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"table": true, "tojson": true }, { "name": "swfwmdtbseg", "title": "Spatial data object of SWFWMD Tampa Bay segments", "object": "swfwmdtbseg", "class": [ "sf", "data.frame" ], "fields": [ "segment", "Shape" ], "rows": 7, "table": false, "tojson": true }, { "name": "swfwmdtbseg2024", "title": "Spatial data object of SWFWMD Tampa Bay segments, 2024", "object": "swfwmdtbseg2024", "class": [ "sf", "data.frame" ], "fields": [ "segment", "geometry" