\bennet_all_NewEngland,images\MidAtlantic\bennet_all_MidAtlantic,NA,images\MidAtlantic\slide_bennet_all_MidAtlantic,images\NewEngland\slide_bennet_all_NewEngland,NA,NA,NA,NA +bennet-all,bennet,bar plot colored by guild,"Total price and volume indicators in 2024 dollars (black) for commercial landings, and individual guild contributions to each indicator from Georges Bank (GB: top panels) and the Gulf of Maine (GOM: bottom panels).","Total price (top) and volume (bottom) indicators in 2024 dollars (black) for commercial landings, and individual guild contributions to each indicator, in the Mid-Atlantic Bight.",NA,images\NewEngland\bennet-all_NewEngland,images\MidAtlantic\bennet-all_MidAtlantic,NA,images\MidAtlantic\slide_bennet-all_MidAtlantic,images\NewEngland\slide_bennet-all_NewEngland,NA,NA,NA,NA benthos,bethos_index,line plot colored by season and faceted by macro/megabenthos,"Changes in spring (blue) and fall (red) benthos abundance in New England for megabenthos (top) and macrobenthos (bottom), with significant long-term increasing (orange), short-term increasing (dark orange), and long-term decreasing (purple) trends. ","Changes in spring (blue) and fall (red) benthos abundance in the Mid-Atlantic Bight for megabenthos (top) and macrobenthos (bottom), with significant long-term increasing trend (orange) for megabenthos and long-term decreasing trend (purple) for macrobenthos in spring.",NA,images\NewEngland\benthos_NewEngland,images\MidAtlantic\benthos_MidAtlantic,NA,images\MidAtlantic\slide_benthos_MidAtlantic,images\NewEngland\slide_benthos_NewEngland,NA,NA,NA,NA -calfin-cog,zooplankton_index,faceted line plot of eastward and northward Calanus center of gravity,Eastward (top) and northward (bottom) shifts in the center of gravity for \textit{Calanus finmarchicus} on the Northeast U.S. Shelf in fall (left) and spring (right). ,NA,NA,images\NewEngland\calfin_cog_NewEngland,NA,NA,NA,images\NewEngland\slide_calfin_cog_NewEngland,NA,NA,NA,NA -chl-month,chl_pp,"faceted monthly median chlorophyll, with one facet for each month","Monthly median chlorophyll a concentration time series for Georges Bank (GB, top) and Gulf of Maine (GOM, bottom), with increasing long-term trends (orange). ",Monthly median chlorophyll a concentration in the Mid-Atlantic Bight (black) with a significant long-term increase present in January (orange) and a significant long-term decline in September (purple).,NA,images\NewEngland\monthly_chl_NewEngland,images\MidAtlantic\monthly_chl_MidAtlantic,NA,images\MidAtlantic\slide_monthly_chl_MidAtlantic,images\NewEngland\slide_monthly_chl_NewEngland,NA,NA,NA,NA -climatevul-land,community_climate_vulnerability,"line plot of landings vulnerability, with background stripes of color showing total vulnerability",New England region total vulnerability of commercial landings (sum of New England port landings weighted by species vulnerability scores). Horizontal colored bars show different environmental variability risk levels.,Mid-Atlantic region Total Vulnerability of commercial landings (sum of Mid-Atlantic port landings weighted by species vulnerability scores). Horizontal colored bars show different environmental variability risk levels. ,NA,images\NewEngland\climatevul_land_NewEngland,images\MidAtlantic\climatevul_land_MidAtlantic,NA,images\MidAtlantic\slide_climatevul_land_MidAtlantic,images\NewEngland\slide_climatevul_land_NewEngland,NA,NA,NA,NA -climatevul-rev,community_climate_vulnerability,"line plot of revenue vulnerability, with background stripes of color showing risk level.",New England region total vulnerability of commercial revenue (sum of New England port landings weighted by species vulnerability scores). Horizontal colored bars show different environmental variability risk levels.,Mid-Atlantic region total vulnerability of commercial revenue (sum of Mid-Atlantic port revenue weighted by species vulnerability scores). Horizontal colored bars show different environmental variability risk levels. ,NA,images\NewEngland\climatevul_rev_NewEngland,images\MidAtlantic\climatevul_rev_MidAtlantic,NA,images\MidAtlantic\slide_climatevul_rev_MidAtlantic,images\NewEngland\slide_climatevul_rev_NewEngland,NA,NA,NA,NA +calfin-cog,zooplankton_index,faceted line plot of eastward and northward Calanus center of gravity,Eastward (top) and northward (bottom) shifts in the center of gravity for \textit{Calanus finmarchicus} on the Northeast U.S. Shelf in fall (left) and spring (right). ,NA,NA,images\NewEngland\calfin-cog_NewEngland,NA,NA,NA,images\NewEngland\slide_calfin-cog_NewEngland,NA,NA,NA,NA +chl-month,chl_pp,"faceted monthly median chlorophyll, with one facet for each month","Monthly median chlorophyll a concentration time series for Georges Bank (GB, top) and Gulf of Maine (GOM, bottom), with increasing long-term trends (orange). ",Monthly median chlorophyll a concentration in the Mid-Atlantic Bight (black) with a significant long-term increase present in January (orange) and a significant long-term decline in September (purple).,NA,images\NewEngland\chl-month_NewEngland,images\MidAtlantic\chl-month_MidAtlantic,NA,images\MidAtlantic\slide_chl-month_MidAtlantic,images\NewEngland\slide_chl-month_NewEngland,NA,NA,NA,NA +climatevul-land,community_climate_vulnerability,"line plot of landings vulnerability, with background stripes of color showing total vulnerability",New England region total vulnerability of commercial landings (sum of New England port landings weighted by species vulnerability scores). Horizontal colored bars show different environmental variability risk levels.,Mid-Atlantic region Total Vulnerability of commercial landings (sum of Mid-Atlantic port landings weighted by species vulnerability scores). Horizontal colored bars show different environmental variability risk levels. ,NA,images\NewEngland\climatevul-land_NewEngland,images\MidAtlantic\climatevul-land_MidAtlantic,NA,images\MidAtlantic\slide_climatevul-land_MidAtlantic,images\NewEngland\slide_climatevul-land_NewEngland,NA,NA,NA,NA +climatevul-rev,community_climate_vulnerability,"line plot of revenue vulnerability, with background stripes of color showing risk level.",New England region total vulnerability of commercial revenue (sum of New England port landings weighted by species vulnerability scores). Horizontal colored bars show different environmental variability risk levels.,Mid-Atlantic region total vulnerability of commercial revenue (sum of Mid-Atlantic port revenue weighted by species vulnerability scores). Horizontal colored bars show different environmental variability risk levels. ,NA,images\NewEngland\climatevul-rev_NewEngland,images\MidAtlantic\climatevul-rev_MidAtlantic,NA,images\MidAtlantic\slide_climatevul-rev_MidAtlantic,images\NewEngland\slide_climatevul-rev_NewEngland,NA,NA,NA,NA cocobloom,NA,statellite image of the Northeast Shelf with cocolithophore bloom off of Long Island,NA,NA,"An OLCI Sentinel 3A true color image with enhanced contrast captured on July 2, 2024. Coccolithophores shed their coccolith plates during the later stages of the bloom cycle, which results in the milky turquoise water color (Image credit: NOAA STAR, OCView and Ocean Color Science Team).",NA,NA,images\BothReports\20240702_Long_Island_algae_bloom-cropped_KimHyde-2025.png,,NA,images\BothReports\20240702_Long_Island_algae_bloom-cropped_KimHyde-2025.png,NA,NA,NA -cold-pool-size,cold_pool,faceted line plot showing cold pool index and extent,NA,NA,"Seasonal cold pool mean temperature (top) and spatial extent index (bottom), based on bias-corrected Regional Ocean Modeling System-Northwest Atlantic (ROMS-NWA) (open circles) and GLORYS (closed circles), with long-term declining trends (purple).",NA,NA,images\BothReports\cold_pool_BothReports,,NA,images\BothReports\slide_cold_pool_BothReports,NA,NA,NA -cold-pool-time,cold_pool,line plot showing cold pool persistence index,NA,NA,"The Mid-Atlantic Bight Cold Pool persistence index based on bias-corrected Regional Ocean Modeling System-Northwest Atlantic(open circles) and GLORYS (closed circles), with significant long-term decline (purple).",NA,NA,images\BothReports\cold_pool_time_BothReports,,NA,images\BothReports\slide_cold_pool_time_BothReports,NA,NA,NA -comdat-profit,comdat_profit,"line plot of cost, profit, and revenue indices","Profitability indices for Georges Bank (GB, top) and the Gulf of Maine (GOM, bottom): cost index (red), profit index (green), and revenue index (blue). Dashed lines represent the long-term annual means for each index. Long-term increasing trend (orange) in the GOM associated with revenue index.","Profitability indices for Mid-Atlantic federally managed species: cost index (red), profit index (green), and revenue index (blue). Dashed lines represent the long-term annual means for each index. Long-term declining trend (purple) associated with revenue index.",NA,images\NewEngland\comdat_profit_NewEngland,images\MidAtlantic\comdat_profit_MidAtlantic,NA,images\MidAtlantic\slide_comdat_profit_MidAtlantic,images\NewEngland\slide_comdat_profit_NewEngland,NA,NA,NA,NA -comm-div-fleet,commercial_div,faceted line plot showing fleet count and fleet diversity in revenue,Commercial fleet count in New England with significant long-term decline (purple line).,Commercial fleet count (top) and fleet diversity in revenue (bottom) in the Mid-Atlantic with significant long-term decline in fleet count (purple line).,NA,images\NewEngland\comm_div_fleet_NewEngland,images\MidAtlantic\comm_div_fleet_MidAtlantic,NA,images\MidAtlantic\slide_comm_div_fleet_MidAtlantic,images\NewEngland\slide_comm_div_fleet_NewEngland,NA,NA,NA,NA -commercial-div-species-div,commercial_div,line plot showing permit revenue species diversity,Species revenue diversity (permit-level species effective Shannon index) in New England.,Species revenue diversity (permit-level species effective Shannon index) in the Mid-Atlantic.,NA,images\NewEngland\commercial_div_species_div_NewEngland,images\MidAtlantic\commercial_div_species_div_MidAtlantic,NA,images\MidAtlantic\slide_commercial_div_species_div_MidAtlantic,images\NewEngland\slide_commercial_div_species_div_NewEngland,NA,NA,NA,NA -commercial-engagement,engagement,point plot showing engagement index and relative engagement index for top fishing communities,Port Commercial Fishing Activity Indicator scores over time in the top 10 commercially active fishing ports in New England.,Port Commercial Fishing Activity Indicator scores over time in the top 10 commercially active fishing ports in the Mid-Atlantic.,NA,images\NewEngland\commercial_engagement_NewEngland,images\MidAtlantic\commercial_engagement_MidAtlantic,NA,images\MidAtlantic\slide_commercial_engagement_MidAtlantic,images\NewEngland\slide_commercial_engagement_NewEngland,NA,NA,NA,NA -comm-landings,comdat,faceted plot showing landings by guild,"Total commercial landings (black) and New England Fishery Management Council managed U.S seafood landings (red) by feeding guild for the Gulf of Maine (GOM, right) and Georges Bank (GB, left), with significant long-term declines (purple).","Total commercial landings in the Mid-Atlantic Bight (black) and Mid-Atlantic Fishery Management Council-managed U.S seafood landings (red) by feeding guild, with significant long-term declines (purple) in total planktivore landings and short-term declines (dark purple) in benthos landings.",NA,images\NewEngland\commercial_landings_NewEngland,images\MidAtlantic\commercial_landings_MidAtlantic,NA,images\MidAtlantic\slide_commercial_landings_MidAtlantic,images\NewEngland\slide_commercial_landings_NewEngland,NA,NA,NA,NA -comm-revenue,comdat,line plot showing council-managed and total revenue,"Commercial revenue through 2024 for Georges Bank (top) and the Gulf of Maine (bottom): total (black) and from New England Fishery Management Council managed species (red), with significant long-term increase (orange), and long-term (light purple) and short-term (dark purple) declines. Dashed lines represent the long-term annual mean.",Commercial revenue (2024 USD) through 2024 for the Mid-Atlantic region: total (black) and from Mid-Atlantic Fishery Managment Councli managed species (red). Dashed lines represent the long-term annual mean. A short-term significant decrease is present for total revenue (purple).,NA,images\NewEngland\comm_revenue_NewEngland,images\MidAtlantic\comm_revenue_MidAtlantic,NA,images\MidAtlantic\slide_comm_revenue_MidAtlantic,images\NewEngland\slide_comm_revenue_NewEngland,NA,NA,NA,NA +cold-pool-size,cold_pool,faceted line plot showing cold pool index and extent,NA,NA,"Seasonal cold pool mean temperature (top) and spatial extent index (bottom), based on bias-corrected Regional Ocean Modeling System-Northwest Atlantic (ROMS-NWA) (open circles) and GLORYS (closed circles), with long-term declining trends (purple).",NA,NA,images\BothReports\cold-pool-size_BothReports,,NA,images\BothReports\slide_cold-pool-size_BothReports,NA,NA,NA +cold-pool-time,cold_pool,line plot showing cold pool persistence index,NA,NA,"The Mid-Atlantic Bight Cold Pool persistence index based on bias-corrected Regional Ocean Modeling System-Northwest Atlantic(open circles) and GLORYS (closed circles), with significant long-term decline (purple).",NA,NA,images\BothReports\cold-pool-time_BothReports,,NA,images\BothReports\slide_cold-pool-time_BothReports,NA,NA,NA +comdat-profit,comdat_profit,"line plot of cost, profit, and revenue indices","Profitability indices for Georges Bank (GB, top) and the Gulf of Maine (GOM, bottom): cost index (red), profit index (green), and revenue index (blue). Dashed lines represent the long-term annual means for each index. Long-term increasing trend (orange) in the GOM associated with revenue index.","Profitability indices for Mid-Atlantic federally managed species: cost index (red), profit index (green), and revenue index (blue). Dashed lines represent the long-term annual means for each index. Long-term declining trend (purple) associated with revenue index.",NA,images\NewEngland\comdat-profit_NewEngland,images\MidAtlantic\comdat-profit_MidAtlantic,NA,images\MidAtlantic\slide_comdat-profit_MidAtlantic,images\NewEngland\slide_comdat-profit_NewEngland,NA,NA,NA,NA +comm-div-fleet,commercial_div,faceted line plot showing fleet count and fleet diversity in revenue,Commercial fleet count in New England with significant long-term decline (purple line).,Commercial fleet count (top) and fleet diversity in revenue (bottom) in the Mid-Atlantic with significant long-term decline in fleet count (purple line).,NA,images\NewEngland\comm-div-fleet_NewEngland,images\MidAtlantic\comm-div-fleet_MidAtlantic,NA,images\MidAtlantic\slide_comm-div-fleet_MidAtlantic,images\NewEngland\slide_comm-div-fleet_NewEngland,NA,NA,NA,NA +commercial-div-species-div,commercial_div,line plot showing permit revenue species diversity,Species revenue diversity (permit-level species effective Shannon index) in New England.,Species revenue diversity (permit-level species effective Shannon index) in the Mid-Atlantic.,NA,images\NewEngland\commercial-div-species-div_NewEngland,images\MidAtlantic\commercial-div-species-div_MidAtlantic,NA,images\MidAtlantic\slide_commercial-div-species-div_MidAtlantic,images\NewEngland\slide_commercial-div-species-div_NewEngland,NA,NA,NA,NA +commercial-engagement,engagement,point plot showing engagement index and relative engagement index for top fishing communities,Port Commercial Fishing Activity Indicator scores over time in the top 10 commercially active fishing ports in New England.,Port Commercial Fishing Activity Indicator scores over time in the top 10 commercially active fishing ports in the Mid-Atlantic.,NA,images\NewEngland\commercial-engagement_NewEngland,images\MidAtlantic\commercial-engagement_MidAtlantic,NA,images\MidAtlantic\slide_commercial-engagement_MidAtlantic,images\NewEngland\slide_commercial-engagement_NewEngland,NA,NA,NA,NA +comm-landings,comdat,faceted plot showing landings by guild,"Total commercial landings (black) and New England Fishery Management Council managed U.S seafood landings (red) by feeding guild for the Gulf of Maine (GOM, right) and Georges Bank (GB, left), with significant long-term declines (purple).","Total commercial landings in the Mid-Atlantic Bight (black) and Mid-Atlantic Fishery Management Council-managed U.S seafood landings (red) by feeding guild, with significant long-term declines (purple) in total planktivore landings and short-term declines (dark purple) in benthos landings.",NA,images\NewEngland\comm-landings_NewEngland,images\MidAtlantic\comm-landings_MidAtlantic,NA,images\MidAtlantic\slide_comm-landings_MidAtlantic,images\NewEngland\slide_comm-landings_NewEngland,NA,NA,NA,NA +comm-revenue,comdat,line plot showing council-managed and total revenue,"Commercial revenue through 2024 for Georges Bank (top) and the Gulf of Maine (bottom): total (black) and from New England Fishery Management Council managed species (red), with significant long-term increase (orange), and long-term (light purple) and short-term (dark purple) declines. Dashed lines represent the long-term annual mean.",Commercial revenue (2024 USD) through 2024 for the Mid-Atlantic region: total (black) and from Mid-Atlantic Fishery Managment Councli managed species (red). Dashed lines represent the long-term annual mean. A short-term significant decrease is present for total revenue (purple).,NA,images\NewEngland\comm-revenue_NewEngland,images\MidAtlantic\comm-revenue_MidAtlantic,NA,images\MidAtlantic\slide_comm-revenue_MidAtlantic,images\NewEngland\slide_comm-revenue_NewEngland,NA,NA,NA,NA commvulex,community_climate_vulnerability,"line plot showing proportion of communities with low, moderate, high, and very high environmental variability risk levels.","Proportion of New England communities at each revenue environmental variability risk level over time. Total vulnerability ranges from low (green), moderate (yellow), high (orange), to very high (red).","Proportion of Mid-Atlantic communities at each revenue environmental variability risk level over time. Total vulnerability ranges from low (green), moderate (yellow), high (orange), to very high (red), with a long-term increase (orange) in very high risk communities and long-term declines (purple) in moderate and low risk communities.",NA,images\NewEngland\commvulex_NewEngland,images\MidAtlantic\commvulex_MidAtlantic,NA,images\MidAtlantic\slide_commvulex_MidAtlantic,images\NewEngland\slide_commvulex_NewEngland,NA,NA,NA,NA docformat,NA,,NA,NA,"Document orientation. a) Key to figures: orange line - significant long-term increasing trend (purple for decreasing), dark orange line - significant increasing short-term trend (dark purple for decreasing), dashed line - time-series mean. b)The Northeast Large Marine Ecosystem: Ecological production units (EPUs) defined for the Gulf of Maine (GOM), Georges Bank (GB), and the Mid-Atlantic Bight (MAB).",NA,NA,,,NA,NA,NA,NA,NA -energy-density,energy_density,faceted line plot showing energy density of multiple forage fish,"Energy density (mean and standard deviation) of eight forage species from Northeast Fisheries Science Center bottom trawl surveys by season and year. Symbol size represents abundance (mean kg/tow) estimated from bottom trawl survey tows in Georges Bank (GB, top) and the GOM (bottom). ",Energy density (mean and standard deviation) of eight forage species from Northeast Fisheries Science Center bottom trawl surveys by season and year for the Mid-Atlantic Bight (MAB). Symbol size represents abundance (mean kg/tow) estimated from bottom trawl survey tows in the MAB.,,images\NewEngland\energy_density_NewEngland,images\MidAtlantic\energy_density_MidAtlantic,,,,,NA,NA,NA -exp-n,exp_n,line plot showing expected number of species from Albatross and Bigelow surveys,"Adult fish diversity for Georges Bank (GB, top) and in the Gulf of Maine (GOM, bottom) with long-term (light orange) and short-term (dark orange) increasing trends, based on expected number of species in a standard number of individuals. Results from survey vessels Albatross (red) and Bigelow (blue) are reported separately due to catchability differences.","Adult fish diversity in the Mid-Atlantic Bight, based on expected number of species in a standard number of individuals. Results from survey vessels Albatross (red) and Bigelow (blue) are reported separately due to catchability differences. A long-term significant decrease is present in the Bigelow time series (purple).",NA,images\NewEngland\exp_n_NewEngland,images\MidAtlantic\exp_n_MidAtlantic,NA,images\MidAtlantic\slide_exp_n_MidAtlantic,images\NewEngland\slide_exp_n_NewEngland,NA,NA,NA,NA +energy-density,energy_density,faceted line plot showing energy density of multiple forage fish,"Energy density (mean and standard deviation) of eight forage species from Northeast Fisheries Science Center bottom trawl surveys by season and year. Symbol size represents abundance (mean kg/tow) estimated from bottom trawl survey tows in Georges Bank (GB, top) and the GOM (bottom). ",Energy density (mean and standard deviation) of eight forage species from Northeast Fisheries Science Center bottom trawl surveys by season and year for the Mid-Atlantic Bight (MAB). Symbol size represents abundance (mean kg/tow) estimated from bottom trawl survey tows in the MAB.,,images\NewEngland\energy-density_NewEngland,images\MidAtlantic\energy-density_MidAtlantic,,,,,NA,NA,NA +exp-n,exp_n,line plot showing expected number of species from Albatross and Bigelow surveys,"Adult fish diversity for Georges Bank (GB, top) and in the Gulf of Maine (GOM, bottom) with long-term (light orange) and short-term (dark orange) increasing trends, based on expected number of species in a standard number of individuals. Results from survey vessels Albatross (red) and Bigelow (blue) are reported separately due to catchability differences.","Adult fish diversity in the Mid-Atlantic Bight, based on expected number of species in a standard number of individuals. Results from survey vessels Albatross (red) and Bigelow (blue) are reported separately due to catchability differences. A long-term significant decrease is present in the Bigelow time series (purple).",NA,images\NewEngland\exp-n_NewEngland,images\MidAtlantic\exp-n_MidAtlantic,NA,images\MidAtlantic\slide_exp-n_MidAtlantic,images\NewEngland\slide_exp-n_NewEngland,NA,NA,NA,NA foragebio,forage_index,line plot showing relative forage biomass over time,"Forage fish index in Georges Bank (GB, top) and the Gulf of Maine (GOM, bottom, significant long-term increase for spring in orange) for spring (blue) and fall (red) surveys. Index values are relative to the maximum observation within a region across surveys.","Forage fish index in the Mid-Atlantic Bight for spring (blue) and fall (red) surveys, with a long-term decline (purple) in fall. Index values are relative to the maximum observation within a region across surveys.",NA,images\NewEngland\foragebio_NewEngland,images\MidAtlantic\foragebio_MidAtlantic,NA,images\MidAtlantic\slide_foragebio_MidAtlantic,images\NewEngland\slide_foragebio_NewEngland,NA,NA,NA,NA -forageshifts,forage_index,faceted line plot showing eastward and northward shifts in forage fish over time,NA,NA,"Eastward (top) and northward (bottom) shifts in the center of gravity for 20 forage fish species on the Northeast U.S. Shelf in fall (left) and spring (right), with long-term increasing trends (orange) for fall eastward and northward and spring northward center of gravity.",NA,NA,images\BothReports\forage_dist_BothReports,NA,NA,images\BothReports\slide_forage_dist_BothReports,NA,NA,NA +forageshifts,forage_index,faceted line plot showing eastward and northward shifts in forage fish over time,NA,NA,"Eastward (top) and northward (bottom) shifts in the center of gravity for 20 forage fish species on the Northeast U.S. Shelf in fall (left) and spring (right), with long-term increasing trends (orange) for fall eastward and northward and spring northward center of gravity.",NA,NA,images\BothReports\forageshifts_BothReports,NA,NA,images\BothReports\slide_forageshifts_BothReports,NA,NA,NA GOMoa,NA,line plot of aragonite saturation by week of year,NA,NA,Weekly average surface aragonite saturation state measured at the long-term buoy location in the Gulf of Maine at 43.02 N and 70.54 W,NA,NA,images\BothReports\GOMoa_image.png,NA,NA,images\BothReports\slide_GOMoa_image.png,NA,NA,NA grayseal,grayseal,line plot showing gray seal bycatch,NA,NA,"Gray seal five-year average bycatch estimate for New England and Mid-Atlantic U.S. gillnet fisheries (blue, with confidence interval shaded) and the potential U.S. biological removal (red). The range-wide potential biological removal (PBR), including both U.S. and Canadian portions of the population, is 12,052 in the draft 2024 SAR. The dashed line (black) represents the annual estimated bycatch.",NA,NA,images\BothReports\grayseal_BothReports,NA,NA,images\BothReports\slide_grayseal_BothReports,NA,NA,NA -GSI,gsi,line plot showing Western GSI over time,NA,NA,"Index representing changes in the location of the western (between 64 and 55 degrees W) Gulf Stream north wall (black). Positive values represent a more northerly Gulf Stream position, with long-term increasing trend (orange).",NA,NA,images\BothReports\west_gsi_BothReports,NA,NA,images\BothReports\slide_west_gsi_BothReports,NA,NA,NA +GSI,gsi,line plot showing Western GSI over time,NA,NA,"Index representing changes in the location of the western (between 64 and 55 degrees W) Gulf Stream north wall (black). Positive values represent a more northerly Gulf Stream position, with long-term increasing trend (orange).",NA,NA,images\BothReports\GSI_BothReports,NA,NA,images\BothReports\slide_GSI_BothReports,NA,NA,NA harborporpoise,harborporpoise,line plot showing harbor porpoise bycatcg,NA,NA,"Harbor porpoise average bycatch estimate for Mid-Atlantic and New England gillnet fisheries (blue, confidence interval shaded) and the potential biological removal (red). The dashed line (black) represents the annual estimated bycatch. ",NA,NA,images\BothReports\harborporpoise_BothReports,NA,NA,images\BothReports\slide_harborporpoise_BothReports,NA,NA,NA -long-term-sst,long_term_sst,line plot showing long term SST,NA,NA,"Northeast U.S. annual sea surface temperature (SST, black), with long-term increasing trend (orange).",NA,NA,images\BothReports\long_term_sst_BothReports,NA,NA,images\BothReports\slide_long_term_sst_BothReports,NA,NA,NA -mab-cf,condition,raster grid showing condition of several fish species,NA,"Condition factor for fish species in the Mid-Atlantic Bight (MAB) based on fall Northeast Fisheries Science Center bottom trawl survey data. MAB data are missing for 2017 due to survey delays, and no survey was conducted in 2020.",NA,NA,images\MidAtlantic\condition_MidAtlantic,NA,images\MidAtlantic\slide_condition_MidAtlantic,NA,NA,NA,NA,NA -macrobenthosshifts,benthos_index,faceted line plot showing eastward and northward shifts in macrobenthos over time,NA,NA,"Eastward (top) and northward (bottom) shifts in the center of gravity for macrobenthos species on the Northeast U.S. Shelf in fall (left) and spring (right), with long-term decreasing trends (purple) for spring eastward and northward center of gravity.",NA,NA,images\BothReports\macrobenthos_dist_BothReports,NA,NA,images\BothReports\slide_macrobenthos_dist_BothReports,NA,NA,NA -mass-biomass,mass_inshore_survey,faceted line plot of guild abundance,"Spring (left) and fall (right) surveyed biomass from the state of Massachusetts inshore survey, with increasing (orange) and decreasing (purple) long-term trends. The shaded area around each annual mean represents 2 standard deviations from the mean.",NA,NA,images\NewEngland\mass_inshore_NewEngland,NA,NA,NA,images\NewEngland\slide_mass_inshore_NewEngland,NA,NA,NA,NA -narw-abundance,narw,line plot showing NARW abundance,NA,NA,Estimated North Atlantic right whale abundance on the Northeast Shelf. 95% confidence interval shaded in gray around the line. ,NA,NA,images\BothReports\narw_abundance_BothReports,NA,NA,images\BothReports\slide_narw_abundance_BothReports,NA,NA,NA -NARW-calf-abundance,narw,line plot showing NARW calf abundance,NA,NA,Number of North Atlantic right whale calf births since 1980. ,NA,NA,images\BothReports\narw_calves_BothReports,NA,NA,images\BothReports\slide_narw_calves_BothReports,NA,NA,NA -ne-cf,condition,raster grid showing condition of several fish species,"Condition factor for fish species in New England (top: Georges Bank, GB; bottom: Gulf of Maine, GOM) based on fall Northeast Fisheries Science Center bottom trawl survey data. No survey was conducted in 2020.",NA,NA,images/NewEngland/condition_NewEngland,NA,NA,NA,images/NewEngland/slide_condition_NewEngland,NA,NA,NA,NA -nefsc-biomass-gb,aggregate_biomass,"faceted line plot showing aggregate biomass of guilds, by season","Spring (left) and fall (right) surveyed biomass on Georges Bank, with long-term increasing (orange), long-term decreasing (purple), and short-term decreasing (dark purple, piscivore spring) trends. The shaded area around each annual mean represents 2 standard deviations from the mean.",NA,NA,images\NewEngland\aggregate_biomass_gb_NewEngland,NA,NA,NA,images\NewEngland\slide_aggregate_biomass_gb_NewEngland,NA,NA,NA,NA -nefsc-biomass-gom,aggregate_biomass,"faceted line plot showing aggregate biomass of guilds, by season","Spring (left) and fall (right) surveyed biomass in the Gulf of Maine, with increasing long-term trends (orange). The shaded area around each annual mean represents 2 standard deviations from the mean.",NA,NA,images\NewEngland\aggregate_biomass_gom_NewEngland,NA,NA,NA,images\NewEngland\slide_aggregate_biomass_gom_NewEngland,NA,NA,NA,NA -nefsc-biomass-mab,aggregate_biomass,"faceted line plot showing aggregate biomass of guilds, by season",NA,"Spring (left) and fall (right) surveyed biomass in the Mid-Atlantic Bight. Data from the Northeast Fisheries Science Center Bottom Trawl Survey are shown in black, with the nearshore Northeast Area Monitoring and Assessment Program (NEAMAP) survey shown in red. Long-term significant increases (orange lines) are present for spring piscivore, fall benthivore, and fall benthos biomass. The shaded area around each annual mean represents 2 standard deviations from the mean.",NA,NA,images\MidAtlantic\aggregate_biomass_mab_MidAtlantic,NA,images\MidAtlantic\slide_aggregate_biomass_mab_MidAtlantic,NA,NA,NA,NA,NA -productivity-anomaly,productivity_anomaly,faceted bar plot showing biomass and recruitment anomalies,"Fish productivity measures. Top: Small-fish-per-large-fish survey biomass anomaly for species managed by the New England Fishery Management Council (NEFMC). Bottom: assessment recruitment per spawning stock biomass anomaly for stocks managed by the NEFMC. The summed anomaly across species is shown by the black line, drawn across all years with the same number of stocks analyzed.","Fish productivity measures. Top: Small fish per large fish survey biomass anomaly of Mid-Atlantic Fishery Management Council (MAFMC) managed species in the Mid-Atlantic Bight. Bottom: assessment recruitment per spawning stock biomass anomaly for stocks managed by the MAFMC. The summed anomaly across species is shown by the black line, drawn across all years with the same number of stocks analyzed.",NA,images\NewEngland\productivity_anomaly_NewEngland,images\MidAtlantic\productivity_anomaly_MidAtlantic,NA,images\MidAtlantic\slide_productivity_anomaly_MidAtlantic,images\NewEngland\slide_productivity_anomaly_NewEngland,NA,NA,NA,NA -protectedspp-dist-shifts,cetacean_dist,faceted map of cetacean distribution shifts by season,NA,NA,"Direction and magnitude of core habitat shifts, represented by the length of the line of the seasonal weighted centroid for species with more than 70 km difference between 2010 and 2017 (tip of arrow).",NA,NA,images\BothReports\cetacean_dist_BothReports,NA,NA,images\BothReports\slide_cetacean_dist_BothReports,NA,NA,NA -recdat-div-catch,recdat,line plot of diversity of recreational catch,"Diversity of recreational catch in New England, with long-term increasing trend (orange). Derived from NOAA Fisheries Marine Recreational Information Program's Catch Time Series Query.",Diversity of recreational catch in the Mid-Atlantic. Derived from NOAA Fisheries Marine Recreational Information Program's Catch Time Series Query.,NA,images\NewEngland\recdat_div_catch_NewEngland,images\MidAtlantic\recdat_div_catch_MidAtlantic,NA,images\MidAtlantic\slide_recdat_div_catch_MidAtlantic,images\NewEngland\slide_recdat_div_catch_NewEngland,NA,NA,NA,NA -rec-div,recdat,line plot of recreational fleet effort diversity,Recreational fleet effort diversity from 1980-2024 in New England.,"Recreational fleet effort diversity from 1980-2024 in the Mid-Atlantic, with significant decrease in long-term (light purple) and short-term (dark purple) trends.",NA,images\NewEngland\rec_div_NewEngland,images\MidAtlantic\rec_div_MidAtlantic,NA,images\MidAtlantic\slide_rec_div_MidAtlantic,images\NewEngland\slide_rec_div_NewEngland,NA,NA,NA,NA -rec-hms,rec_hms,faceted line plot showing recreational shark landings and recreational pelagic shark landings,Recreational shark landings in the New England region from NOAA Fisheries' Large Pelagics Survey.,"Recreational shark landings in the Mid-Atlantic region from NOAA Fisheries Large Pelagics Survey (top, with short-term sigificant decline in dark purple) and Marine Recreational Information Program (MRIP, bottom) with long-term declining trend (purple). Note that the trend line is associated with the Large Coastal group, which has had no reported MRIP landings after 2020.",NA,images\NewEngland\rec_hms_NE_NewEngland,images\MidAtlantic\rec_hms_MidAtlantic,NA,images\MidAtlantic\slide_rec_hms_MidAtlantic,images\NewEngland\slide_rec_hms_NewEngland,NA,NA,NA,NA -rec-landings,recdat,line plot showing recreational seafood harvest,"Total recreational seafood harvest (millions of pounds, black, long-term significant decrease, purple) in the New England region.","Total recreational seafood harvest (millions of pounds, black, long-term significant decrease, purple) in the Mid-Atlantic region.",NA,images\NewEngland\rec_landings_NewEngland,images\MidAtlantic\rec_landings_MidAtlantic,NA,images\MidAtlantic\slide_rec_landings_MidAtlantic,images\NewEngland\slide_rec_landings_NewEngland,NA,NA,NA,NA -rec-op,recdat,line plot showing recreational angler trips over time,Recreational effort (total number of recreational angler trips from 1980-2024) in New England. Derived from NOAA Fisheries Marine Recreational Information Program's Effort Time Series Query.,Recreational effort (total number of recreational angler trips from 1980-2024) in the Mid-Atlantic. Derived from NOAA Fisheries Marine Recreational Information Program Effort Time Series Query.,NA,images\NewEngland\rec_op_NewEngland,images\MidAtlantic\rec_op_MidAtlantic,NA,images\MidAtlantic\slide_rec_op_MidAtlantic,images\NewEngland\slide_rec_op_NewEngland,NA,NA,NA,NA -recreational-engagement,engagement,point plot showing engagement index and relative engagement index for top recreational fishing communities,Recreational engagement and population relative engagement with labels for the top recreationally engaged fishing communities in New England (last updated 2024).,Recreational engagement and population relative engagement with labels for the top recreationally engaged fishing communities in the Mid-Atlantic (last updated 2024).,NA,images\NewEngland\recreational_engagement_NewEngland,images\MidAtlantic\recreational_engagement_MidAtlantic,NA,images\MidAtlantic\slide_recreational_engagement_MidAtlantic,images\NewEngland\slide_recreational_engagement_NewEngland,NA,NA,NA,NA +long-term-sst,long_term_sst,line plot showing long term SST,NA,NA,"Northeast U.S. annual sea surface temperature (SST, black), with long-term increasing trend (orange).",NA,NA,images\BothReports\long-term-sst_BothReports,NA,NA,images\BothReports\slide_long-term-sst_BothReports,NA,NA,NA +mab-cf,condition,raster grid showing condition of several fish species,NA,"Condition factor for fish species in the Mid-Atlantic Bight (MAB) based on fall Northeast Fisheries Science Center bottom trawl survey data. MAB data are missing for 2017 due to survey delays, and no survey was conducted in 2020.",NA,NA,images\MidAtlantic\mab-cf_MidAtlantic,NA,images\MidAtlantic\slide_mab-cf_MidAtlantic,NA,NA,NA,NA,NA +macrobenthosshifts,benthos_index,faceted line plot showing eastward and northward shifts in macrobenthos over time,NA,NA,"Eastward (top) and northward (bottom) shifts in the center of gravity for macrobenthos species on the Northeast U.S. Shelf in fall (left) and spring (right), with long-term decreasing trends (purple) for spring eastward and northward center of gravity.",NA,NA,images\BothReports\macrobenthosshifts_BothReports,NA,NA,images\BothReports\slide_macrobenthosshifts_BothReports,NA,NA,NA +mass-biomass,mass_inshore_survey,faceted line plot of guild abundance,"Spring (left) and fall (right) surveyed biomass from the state of Massachusetts inshore survey, with increasing (orange) and decreasing (purple) long-term trends. The shaded area around each annual mean represents 2 standard deviations from the mean.",NA,NA,images\NewEngland\mass-biomass_NewEngland,NA,NA,NA,images\NewEngland\slide_mass-biomass_NewEngland,NA,NA,NA,NA +narw-abundance,narw,line plot showing NARW abundance,NA,NA,Estimated North Atlantic right whale abundance on the Northeast Shelf. 95% confidence interval shaded in gray around the line. ,NA,NA,images\BothReports\narw-abundance_BothReports,NA,NA,images\BothReports\slide_narw-abundance_BothReports,NA,NA,NA +NARW-calf-abundance,narw,line plot showing NARW calf abundance,NA,NA,Number of North Atlantic right whale calf births since 1980. ,NA,NA,images\BothReports\NARW-calf-abundance_BothReports,NA,NA,images\BothReports\slide_NARW-calf-abundance_BothReports,NA,NA,NA +ne-cf,condition,raster grid showing condition of several fish species,"Condition factor for fish species in New England (top: Georges Bank, GB; bottom: Gulf of Maine, GOM) based on fall Northeast Fisheries Science Center bottom trawl survey data. No survey was conducted in 2020.",NA,NA,images/NewEngland/ne-cf_NewEngland,NA,NA,NA,images/NewEngland/slide_ne-cf_NewEngland,NA,NA,NA,NA +nefsc-biomass-gb,aggregate_biomass,"faceted line plot showing aggregate biomass of guilds, by season","Spring (left) and fall (right) surveyed biomass on Georges Bank, with long-term increasing (orange), long-term decreasing (purple), and short-term decreasing (dark purple, piscivore spring) trends. The shaded area around each annual mean represents 2 standard deviations from the mean.",NA,NA,images\NewEngland\nefsc-biomass-gb_NewEngland,NA,NA,NA,images\NewEngland\slide_nefsc-biomass-gb_NewEngland,NA,NA,NA,NA +nefsc-biomass-gom,aggregate_biomass,"faceted line plot showing aggregate biomass of guilds, by season","Spring (left) and fall (right) surveyed biomass in the Gulf of Maine, with increasing long-term trends (orange). The shaded area around each annual mean represents 2 standard deviations from the mean.",NA,NA,images\NewEngland\nefsc-biomass-gom_NewEngland,NA,NA,NA,images\NewEngland\slide_nefsc-biomass-gom_NewEngland,NA,NA,NA,NA +nefsc-biomass-mab,aggregate_biomass,"faceted line plot showing aggregate biomass of guilds, by season",NA,"Spring (left) and fall (right) surveyed biomass in the Mid-Atlantic Bight. Data from the Northeast Fisheries Science Center Bottom Trawl Survey are shown in black, with the nearshore Northeast Area Monitoring and Assessment Program (NEAMAP) survey shown in red. Long-term significant increases (orange lines) are present for spring piscivore, fall benthivore, and fall benthos biomass. The shaded area around each annual mean represents 2 standard deviations from the mean.",NA,NA,images\MidAtlantic\nefsc-biomass-mab_MidAtlantic,NA,images\MidAtlantic\slide_nefsc-biomass-mab_MidAtlantic,NA,NA,NA,NA,NA +productivity-anomaly,productivity_anomaly,faceted bar plot showing biomass and recruitment anomalies,"Fish productivity measures. Top: Small-fish-per-large-fish survey biomass anomaly for species managed by the New England Fishery Management Council (NEFMC). Bottom: assessment recruitment per spawning stock biomass anomaly for stocks managed by the NEFMC. The summed anomaly across species is shown by the black line, drawn across all years with the same number of stocks analyzed.","Fish productivity measures. Top: Small fish per large fish survey biomass anomaly of Mid-Atlantic Fishery Management Council (MAFMC) managed species in the Mid-Atlantic Bight. Bottom: assessment recruitment per spawning stock biomass anomaly for stocks managed by the MAFMC. The summed anomaly across species is shown by the black line, drawn across all years with the same number of stocks analyzed.",NA,images\NewEngland\productivity-anomaly_NewEngland,images\MidAtlantic\productivity-anomaly_MidAtlantic,NA,images\MidAtlantic\slide_productivity-anomaly_MidAtlantic,images\NewEngland\slide_productivity-anomaly_NewEngland,NA,NA,NA,NA +protectedspp-dist-shifts,cetacean_dist,faceted map of cetacean distribution shifts by season,NA,NA,"Direction and magnitude of core habitat shifts, represented by the length of the line of the seasonal weighted centroid for species with more than 70 km difference between 2010 and 2017 (tip of arrow).",NA,NA,images\BothReports\protectedspp-dist-shifts_BothReports,NA,NA,images\BothReports\slide_protectedspp-dist-shifts_BothReports,NA,NA,NA +recdat-div-catch,recdat,line plot of diversity of recreational catch,"Diversity of recreational catch in New England, with long-term increasing trend (orange). Derived from NOAA Fisheries Marine Recreational Information Program's Catch Time Series Query.",Diversity of recreational catch in the Mid-Atlantic. Derived from NOAA Fisheries Marine Recreational Information Program's Catch Time Series Query.,NA,images\NewEngland\recdat-div-catch_NewEngland,images\MidAtlantic\recdat-div-catch_MidAtlantic,NA,images\MidAtlantic\slide_recdat-div-catch_MidAtlantic,images\NewEngland\slide_recdat-div-catch_NewEngland,NA,NA,NA,NA +rec-div,recdat,line plot of recreational fleet effort diversity,Recreational fleet effort diversity from 1980-2024 in New England.,"Recreational fleet effort diversity from 1980-2024 in the Mid-Atlantic, with significant decrease in long-term (light purple) and short-term (dark purple) trends.",NA,images\NewEngland\rec-div_NewEngland,images\MidAtlantic\rec-div_MidAtlantic,NA,images\MidAtlantic\slide_rec-div_MidAtlantic,images\NewEngland\slide_rec-div_NewEngland,NA,NA,NA,NA +rec-hms,rec_hms,faceted line plot showing recreational shark landings and recreational pelagic shark landings,Recreational shark landings in the New England region from NOAA Fisheries' Large Pelagics Survey.,"Recreational shark landings in the Mid-Atlantic region from NOAA Fisheries Large Pelagics Survey (top, with short-term sigificant decline in dark purple) and Marine Recreational Information Program (MRIP, bottom) with long-term declining trend (purple). Note that the trend line is associated with the Large Coastal group, which has had no reported MRIP landings after 2020.",NA,images\NewEngland\rec-hms-NE_NewEngland,images\MidAtlantic\rec-hms_MidAtlantic,NA,images\MidAtlantic\slide_rec-hms_MidAtlantic,images\NewEngland\slide_rec-hms_NewEngland,NA,NA,NA,NA +rec-landings,recdat,line plot showing recreational seafood harvest,"Total recreational seafood harvest (millions of pounds, black, long-term significant decrease, purple) in the New England region.","Total recreational seafood harvest (millions of pounds, black, long-term significant decrease, purple) in the Mid-Atlantic region.",NA,images\NewEngland\rec-landings_NewEngland,images\MidAtlantic\rec-landings_MidAtlantic,NA,images\MidAtlantic\slide_rec-landings_MidAtlantic,images\NewEngland\slide_rec-landings_NewEngland,NA,NA,NA,NA +rec-op,recdat,line plot showing recreational angler trips over time,Recreational effort (total number of recreational angler trips from 1980-2024) in New England. Derived from NOAA Fisheries Marine Recreational Information Program's Effort Time Series Query.,Recreational effort (total number of recreational angler trips from 1980-2024) in the Mid-Atlantic. Derived from NOAA Fisheries Marine Recreational Information Program Effort Time Series Query.,NA,images\NewEngland\rec-op_NewEngland,images\MidAtlantic\rec-op_MidAtlantic,NA,images\MidAtlantic\slide_rec-op_MidAtlantic,images\NewEngland\slide_rec-op_NewEngland,NA,NA,NA,NA +recreational-engagement,engagement,point plot showing engagement index and relative engagement index for top recreational fishing communities,Recreational engagement and population relative engagement with labels for the top recreationally engaged fishing communities in New England (last updated 2024).,Recreational engagement and population relative engagement with labels for the top recreationally engaged fishing communities in the Mid-Atlantic (last updated 2024).,NA,images\NewEngland\recreational-engagement_NewEngland,images\MidAtlantic\recreational-engagement_MidAtlantic,NA,images\MidAtlantic\slide_recreational-engagement_MidAtlantic,images\NewEngland\slide_recreational-engagement_NewEngland,NA,NA,NA,NA salmon,gom_salmon,faceted line plot of salmon percent return and number of salmon,Percent return rate of two year old hatchery Atlantic salmon (top) and number (bottom) of all Atlantic salmon returns to the Penobscot River Gulf of Maine rivers since 1972. Long-term decreasing trend for percent return rate in purple.,NA,NA,images\NewEngland\salmon_NewEngland,NA,NA,NA,images\NewEngland\slide_salmon_NewEngland,NA,NA,NA,NA -seabird-ne-productivity,seabird_ne,line plot of fledged chicks per nest,"Common tern productivity - the number of fledged chicks per nest - at seven Gulf of Maine colonies managed by the National Audubon Society's Seabird Restoration Program, with significant long-term (purple) and short-term (dark purple) declines.",NA,NA,images\NewEngland\seabird_productivity_NewEngland,NA,NA,NA,images\NewEngland\slide_seabird_productivity_NewEngland,NA,NA,NA,NA -seals,seal_pups,"line plot of gray seal pup births, colored by colony",NA,NA,Estimated number of gray seal pups born at four United States pupping colonies at various times from 1988 to 2021. ,NA,NA,images\BothReports\seal_pups_BothReports,NA,NA,images\BothReports\slide_seal_pups_BothReports,NA,NA,NA +seabird-ne-productivity,seabird_ne,line plot of fledged chicks per nest,"Common tern productivity - the number of fledged chicks per nest - at seven Gulf of Maine colonies managed by the National Audubon Society's Seabird Restoration Program, with significant long-term (purple) and short-term (dark purple) declines.",NA,NA,images\NewEngland\seabird-ne-productivity_NewEngland,NA,NA,NA,images\NewEngland\slide_seabird-ne-productivity_NewEngland,NA,NA,NA,NA +seals,seal_pups,"line plot of gray seal pup births, colored by colony",NA,NA,Estimated number of gray seal pups born at four United States pupping colonies at various times from 1988 to 2021. ,NA,NA,images\BothReports\seals_BothReports,NA,NA,images\BothReports\slide_seals_BothReports,NA,NA,NA slopesea-bottom,NA,map of temperature anomalies in the Northeast US Shelf,NA,NA,NA,NA,NA,images\BothReports\Highlights_2026-BTemp_Anomaly-202501-NES.png,NA,NA,images\BothReports\slide_Highlights_2026-BTemp_Anomaly-202501-NES.png,NA,NA,NA slopesea,NA,map of temperature anomalies in the Northeast US Shelf,NA,NA,January 2025 sea surface (left) and bottom (right) temperature differences compared to the January climatological means. Sea Surface Temperature (SST) is from the NOAA Advanced Clear-Sky Processor for Ocean (ACSPO) Super-collated SST (climatology range 2000-2020); Bottom temperature is from the GLORYS reanalysis model (climatological range 1990-2020).,NA,NA,images\BothReports\Highlights_2026-SST_Anomaly-202501-NES.png,NA,NA,images\BothReports\Feb2024-SST-ANOM_KHyde_2025.png,NA,NA,NA slopewater,slopewater,line plot showing Labrador and Warm Slope Waters,NA,NA,The proportion of Warm Slope Water (WSW) and Labrador Slope Water (LSW) entering the Gulf of Maine through the Northeast Channel from 1977 to 2024. The red and teal dashed lines represent the long-term proportion averages for the WSW and LSW respectively.,NA,NA,images\BothReports\slopewater_BothReports,NA,NA,images\BothReports\slide_slopewater_BothReports,NA,NA,NA -spawntiming,spawn_timing,faceted line plot of spring resting maturity stage for several fish,NA,NA,"Percent resting stage (non-spawning) mature female fish (black) from spring Northeast Fisheries Science Center bottom trawl survey with significant long-term increases (orange), short-term decreases (dark purple), and long-term decreases (purple) from two haddock and three yellowtail flounder stocks: CC = Cape Cod, Gulf of Maine, GOM = Gulf of Maine, GB = Georges Bank, SNE = Southern New England.",NA,NA,images\BothReports\spawn_timing_BothReports,NA,NA,images\BothReports\slide_spawn_timing_BothReports,NA,NA,NA -species-dist,species_dist,faceted line plot showing along-shelf distance and depth ,NA,NA,"Aggregate species distribution metrics for species in the Northeast Large Marine Ecosystem: along shelf distance with long-term increasing trend (orange), and depth with long-term decreasing trend indicating deeper water (purple).",NA,NA,images\BothReports\species_dist_BothReports,NA,NA,images\BothReports\slide_species_dist_BothReports,NA,NA,NA -stock-status,stock_status,Kobe plot of stock status,"Summary of single species status for New England Fishery Management Council and jointly federally managed stocks (goosefish and spiny dogfish). The dotted vertical line at one is the target biomass reference point of B. The dashed lines are the management thresholds of B (vertical) or F (horizontal). Stocks with a $B/B_{MSY}$ estimate but without an $F/F_{MSY}$ estimate are denoted in a separate box plot (top). Colors denote stocks with $B/B_{MSY}$ < 0.5 or $F/F_{MSY}$ (orange), stocks 0.5<$B/B_{MSY}$<1 (blue), and stocks $B/B_{MSY}$>1 (green).CCGOM = Cape Cod Gulf of Maine, GOM = Gulf of Maine, GB = Georges Bank, SNEMA = Southern New England Mid-Atlantic","Summary of single species status for Mid-Atlantic Fishery Management Council and jointly federally managed stocks (spiny dogfish; goosefish has unknown status). The dotted vertical line is the target biomass reference point of $B_{MSY}$. The dashed lines are the management thresholds of one half $B_{MSY}$ (vertical) or $F_{MSY}$ (horizontal). Stocks with a $B/B_{MSY}$ estimate but without an $F/F_{MSY}$ estimate are denoted in a separate box plot (top). Colors denote stocks with $B/B_{MSY}$ < 0.5 or $F/F_{MSY}$>1 (orange), stocks 0.5<$B/B_{MSY}$<1 (blue), and stocks $B/B_{MSY}$>1 (green).",NA,images\NewEngland\stock_status_NewEngland,images\MidAtlantic\stock_status_MidAtlantic,NA,images\MidAtlantic\slide_stock_status_MidAtlantic,images\NewEngland\slide_stock_status_NewEngland,NA,NA,NA,NA -therm-hab-persist-2024,thermal_habitat_gridded,faceted map of number of days with temperatures above thresholds,NA,NA,The number of days in 2025 where bottom temperature exceeds 15 degrees (left) and 24 degrees (right) based on the GLORYS 1/12 degree grid.,NA,NA,images\BothReports\therm_hab_persist_BothReports,NA,NA,images\BothReports\slide_therm_hab_persist_BothReports,NA,NA,NA -total-landings,comdat,"line plot of total, council, and seafood landings","Total commercial landings (black), total U.S. seafood landings (blue), and New England managed U.S. seafood landings (red) for Georges Bank (GB, top) and the Gulf of Maine (GOM, bottom), with long-term significant declines (purple).","Total commercial landings (black), total U.S. seafood landings (blue), and Mid-Atlantic managed U.S. seafood landings (red), with long-term significant decline (purple) in total landings.",NA,images/NewEngland/total_landings_NewEngland,images/MidAtlantic/total_landings_MidAtlantic,NA,images/MidAtlantic/slide_total_landings_MidAtlantic,images/NewEngland/slide_total_landings_NewEngland,NA,NA,NA,NA +spawntiming,spawn_timing,faceted line plot of spring resting maturity stage for several fish,NA,NA,"Percent resting stage (non-spawning) mature female fish (black) from spring Northeast Fisheries Science Center bottom trawl survey with significant long-term increases (orange), short-term decreases (dark purple), and long-term decreases (purple) from two haddock and three yellowtail flounder stocks: CC = Cape Cod, Gulf of Maine, GOM = Gulf of Maine, GB = Georges Bank, SNE = Southern New England.",NA,NA,images\BothReports\spawntiming_BothReports,NA,NA,images\BothReports\slide_spawntiming_BothReports,NA,NA,NA +species-dist,species_dist,faceted line plot showing along-shelf distance and depth ,NA,NA,"Aggregate species distribution metrics for species in the Northeast Large Marine Ecosystem: along shelf distance with long-term increasing trend (orange), and depth with long-term decreasing trend indicating deeper water (purple).",NA,NA,images\BothReports\species-dist_BothReports,NA,NA,images\BothReports\slide_species-dist_BothReports,NA,NA,NA +stock-status,stock_status,Kobe plot of stock status,"Summary of single species status for New England Fishery Management Council and jointly federally managed stocks (goosefish and spiny dogfish). The dotted vertical line at one is the target biomass reference point of B. The dashed lines are the management thresholds of B (vertical) or F (horizontal). Stocks with a $B/B_{MSY}$ estimate but without an $F/F_{MSY}$ estimate are denoted in a separate box plot (top). Colors denote stocks with $B/B_{MSY}$ < 0.5 or $F/F_{MSY}$ (orange), stocks 0.5<$B/B_{MSY}$<1 (blue), and stocks $B/B_{MSY}$>1 (green).CCGOM = Cape Cod Gulf of Maine, GOM = Gulf of Maine, GB = Georges Bank, SNEMA = Southern New England Mid-Atlantic","Summary of single species status for Mid-Atlantic Fishery Management Council and jointly federally managed stocks (spiny dogfish; goosefish has unknown status). The dotted vertical line is the target biomass reference point of $B_{MSY}$. The dashed lines are the management thresholds of one half $B_{MSY}$ (vertical) or $F_{MSY}$ (horizontal). Stocks with a $B/B_{MSY}$ estimate but without an $F/F_{MSY}$ estimate are denoted in a separate box plot (top). Colors denote stocks with $B/B_{MSY}$ < 0.5 or $F/F_{MSY}$>1 (orange), stocks 0.5<$B/B_{MSY}$<1 (blue), and stocks $B/B_{MSY}$>1 (green).",NA,images\NewEngland\stock-status_NewEngland,images\MidAtlantic\stock-status_MidAtlantic,NA,images\MidAtlantic\slide_stock-status_MidAtlantic,images\NewEngland\slide_stock-status_NewEngland,NA,NA,NA,NA +therm-hab-persist-2024,thermal_habitat_gridded,faceted map of number of days with temperatures above thresholds,NA,NA,The number of days in 2025 where bottom temperature exceeds 15 degrees (left) and 24 degrees (right) based on the GLORYS 1/12 degree grid.,NA,NA,images\BothReports\therm-hab-persist-2024_BothReports,NA,NA,images\BothReports\slide_therm-hab-persist-2024_BothReports,NA,NA,NA +total-landings,comdat,"line plot of total, council, and seafood landings","Total commercial landings (black), total U.S. seafood landings (blue), and New England managed U.S. seafood landings (red) for Georges Bank (GB, top) and the Gulf of Maine (GOM, bottom), with long-term significant declines (purple).","Total commercial landings (black), total U.S. seafood landings (blue), and Mid-Atlantic managed U.S. seafood landings (red), with long-term significant decline (purple) in total landings.",NA,images/NewEngland/total-landings_NewEngland,images/MidAtlantic/total-landings_MidAtlantic,NA,images/MidAtlantic/slide_total-landings_MidAtlantic,images/NewEngland/slide_total-landings_NewEngland,NA,NA,NA,NA totpp,annual_chl_pp,line plot of annual primary production,"Total areal annual primary production by ecological production unit (Georges Bank, top; Gulf of Maine, bottom). The dashed line represents the long-term (1998-2025) annual mean.",Total areal annual primary production for the Mid-Atlantic Bight. The dashed line represents the long-term (1998-2025) annual mean.,NA,images\NewEngland\totpp_NewEngland,images\MidAtlantic\totpp_MidAtlantic,NA,images\MidAtlantic\slide_totpp_MidAtlantic,images\NewEngland\slide_totpp_NewEngland,NA,NA,NA,NA traits,finfish_traits,line plot of length at maturity in spring and fall,"Fish community functional traits in New England based on Fall (red) and Spring (blue) survey data for Georges Bank (GB, top) and the Gulf of Maine (bottom) with significant long-term declines (purple). Dashed lines represent the long term annual mean. ","Fish community functional traits in the Mid-Atlantic Bight based on Fall (red) and Spring (blue) survey data. Length at maturity for the full finfish community has increased in spring (orange line), but decreased in fall (purple lines)",NA,images\NewEngland\traits_NewEngland,images\MidAtlantic\traits_MidAtlantic,NA,images\MidAtlantic\slide_traits_MidAtlantic,images\NewEngland\slide_traits_NewEngland,NA,NA,NA,NA -traits-tl,finfish_traits,line plot of trophic level over time,"Fish community functional traits (trophic level) in Georges Bank (GB, top) and the Gulf of Maine (GOM, bottom) based on Fall (red) and Spring (blue) survey data with increasing long-term trend (orange) and increasing short-term trend (dark orange). Dashed lines represent the long-term annual mean for each survey.",Fish community functional traits (trophic level) in the Mid-Atlantic Bight based on Fall (red) and Spring (blue) survey data with a significant long-term decrease (purple) present in the fall. Dashed lines represent the long-term annual mean for each survey.,NA,images\NewEngland\traits_tl_NewEngland,images\MidAtlantic\traits_tl_MidAtlantic,NA,images\MidAtlantic\slide_traits_tl_MidAtlantic,images\NewEngland\slide_traits_tl_NewEngland,NA,NA,NA,NA -traits-k,finfish_traits,"line plot of growth rate, colored by season","Fish community functional traits (growth rate) in Georges Bank (GB, top) and the Gulf of Maine (GOM, bottom) based on Fall (red) and Spring (blue) survey data with an increasing long-term trend (orange). Dashed lines represent the long-term annual mean for each survey.",Fish community functional traits (growth rate) in the Mid-Atlantic Bight based on Fall (red) and Spring (blue) survey data with a significant long-term increase (orange) present in the fall. Dashed lines represent the long-term annual mean for each survey.,,images\NewEngland\traits_k_NewEngland,images\MidAtlantic\traits_k_MidAtlantic,,images\MidAtlantic\slide_traits_k_MidAtlantic,images\NewEngland\slide_traits_k_NewEngland,NA,NA,NA,NA -transition,trans_dates,line plot of time between spring and fall transition dates,"Ocean summer length in New England (Georges Bank (GB), top; Gulf of Maine (GOM), bottom): the annual total number of days between the spring thermal transition date and the fall thermal transition date (black), with a long-term increasing trend (orange). Transition dates are based on sea surface temperatures.","Ocean summer length in the Mid-Atlantic Bight: the annual total number of days between the spring thermal transition date and the fall thermal transition date (black), with a long-term increasing trend (orange). Transition dates are based on sea surface temperatures.",NA,images\NewEngland\transition_date_NewEngland,images\MidAtlantic\transition_date_MidAtlantic,NA,images\MidAtlantic\slide_transition_date_MidAtlantic,images\NewEngland\slide_transition_date_NewEngland,NA,NA,NA,NA -wbts-zoo,wbts_zoo,scatter plot with trend line of total dry weight of zooplankton by month,Mesozooplankton biomass phenology at Wilkinson Basin Time Series station: 2005 to 2025. Fitted line (black) shows GAM prediction for 2012 with 95% confidence interval (shaded). Shapes indicate observation year. Vertical lines denote season boundaries. Data for 2025 is incomplete.,NA,NA,images\NewEngland\wbts_zoo_NewEngland,NA,NA,NA,images\NewEngland\slide_wbts_zoo_NewEngland,NA,NA,NA,NA -wea-port-rev,wind_port,stacked bar plot of percent port revenue from leased areas,"Percent of New England port fisheries revenue from wind lease areas from all leases (green), leases not under construction (blue), and active leases (orange).","Percent of Mid-Atlantic port revenue from wind lease areas from leases not under construction (blue) and active leases (orange). Note that North Carolina fisheries management is split between the Northeast and Southeast, and this plot only includes data reported to the Northeast Fisheries Science Center.",NA,images\NewEngland\wea_port_rev_NewEngland,images\MidAtlantic\wea_port_rev_MidAtlantic,NA,images\MidAtlantic\slide_wea_port_rev_MidAtlantic,images\NewEngland\slide_wea_port_rev_NewEngland,NA,NA,NA,NA -wea-spp-rev,wind_revenue,"line plot of revenue in lease areas, colored by species","Revenue of species managed by the New England Fishery Management Council within existing offshore wind lease areas, with significant long-term declines (purple) in Atlantic sea scallop, Atlantic herring, monkfish, and silver hake.",Revenue of species managed by the Mid-Atlantic Fishery Management Council within Active Projects. The declining trendline (purple) is associated with monkfish. ,NA,images/NewEngland/wind_revenue_NewEngland,images/MidAtlantic/wind_revenue_MidAtlantic,NA,images/MidAtlantic/slide_wind_revenue_MidAtlantic,images/NewEngland/slide_wind_revenue_NewEngland,NA,NA,NA,NA +traits-tl,finfish_traits,line plot of trophic level over time,"Fish community functional traits (trophic level) in Georges Bank (GB, top) and the Gulf of Maine (GOM, bottom) based on Fall (red) and Spring (blue) survey data with increasing long-term trend (orange) and increasing short-term trend (dark orange). Dashed lines represent the long-term annual mean for each survey.",Fish community functional traits (trophic level) in the Mid-Atlantic Bight based on Fall (red) and Spring (blue) survey data with a significant long-term decrease (purple) present in the fall. Dashed lines represent the long-term annual mean for each survey.,NA,images\NewEngland\traits-tl_NewEngland,images\MidAtlantic\traits-tl_MidAtlantic,NA,images\MidAtlantic\slide_traits-tl_MidAtlantic,images\NewEngland\slide_traits-tl_NewEngland,NA,NA,NA,NA +traits-k,finfish_traits,"line plot of growth rate, colored by season","Fish community functional traits (growth rate) in Georges Bank (GB, top) and the Gulf of Maine (GOM, bottom) based on Fall (red) and Spring (blue) survey data with an increasing long-term trend (orange). Dashed lines represent the long-term annual mean for each survey.",Fish community functional traits (growth rate) in the Mid-Atlantic Bight based on Fall (red) and Spring (blue) survey data with a significant long-term increase (orange) present in the fall. Dashed lines represent the long-term annual mean for each survey.,,images\NewEngland\traits-k_NewEngland,images\MidAtlantic\traits-k_MidAtlantic,,images\MidAtlantic\slide_traits-k_MidAtlantic,images\NewEngland\slide_traits-k_NewEngland,NA,NA,NA,NA +transition,trans_dates,line plot of time between spring and fall transition dates,"Ocean summer length in New England (Georges Bank (GB), top; Gulf of Maine (GOM), bottom): the annual total number of days between the spring thermal transition date and the fall thermal transition date (black), with a long-term increasing trend (orange). Transition dates are based on sea surface temperatures.","Ocean summer length in the Mid-Atlantic Bight: the annual total number of days between the spring thermal transition date and the fall thermal transition date (black), with a long-term increasing trend (orange). Transition dates are based on sea surface temperatures.",NA,images\NewEngland\transition_NewEngland,images\MidAtlantic\transition_MidAtlantic,NA,images\MidAtlantic\slide_transition_MidAtlantic,images\NewEngland\slide_transition_NewEngland,NA,NA,NA,NA +wbts-zoo,wbts_zoo,scatter plot with trend line of total dry weight of zooplankton by month,Mesozooplankton biomass phenology at Wilkinson Basin Time Series station: 2005 to 2025. Fitted line (black) shows GAM prediction for 2012 with 95% confidence interval (shaded). Shapes indicate observation year. Vertical lines denote season boundaries. Data for 2025 is incomplete.,NA,NA,images\NewEngland\wbts-zoo_NewEngland,NA,NA,NA,images\NewEngland\slide_wbts-zoo_NewEngland,NA,NA,NA,NA +wea-port-rev,wind_port,stacked bar plot of percent port revenue from leased areas,"Percent of New England port fisheries revenue from wind lease areas from all leases (green), leases not under construction (blue), and active leases (orange).","Percent of Mid-Atlantic port revenue from wind lease areas from leases not under construction (blue) and active leases (orange). Note that North Carolina fisheries management is split between the Northeast and Southeast, and this plot only includes data reported to the Northeast Fisheries Science Center.",NA,images\NewEngland\wea-port-rev_NewEngland,images\MidAtlantic\wea-port-rev_MidAtlantic,NA,images\MidAtlantic\slide_wea-port-rev_MidAtlantic,images\NewEngland\slide_wea-port-rev_NewEngland,NA,NA,NA,NA +wea-spp-rev,wind_revenue,"line plot of revenue in lease areas, colored by species","Revenue of species managed by the New England Fishery Management Council within existing offshore wind lease areas, with significant long-term declines (purple) in Atlantic sea scallop, Atlantic herring, monkfish, and silver hake.",Revenue of species managed by the Mid-Atlantic Fishery Management Council within Active Projects. The declining trendline (purple) is associated with monkfish. ,NA,images/NewEngland/wea-spp-rev_NewEngland,images/MidAtlantic/wea-spp-rev_MidAtlantic,NA,images/MidAtlantic/slide_wea-spp-rev_MidAtlantic,images/NewEngland/slide_wea-spp-rev_NewEngland,NA,NA,NA,NA whales-wind,NA,"map of whale hotspots, with lease areas overlaid",NA,NA,North Atlantic Right Whale persistent hotspots (red shading) and wind lease areas (black outlines).,NA,NA,images\BothReports\NARW_hotspots_final_2024.jpg,NA,NA,images\BothReports\NARW_hotspots_final_2024.jpg,NA,NA,NA wind-dev-cumul,NA,"map of proposed wind development areas, with overlaid table of lease information",NA,NA,"All Northeast wind energy lease areas, colored by lease construction status.",NA,NA,images\BothReports\OffshoreWindDevelopmentMap_V3_NicoleMucci,NA,NA,images\BothReports\UpdatedWind_AngelaSilva_2025.png,NA,NA,NA -wind-proposed-dev,wind_dev_speed,"line plot of total area developed, colored by year reported",NA,NA,Total area proposed for wind development on the Northeast Shelf through 2030.,NA,NA,images\BothReports\wind_dev_speed_BothReports,NA,NA,images\BothReports\slide_wind_dev_speed_BothReports,NA,NA,NA +wind-proposed-dev,wind_dev_speed,"line plot of total area developed, colored by year reported",NA,NA,Total area proposed for wind development on the Northeast Shelf through 2030.,NA,NA,images\BothReports\wind-proposed-dev_BothReports,NA,NA,images\BothReports\slide_wind-proposed-dev_BothReports,NA,NA,NA wind-rev,NA,stacked bar plot of percent port revenue from leased areas,Percent of port revenue from wind lease areas for Mid-Atlantic ports that land a majority of New England Fishery Management Council-managed species within the wind lease areas. Percent of revenue is shown for leases not under construction (blue) and active leases (orange).,"Percent of port revenue from wind lease areas for New England ports that land a majority of Mid-Atlantic Fishery Management Council-managed species within the wind lease areas. Percent of revenue is shown for leases not under construction (blue), active leases (orange), and all leases (green).",NA,images\NewEngland\midatlantic_nefmc,images\MidAtlantic\newengland_mafmc,NA,images\MidAtlantic\slide_newengland_mafmc,images\NewEngland\slide_midatlantic_nefmc,NA,NA,NA,NA -zoo-community,zoo_community,line plot of PCA 1 and 2,"Principal component analysis of zooplankton community composition for Georges Bank (GB, top) and the Gulf of Maine (GOM, bottom). Lines show the first two principal components (colors), with a long-term increase in GB (orange).","Principal component analysis of zooplankton community composition in the Mid-Atlantic Bight. Lines show the first two principal components (colors). The long-term declining trendline (purple) is associated with the first principal component. This trend is driven by an increasing abundance of sea butterflies, hyperiid amphipods, echinoderm larvae, arrow worms, and the copepod \textit{Calanus minor}, and a decreasing abundance of the copepods \textit{Pseudocalanus spp.}, \textit{Centropages hamatus}, \textit{Acartia spp.}, and \textit{Temora longicornis}.",,images\NewEngland\zoo_community_NewEngland,images\MidAtlantic\zoo_community_MidAtlantic,NA,images\MidAtlantic\slide_zoo_community_MidAtlantic,images\NewEngland\slide_zoo_community_NewEngland,NA,NA,NA,NA -zoo-diversity,zoo_diversity,line plot of zooplankton Shannon index,"Zooplankton diversity on Georges Bank and in the Gulf of Maine with long term significant increase (orange, GB), based on Shannon diversity index. 2020 surveys were incomplete due to COVID-19.","Zooplankton diversity in the Mid-Atlantic Bight, Shannon diversity index (black) with significant increase (orange line).",NA,images\NewEngland\zoo_diversity_NewEngland,images\MidAtlantic\zoo_diversity_MidAtlantic,NA,images\MidAtlantic\slide_zoo_diversity_MidAtlantic,images\NewEngland\slide_zoo_diversity_NewEngland,NA,NA,NA,NA -zoopanom,zooplankton_index,faceted line plot of 3 guilds of copepods,"Changes in the abundance anomalies of three zooplankton groups in Georges Bank (GB, left) and the Gulf of Maine (GOM, right): large copepods (includes \textit{Calanus finmarchicus}, top), small copepods (including \textit{C. typicus} and \textit{Pseudocalanus spp.}), and Euphausiids (bottom), with significant decreases (short-term, dark purple) in large copepods and long-term increases (orange) in GOM small copepods and GB and GOM euphausiids.","Changes in the abundance anomalies of three zooplankton groups in the Mid-Atlantic Bight: large copepods (includes \textit{Calanus finmarchicus}, top), small copepods (including \textit{C. typicus} and \textit{Pseudocalanus spp.}), and Euphausiids (bottom), with significant decreases (short-term, dark purple; long-term, light purple) in small copepods and long-term increases (orange) in Euphausiids.",NA,images\NewEngland\zooplankton_anomaly_NewEngland,images\MidAtlantic\zooplankton_anomaly_MidAtlantic,NA,images\MidAtlantic\slide_zooplankton_anomaly_MidAtlantic,images\NewEngland\slide_zooplankton_anomaly_NewEngland,NA,NA,NA,NA +zoo-community,zoo_community,line plot of PCA 1 and 2,"Principal component analysis of zooplankton community composition for Georges Bank (GB, top) and the Gulf of Maine (GOM, bottom). Lines show the first two principal components (colors), with a long-term increase in GB (orange).","Principal component analysis of zooplankton community composition in the Mid-Atlantic Bight. Lines show the first two principal components (colors). The long-term declining trendline (purple) is associated with the first principal component. This trend is driven by an increasing abundance of sea butterflies, hyperiid amphipods, echinoderm larvae, arrow worms, and the copepod \textit{Calanus minor}, and a decreasing abundance of the copepods \textit{Pseudocalanus spp.}, \textit{Centropages hamatus}, \textit{Acartia spp.}, and \textit{Temora longicornis}.",,images\NewEngland\zoo-community_NewEngland,images\MidAtlantic\zoo-community_MidAtlantic,NA,images\MidAtlantic\slide_zoo-community_MidAtlantic,images\NewEngland\slide_zoo-community_NewEngland,NA,NA,NA,NA +zoo-diversity,zoo_diversity,line plot of zooplankton Shannon index,"Zooplankton diversity on Georges Bank and in the Gulf of Maine with long term significant increase (orange, GB), based on Shannon diversity index. 2020 surveys were incomplete due to COVID-19.","Zooplankton diversity in the Mid-Atlantic Bight, Shannon diversity index (black) with significant increase (orange line).",NA,images\NewEngland\zoo-diversity_NewEngland,images\MidAtlantic\zoo-diversity_MidAtlantic,NA,images\MidAtlantic\slide_zoo-diversity_MidAtlantic,images\NewEngland\slide_zoo-diversity_NewEngland,NA,NA,NA,NA +zoopanom,zooplankton_index,faceted line plot of 3 guilds of copepods,"Changes in the abundance anomalies of three zooplankton groups in Georges Bank (GB, left) and the Gulf of Maine (GOM, right): large copepods (includes \textit{Calanus finmarchicus}, top), small copepods (including \textit{C. typicus} and \textit{Pseudocalanus spp.}), and Euphausiids (bottom), with significant decreases (short-term, dark purple) in large copepods and long-term increases (orange) in GOM small copepods and GB and GOM euphausiids.","Changes in the abundance anomalies of three zooplankton groups in the Mid-Atlantic Bight: large copepods (includes \textit{Calanus finmarchicus}, top), small copepods (including \textit{C. typicus} and \textit{Pseudocalanus spp.}), and Euphausiids (bottom), with significant decreases (short-term, dark purple; long-term, light purple) in small copepods and long-term increases (orange) in Euphausiids.",NA,images\NewEngland\zoopanom_NewEngland,images\MidAtlantic\zoopanom_MidAtlantic,NA,images\MidAtlantic\slide_zoopanom_MidAtlantic,images\NewEngland\slide_zoopanom_NewEngland,NA,NA,NA,NA zooplankton-season,NA,faceted dot plot of zooplankton abundance,"Abundance (no $m^-2$) of \textit{Calanus finmarchicus} C3-C6 estimated from 200$\mu$ vertical ring net tows. Individual data with fitted lines. Data from 2005-2010 (circles), 2011-2021 (triangles), and 2022-2024 (squares). WBTS station seasonal abundance time series for B) spring, C) summer, D) fall, E) winter. Vertical lines denote season boudnaries. If the seasonal abundance time series is significant, GAM predictions are calculated with day of year set to 1, 100, 200, and 300 for winter, spring, summer, and fall, respectively.",NA,NA,images\NewEngland\Calanusfinmarchicus-JeffreyRunge_2025.png,NA,NA,NA,images\NewEngland\Calanusfinmarchicus-JeffreyRunge_2025.png,NA,NA,NA,NA -megabenthosshifts,benthos_index,faceted line plot showing eastward and northward shifts in megabenthos over time,NA,NA,"Eastward (top) and northward (bottom) shifts in the center of gravity for megabenthos species on the Northeast U.S. Shelf in fall (left) and spring (right), with short-term increasing trend (orange) for spring eastward center of gravity.",NA,NA,images\BothReports\megabenthos_dist_BothReports,NA,NA,images\BothReports\slide_megabenthos_dist_BothReports,NA,NA,NA -smallcopeall-cog,zooplankton_index,faceted line plot of eastward and northward small copepod center of gravity,NA,NA,"Eastward (top) and northward (bottom) shifts in the center of gravity for small copepod species on the Northeast U.S. Shelf in fall (left) and spring (right), with long-term increasing trends (orange) in fall eastward and fall and spring northward center of gravity",NA,NA,images\BothReports\smallcopeall_cog_BothReports,NA,NA,images\BothReports\slide_smallcopeall_cog_BothReports,NA,NA,NA -lgcopeall-cog,zooplankton_index,faceted line plot of eastward and northward large copepod center of gravity,NA,NA,"Eastward (top) and northward (bottom) shifts in the center of gravity for large copepod species (\textit{Calanus finmarchicus}, \textit{Metridia lucens}, \textit{Calanus minor}, \textit{Eucalanus sp.}, \textit{Calanus spp.}) on the Northeast U.S. Shelf in fall (left) and spring (right). ",NA,NA,images\BothReports\lgcopeall_cog_BothReports,NA,NA,images\BothReports\slide_lgcopeall_cog_BothReports,NA,NA,NA -euph-cog,zooplankton_index,faceted line plot of eastward and northward euphausiid center of gravity,NA,NA,Eastward (top) and northward (bottom) shifts in the center of gravity for Euphausiid species on the Northeast U.S. Shelf in fall (left) and spring (right). ,NA,NA,images\BothReports\euph_cog_BothReports,NA,NA,images\BothReports\slide_euph_cog_BothReports,NA,NA,NA +megabenthosshifts,benthos_index,faceted line plot showing eastward and northward shifts in megabenthos over time,NA,NA,"Eastward (top) and northward (bottom) shifts in the center of gravity for megabenthos species on the Northeast U.S. Shelf in fall (left) and spring (right), with short-term increasing trend (orange) for spring eastward center of gravity.",NA,NA,images\BothReports\megabenthosshifts_BothReports,NA,NA,images\BothReports\slide_megabenthosshifts_BothReports,NA,NA,NA +smallcopeall-cog,zooplankton_index,faceted line plot of eastward and northward small copepod center of gravity,NA,NA,"Eastward (top) and northward (bottom) shifts in the center of gravity for small copepod species on the Northeast U.S. Shelf in fall (left) and spring (right), with long-term increasing trends (orange) in fall eastward and fall and spring northward center of gravity",NA,NA,images\BothReports\smallcopeall-cog_BothReports,NA,NA,images\BothReports\slide_smallcopeall-cog_BothReports,NA,NA,NA +lgcopeall-cog,zooplankton_index,faceted line plot of eastward and northward large copepod center of gravity,NA,NA,"Eastward (top) and northward (bottom) shifts in the center of gravity for large copepod species (\textit{Calanus finmarchicus}, \textit{Metridia lucens}, \textit{Calanus minor}, \textit{Eucalanus sp.}, \textit{Calanus spp.}) on the Northeast U.S. Shelf in fall (left) and spring (right). ",NA,NA,images\BothReports\lgcopeall-cog_BothReports,NA,NA,images\BothReports\slide_lgcopeall-cog_BothReports,NA,NA,NA +euph-cog,zooplankton_index,faceted line plot of eastward and northward euphausiid center of gravity,NA,NA,Eastward (top) and northward (bottom) shifts in the center of gravity for Euphausiid species on the Northeast U.S. Shelf in fall (left) and spring (right). ,NA,NA,images\BothReports\euph-cog_BothReports,NA,NA,images\BothReports\slide_euph-cog_BothReports,NA,NA,NA mab-oa,,map of glider tracks and aragonite measurements in New York Bight,NA,NA,"Locations where bottom aragonite saturation state ($\Omega_{Arag}$; summer only: June-August) were at or below the laboratory-derived sensitivity level for Atlantic sea scallop (left panel) and longfin squid (right panel) for the time periods 2007-2022 (dark cyan), 2023 only (magenta) and 2024 only (cyan). Gray circles indicate locations where bottom $\Omega_{Arag}$ values were above the species specific sensitivity values.",NA,NA,images\BothReports\final_bottom_omega_2026,NA,NA,images\BothReports\slide_final_bottom_omega_2026,NA,NA,NA priority-2025,2025_prioritization,table of 2025 high prioirty items,,,NA,NA,NA,images\Both_Regions\SOE Prioritization 2025,NA,NA,images\Both_Regions\SOE Prioritization 2025,NA,NA,NA -advection-index,advection,line plot of net advection at 3 depths,"Net advection in June across the Southern New England and Georges Bank continental shelf break within 3 depth bands, with increasing long-term trends in the middle and bottom depths (orange).","Net advection in June across the Mid-Atlantic continental shelf break within 3 depth bands, with significant long-term declines (purple) in >40m and <15m. ",NA,images\NewEngland\advection_index_NewEngland,images\MidAtlantic\advection_index_MidAtlantic,NA,images\MidAtlantic\slide_advection_index_MidAtlantic,images\NewEngland\slide_advection_index_NewEngland,NA,NA,NA,NA -seasonal-oisst-anom,seasonal_oisst_anom,faceted line plot of temperature anomalies by season,"Seasonal Optimum Interpolation Sea Surface Temperature (OISST) anomaly by season for the Gulf of Maine (GOM, top) and Georges Bank (GB, bottom), with long-term increasing trends (orange).","Seasonal Optimum Interpolation Sea Surface Temperature (OISST) anomaly by season for the Mid-Atlantic Bight, with long-term increasing trends (orange) in spring, summer, and fall, and short-term increasing trend in spring.",NA,images\NewEngland\seasonal_oisst_anom_NewEngland,images\MidAtlantic\seasonal_oisst_anom_MidAtlantic,NA,images\MidAtlantic\slide_seasonal_oisst_anom_MidAtlantic,NA,NA,NA,NA,NA -bottom-temp-anom,bottom_temp_model_anom,faceted line plot of temperature anomalies by season,"GLORYS (black) and debiased Regional Ocean Modeling System (ROMS) (red) seasonal bottom temperature anomaly for the Gulf of Maine (GOM, top) and Georges Bank (GB, bottom), with long-term increasing trends (orange).","GLORYS (black) and debiased Regional Ocean Modeling System (ROMS) (red) seasonal bottom temperature anomaly in the Mid-Atlantic Bight, with long-term increasing trends (orange).",NA,images\NewEngland\bottom_temp_anom_NewEngland,images\MidAtlantic\bottom_temp_anom_MidAtlantic,NA,images\MidAtlantic\slide_bottom_temp_anom_MidAtlantic,NA,NA,NA,NA,NA -bottom-temp-insitu,bottom_temp_insitu,line plot of insitu bottom temperature ,"Annual in situ bottom temperature anomaly for Georges Bank (GB, top) and the Gulf of Maine (GOM, bottom), with long-term increasing trends (orange).","Annual in situ bottom temperature anomaly in the Mid-Atlantic, with long-term increasing trends (orange).",NA,images\NewEngland\bottom_temp_insitu_NewEngland,images\MidAtlantic\bottom_temp_insitu_MidAtlantic,NA,images\MidAtlantic\slide_bottom_temp_insitu_MidAtlantic,images\NewEngland\bottom_temp_insitu_NewEngland,NA,NA,NA,NA +advection-index,advection,line plot of net advection at 3 depths,"Net advection in June across the Southern New England and Georges Bank continental shelf break within 3 depth bands, with increasing long-term trends in the middle and bottom depths (orange).","Net advection in June across the Mid-Atlantic continental shelf break within 3 depth bands, with significant long-term declines (purple) in >40m and <15m. ",NA,images\NewEngland\advection-index_NewEngland,images\MidAtlantic\advection-index_MidAtlantic,NA,images\MidAtlantic\slide_advection-index_MidAtlantic,images\NewEngland\slide_advection-index_NewEngland,NA,NA,NA,NA +seasonal-oisst-anom,seasonal_oisst_anom,faceted line plot of temperature anomalies by season,"Seasonal Optimum Interpolation Sea Surface Temperature (OISST) anomaly by season for the Gulf of Maine (GOM, top) and Georges Bank (GB, bottom), with long-term increasing trends (orange).","Seasonal Optimum Interpolation Sea Surface Temperature (OISST) anomaly by season for the Mid-Atlantic Bight, with long-term increasing trends (orange) in spring, summer, and fall, and short-term increasing trend in spring.",NA,images\NewEngland\seasonal-oisst-anom_NewEngland,images\MidAtlantic\seasonal-oisst-anom_MidAtlantic,NA,images\MidAtlantic\slide_seasonal-oisst-anom_MidAtlantic,NA,NA,NA,NA,NA +bottom-temp-anom,bottom_temp_model_anom,faceted line plot of temperature anomalies by season,"GLORYS (black) and debiased Regional Ocean Modeling System (ROMS) (red) seasonal bottom temperature anomaly for the Gulf of Maine (GOM, top) and Georges Bank (GB, bottom), with long-term increasing trends (orange).","GLORYS (black) and debiased Regional Ocean Modeling System (ROMS) (red) seasonal bottom temperature anomaly in the Mid-Atlantic Bight, with long-term increasing trends (orange).",NA,images\NewEngland\bottom-temp-anom_NewEngland,images\MidAtlantic\bottom-temp-anom_MidAtlantic,NA,images\MidAtlantic\slide_bottom-temp-anom_MidAtlantic,NA,NA,NA,NA,NA +bottom-temp-insitu,bottom_temp_insitu,line plot of insitu bottom temperature ,"Annual in situ bottom temperature anomaly for Georges Bank (GB, top) and the Gulf of Maine (GOM, bottom), with long-term increasing trends (orange).","Annual in situ bottom temperature anomaly in the Mid-Atlantic, with long-term increasing trends (orange).",NA,images\NewEngland\bottom-temp-insitu_NewEngland,images\MidAtlantic\bottom-temp-insitu_MidAtlantic,NA,images\MidAtlantic\slide_bottom-temp-insitu_MidAtlantic,images\NewEngland\bottom-temp-insitu_NewEngland,NA,NA,NA,NA mcs-bottom-gom,NA,bottom marine cold spell for GOM,Marine cold spells based on detrended GLORYS12V1 bottom temperature from October 2024 though October 2025 in the Gulf of Maine. Cold spells defined by events where observered temperature (black) exceeds a threshold (green) based on the climatology (blue). Blue shaded areas show the cold spell events with the largest event in dark blue. ,NA,NA,images\NewEngland\SOE_2026_GOM_Bottom_MCS.pdf,NA,NA,NA,images\NewEngland\SOE_2026_GOM_Bottom_MCS.pdf,NA,NA,NA,NA mcs-bottom-gb,NA,bottom marine cold spell for GB,Marine cold spells based on detrended GLORYS12V1 bottom temperature from January 2024 though June 2025 in Georges Bank. Cold spells defined by events where observered temperature (black) exceeds a threshold (green) based on the climatology (blue). Blue shaded areas show the cold spell events with the largest event in dark blue. ,NA,NA,images\NewEngland\SOE_2026_GB_Bottom_MCS.pdf,NA,NA,NA,images\NewEngland\SOE_2026_GB_Bottom_MCS.pdf,NA,NA,NA,NA mcs-bottom-mab,NA,bottom marine cold spell for MAB,NA,Marine cold spells based on detrended GLORYS12V1 bottom temperature from July 2024 though December 2025 in the MAB. Cold spells defined by events where observered temperature (black) exceeds a threshold (green) based on the climatology (blue). Blue shaded areas show the cold spell events with the largest event in dark blue. ,NA,NA,images\MidAtlantic\SOE_2026_MAB_Bottom_MCS.pdf,NA,images\MidAtlantic\SOE_2026_MAB_Bottom_MCS.pdf,NA,NA,NA,NA,NA diff --git a/utils/figure_stats_summaries.csv b/utils/figure_stats_summaries.csv new file mode 100644 index 00000000..9fb4b130 --- /dev/null +++ b/utils/figure_stats_summaries.csv @@ -0,0 +1,9 @@ +"Indicator","Region","File_Generated","Group1","Group2","mean","min","max","median","sd","upper","lower","recent_value","status","aicc_long_term_linear_normal_error","aicc_long_term_linear_ar1_error","aicc_short_term_ar1_10_years","trend_long_term_linear_normal_error","trend_long_term_linear_ar1_error","trend_short_term_ar1_10_years","pval_long_term_linear_normal_error","pval_long_term_linear_ar1_error","pval_short_term_ar1_10_years","sig_long_term_linear_normal_error","sig_long_term_linear_ar1_error","sig_short_term_ar1_10_years" +"NARW-calf-abundance","BothReports","C:/Users/abigail.tyrell/Documents/code/READ-EDAB-SOE_reports/images/MidAtlantic/NARW-calf-abundance_BothReports_2026-06-05.png","Unit",NA,14.0217391304348,0,39,12,7.84995153682077,21.8716906672556,6.17178759361401,11,"near average",324.982523304814,320.465694635366,NA,"negative","negative","positive",0.196154343776347,0.350345003505441,0.464,FALSE,FALSE,FALSE +"forage_dist","BothReports","C:/Users/abigail.tyrell/Documents/code/READ-EDAB-SOE_reports/images/MidAtlantic/forage_dist_BothReports_2026-06-05.png","Eastward","Fall", 368.2233, 296.0486, 422.6559, 372.3723,26.65062, 394.8739, 341.5726, 377.5155,near average,389.2504,385.0883,NA,negative,negative,positive,0.0068080635,0.041279516,0.248,TRUE,TRUE,FALSE +"forage_dist","BothReports","C:/Users/abigail.tyrell/Documents/code/READ-EDAB-SOE_reports/images/MidAtlantic/forage_dist_BothReports_2026-06-05.png","Eastward","Spring", 365.4830, 280.2950, 434.0439, 368.2428,39.81883, 405.3018, 325.6641, 400.7611,near average,423.3014,422.5800,NA,negative,negative,negative,0.0213540262,0.063833417,0.740,TRUE,FALSE,FALSE +"forage_dist","BothReports","C:/Users/abigail.tyrell/Documents/code/READ-EDAB-SOE_reports/images/MidAtlantic/forage_dist_BothReports_2026-06-05.png","Northward","Fall",4532.9245,4477.0147,4565.9099,4537.7385,20.39933,4553.3238,4512.5252,4545.7290,near average,361.9699,362.4382,NA,positive,positive,positive,0.0002368742,0.003268341,0.578,TRUE,TRUE,FALSE +"forage_dist","BothReports","C:/Users/abigail.tyrell/Documents/code/READ-EDAB-SOE_reports/images/MidAtlantic/forage_dist_BothReports_2026-06-05.png","Northward","Spring",4534.0735,4461.5463,4595.1873,4533.4704,30.47439,4564.5479,4503.5991,4560.4094,near average,400.4968,400.0005,NA,positive,positive,negative,0.0092369891,0.038844195,0.186,TRUE,TRUE,FALSE +"comdat_profit","MidAtlantic","C:/Users/abigail.tyrell/Documents/code/READ-EDAB-SOE_reports/images/MidAtlantic/comdat_profit_MidAtlantic_2026-06-05.png","Cost Index",NA,1.4721200,0.9770000,2.368000,1.4990000,0.3105276,1.7826476,1.1615924,1.4080000,near average,26.938960543, 23.611039,NA,negative,negative,positive,6.878967e-02,0.203677064,0.308,FALSE,FALSE,FALSE +"comdat_profit","MidAtlantic","C:/Users/abigail.tyrell/Documents/code/READ-EDAB-SOE_reports/images/MidAtlantic/comdat_profit_MidAtlantic_2026-06-05.png","Profit Index",NA,0.6459368,0.1789216,1.176049,0.6199869,0.2862698,0.9322065,0.3596670,0.2485795,below average,-0.857427202,-10.744646,NA,positive,positive,negative,5.713483e-08,0.005297415,0.080,TRUE,TRUE,FALSE +"comdat_profit","MidAtlantic","C:/Users/abigail.tyrell/Documents/code/READ-EDAB-SOE_reports/images/MidAtlantic/comdat_profit_MidAtlantic_2026-06-05.png","Revenue Index",NA,0.8938800,0.3060000,1.357000,0.9430000,0.2877061,1.1815861,0.6061739,0.3500000,below average,-0.004148016, -2.795973,NA,positive,positive,negative,8.104270e-08,0.004908972,0.062,TRUE,TRUE,FALSE diff --git a/utils/image_functions.R b/utils/image_functions.R new file mode 100644 index 00000000..16ae8872 --- /dev/null +++ b/utils/image_functions.R @@ -0,0 +1,448 @@ +#' Create a Standardized Filename +#' +#' Constructs a standardized file path by combining an indicator name, a geographical region, +#' the current system date, and a file extension. +#' +#' @param indicator A character string specifying the metric or indicator name. +#' @param file_region A character string specifying the geographical region or strata. +#' @param dir A character string specifying the target directory path. Defaults to +#' the variable \code{out_dir} evaluated from the calling environment. +#' @param extension A character string specifying the file extension (including the period). +#' Defaults to \code{".png"}. +#' +#' @return A character string containing the concatenated file path structured as: +#' \code{dir/indicator_file_region_YYYY-MM-DD.extension} +#' +#' @export +#' +#' @examples +#' \dontrun{ +#' # Uses out_dir from environment +#' out_dir <- "output/plots" +#' create_filename("benthic_biomass", "georges_bank") +#' +#' # Overriding defaults +#' create_filename("sst", "mid_atlantic", dir = "data/raw", extension = ".csv") +#' } +create_filename <- function( + indicator, + file_region, + dir = out_dir, + extension = ".png" +) { + file.path( + dir, + paste0( + indicator, + "_", + file_region, + "_", + Sys.Date(), + extension + ) + ) +} + +#' Add Ecodata Source Attribution Caption to ggplot +#' +#' Appends a standardized data provenance caption to an existing \code{ggplot2} object. +#' The caption dynamically extracts tracking metadata (branch name, abbreviated commit SHA, +#' and packaging date) directly from the installed \code{ecodata} package description. +#' +#' @param p A \code{ggplot2} plot object to be annotated. +#' @param plt_indicator A character string matching a \code{chunkName} key within the reference CSV file. +#' @param plt_key A character string mapping the file path to a figure caption summary CSV file. +#' Defaults to a file named \code{"figure_captions_summary.csv"} located inside a \code{utils/} +#' directory relative to the project root (via \code{here::here()}). +#' +#' @return An updated \code{ggplot2} plot object incorporating the wrapped, small-font source caption. +#' +#' @export +#' +#' @examples +#' \dontrun{ +#' library(ggplot2) +#' p <- ggplot(mtcars, aes(mpg, wt)) + geom_point() +#' # Appends ecodata package provenance info based on matching chunk ID +#' add_ecodata_name(p, plt_indicator = "sst_anomaly_chunk") +#' } + +add_ecodata_name <- function( + p, + plt_indicator, + plt_key = here::here("utils/figure_captions_summary.csv") +) { + key <- read.csv(plt_key) + name <- key$ecodata_object[key$chunkName == plt_indicator] + p <- p + + ggplot2::labs( + caption = paste0( + "Source: ecodata::", + name, + " (", + packageDescription("ecodata")$RemoteRef, + " branch, commit ", + packageDescription("ecodata")$RemoteSha |> substr(1, 7), + ", packaged ", + packageDescription("ecodata")$Packaged |> substr(1, 10), + ")" + ) |> + stringr::str_wrap(width = 50) + ) + + ggplot2::theme(plot.caption = ggplot2::element_text(size = 8)) + + return(p) +} + +#' Extract Data from a ggplot Point Layer +#' +#' Iterates through all geometric layers of a built or unbuilt \code{ggplot2} object +#' to identify and return the data matrix driving a scatter or point geometry layer +#' (such as \code{geom_point}), using the structural presence of the \code{shape} +#' column as the layer identifier. +#' +#' @details +#' The function relies on \code{\link[ggplot2]{layer_data}} to extract evaluated +#' aesthetics. If a plot contains multiple point layers, this function will overwrite +#' the \code{plt_data} object sequentially and return data exclusively from the +#' \emph{last} identified point layer. If no layers contain a \code{shape} column, +#' the function will trigger an error due to an unassigned return variable. +#' +#' @param p A \code{ggplot2} plot object containing at least one point layer. +#' +#' @return A data frame containing the evaluated aesthetic mapping data (e.g., +#' \code{x}, \code{y}, \code{shape}, \code{colour}, \code{size}) corresponding +#' to the isolated point layer. +#' +#' @export +#' +#' @examples +#' \dontrun{ +#' library(ggplot2) +#' # Construct a multi-layered plot +#' p <- ggplot(mtcars, aes(mpg, wt)) + +#' geom_line() + +#' geom_point(shape = 21, fill = "blue") +#' +#' # Extract structural coordinate matrix for the geom_point layer +#' pt_data <- return_point_data(p) +#' head(pt_data) +#' } + +return_point_data <- function(p) { + n_layers <- length(p$layers) + + for (i in 1:n_layers) { + dat <- ggplot2::layer_data(p, i) + # print(head(dat)) + # shape is only for points, so this will grab data from the point layer + if ("shape" %in% names(dat)) { + plt_data <- dat + } + } + + return(plt_data) +} + +#' Map Faceted Plot Points to Layout Metadata +#' +#' Extracts built layer data from a ggplot object and joins it back to the +#' plot's structural layout matrix to explicitly decode which panel corresponds +#' to which facet variables. +#' +#' @param p A \code{ggplot2} plot object containing facet layers (e.g., \code{facet_wrap} +#' or \code{facet_grid}). +#' @param p_dat A data frame representing a built plot layer (typically extracted from +#' \code{ggplot2::ggplot_build(p)$data[[i]]}) containing columns \code{x}, \code{y}, and \code{PANEL}. +#' +#' @return A data frame/tibble containing the raw coordinates (\code{x} and \code{y}) +#' bound to their explicit facet mapping variables, with the internal \code{PANEL} column removed. +#' +#' @export +#' +#' @examples +#' \dontrun{ +#' library(ggplot2) +#' p <- ggplot(mpg, aes(displ, hwy)) + geom_point() + facet_wrap(~class) +#' built_p <- ggplot_build(p) +#' +#' # Extract layer 1 data and map panels to 'class' labels +#' facet_data <- return_faceted_plt_data(p, built_p$data[[1]]) +#' } + +return_faceted_plt_data <- function(p, p_dat) { + plt_data <- p_dat |> + dplyr::select(x, y, PANEL) + + # get facet data to join + metadata <- ggplot2::ggplot_build(p) + facet_labels <- metadata$layout$layout |> + dplyr::select(-c(ROW, COL, SCALE_X, SCALE_Y, COORD)) + + output <- dplyr::left_join(plt_data, facet_labels, by = "PANEL") |> + dplyr::select(-PANEL) + + return(output) +} + +#' Decode Hex Colors to Categorical Scale Labels +#' +#' Extracts built layer data containing hexadecimal color assignments and cross-references +#' them against the plot's active color scale mapping key to append the human-readable +#' variable label names. +#' +#' @param p A \code{ggplot2} plot object containing an active discrete or continuous color scale. +#' @param p_dat A data frame representing a built plot layer (typically extracted from +#' \code{ggplot2::ggplot_build(p)$data[[i]]}) containing columns \code{x}, \code{y}, and \code{colour}. +#' +#' @return A data frame/tibble containing the coordinates (\code{x} and \code{y}) +#' bound to a new column \code{Var} containing the decoded categorical text labels, +#' with the internal \code{colour} hex values removed. +#' +#' @export +#' +#' @examples +#' \dontrun{ +#' library(ggplot2) +#' p <- ggplot(iris, aes(Sepal.Length, Sepal.Width, color = Species)) + geom_point() +#' built_p <- ggplot_build(p) +#' +#' # Extract layer 1 data and map hex values back to "Species" categories +#' colored_data <- return_color_plt_data(p, built_p$data[[1]]) +#' } + +return_color_plt_data <- function(p, p_dat) { + plt_data <- p_dat |> + # might need to keep more of the columns if the plot is faceted? + dplyr::select(x, y, colour) + + # get color data to join + metadata <- ggplot2::ggplot_build(p) + color_scale <- metadata$plot$scales$get_scales("colour") + + # Map the labels to their hex colors + color_key <- tibble::tibble( + hex = color_scale$map(color_scale$get_breaks()), + Var = color_scale$get_labels() + ) + + output <- dplyr::left_join(plt_data, color_key, by = c("colour" = "hex")) |> + dplyr::select(-colour) + + return(output) +} + +# # A flexible function to generate and save a plot +# save_plot <- function( +# plot_expression, +# indicator, +# report = region, +# save_dir = out_dir, +# ... +# ) { +# # Execute the code to create the plot +# p <- eval(plot_expression) +# +# # Check if the plot object is valid before saving +# if (inherits(p, "ggplot") || inherits(p, "ggarrange")) { +# message(report) +# message(indicator) +# message(out_dir) +# fname <- create_filename( +# indicator = indicator, +# file_region = report, +# dir = save_dir +# ) +# ggplot2::ggsave( +# filename = fname, +# plot = p, +# bg = "white", +# ... +# ) +# message("Plot saved to: ", fname) +# } else { +# stop("Plot object is not a valid ggplot or ggarrange object.") +# } +# } + +#' Evaluate, Save, and Log Plot Trend Metrics +#' +#' Evaluates a plot expression, annotates it with data source information, exports the +#' image to disk, and conditionally decomposes the plot's point layers to calculate +#' and append descriptive summary metrics and trend indicators to a shared log file. +#' +#' @details +#' The function uses conditional logic based on the structural properties of the parsed +#' plot (such as facet definitions via \code{FacetNull} or unique aesthetic hexadecimal values) +#' to isolate stratification layers. It relies heavily on parent environment variables if +#' default parameters are left unassigned. +#' +#' \strong{Warning:} There is a typographical bug in an internal error message (\code{inidcator} +#' instead of \code{indicator}). If a structural extraction fails, a console notification will +#' print but execution won't break so the image asset is preserved. +#' +#' @param plot_expression An unevaluated R expression or language object that returns a +#' \code{ggplot} or \code{ggarrange} object when evaluated (e.g., \code{quote(my_plot_function())}). +#' @param indicator A character string defining the target metric code name. Used both for +#' file naming and log tracking. +#' @param report A character string specifying the geographic region or report strata. +#' Defaults to the variable \code{region} looked up in the parent calling environment. +#' @param save_dir A character string tracking the plot storage path. Defaults to the variable +#' \code{out_dir} looked up in the parent calling environment. +#' @param output_summary A logical value indicating whether the internal data matrix should +#' be reverse-engineered to yield statistical and trend records. Defaults to \code{TRUE}. +#' @param summary_file A character string defining the storage path for the aggregated project +#' statistics summary spreadsheet. Defaults to \code{"figure_stats_summaries.csv"} inside +#' \code{utils/} via \code{here::here()}. +#' @param key A character string mapping the location of the figure captions indexing CSV. +#' Defaults to \code{"figure_captions_summary.csv"} inside \code{utils/} via \code{here::here()}. +#' @param ... Additional keyword arguments passed directly to \code{\link[ggplot2]{ggsave}} +#' (such as \code{width}, \code{height}, or \code{dpi}). +#' +#' @return No return value. The function acts entirely through structural side effects: +#' writing an image file to disk and appending tabular summary logs to an external file. +#' +#' @export +#' +#' @seealso +#' \code{\link{create_filename}}, \code{\link{add_ecodata_name}}, +#' \code{\link{return_point_data}}, \code{\link{summary_stats}}, \code{\link{trend_summaries}} +#' +#' @examples +#' \dontrun{ +#' # Assign necessary environment tokens assumed by function defaults +#' region <- "mid_atlantic" +#' out_dir <- "./outputs" +#' +#' # Define an expression generating a point plot +#' expr <- quote({ +#' ggplot2::ggplot(mtcars, ggplot2::aes(mpg, wt)) + ggplot2::geom_point() +#' }) +#' +#' # Run pipeline +#' save_plot( +#' plot_expression = expr, +#' indicator = "vehicle_weight_metrics", +#' output_summary = TRUE +#' ) +#' } + +save_plot <- function( + plot_expression, + indicator, + report = region, + save_dir = out_dir, + output_summary = TRUE, + summary_file = here::here("utils/figure_stats_summaries.csv"), + key = here::here("utils/figure_captions_summary.csv"), + ... +) { + # Execute the code to create the plot + p <- eval(plot_expression) |> + add_ecodata_name( + plt_indicator = indicator, + plt_key = key + ) + + if (inherits(p, "ggplot") || inherits(p, "ggarrange")) { + message(report) + message(indicator) + message(out_dir) + + fname <- create_filename( + indicator = indicator, + file_region = report, + dir = save_dir + ) + + ggplot2::ggsave( + filename = fname, + plot = p, + bg = "white", + ... + ) + message("Plot saved to: ", fname) + + #### extract data for summary table ============================================ + if (output_summary) { + target_plot <- if (inherits(p, "ggarrange")) p$plots[[1]] else p + + raw_dat <- return_point_data(target_plot) + + # extract simple data if there are no facets or colors + if ( + length(unique(raw_dat$colour)) == 1 & + inherits(target_plot$facet, "FacetNull") + ) { + dat <- raw_dat |> + dplyr::select(x, y) + } else if (!inherits(target_plot$facet, "FacetNull")) { + # extract data by facet if there are facets + dat <- return_faceted_plt_data(target_plot, p_dat = raw_dat) + } else if (length(unique(raw_dat$colour)) > 1) { + # extract data by color if there are colors + dat <- return_color_plt_data(target_plot, p_dat = raw_dat) + } else { + message(paste0( + "Unable to extract plot data for ", + inidcator, + ". The underlying ggplot may be missing the geom_point aesthetic, or the plot structure may be too complex for the current extraction functions." + )) + # exit without throwing error so the plot can still be saved without summary stats + return() + } + + # 5. Group by our new literal labels and execute summary functions + group <- colnames(dat)[-which(colnames(dat) %in% c("x", "y"))] + + if (length(group) == 0) { + summary_rows <- dplyr::bind_cols( + dat |> summary_stats(), + dat |> trend_summaries() + ) |> + dplyr::mutate(Group1 = "Unit", Group2 = NA, .before = 1) + } else { + summary_rows <- dat |> + dplyr::group_by(dplyr::across(dplyr::all_of(group))) |> + dplyr::reframe( + stats = summary_stats(dplyr::pick(dplyr::everything())), + trends = trend_summaries(dplyr::pick(dplyr::everything())) + ) + } + + if (length(group) == 1) { + summary_rows <- summary_rows |> + # add dummy group 2 col so they line up + dplyr::mutate(Group2 = NA, .after = 1) + } + + output <- summary_rows |> + dplyr::mutate( + Indicator = indicator, + Region = report, + File_Generated = file.path(fname), + .before = 1 + ) + + # 6. Append to the shared summary CSV file + summary_path <- file.path(summary_file) + append_mode <- file.exists(summary_path) + + write.table( + output, + file = summary_path, + append = append_mode, + sep = ",", + row.names = FALSE, + col.names = !append_mode + ) + + message( + "Grouped summary metrics appended to: ", + summary_path + ) + } + } else { + stop("Plot object is not a valid ggplot or ggarrange object.") + } +}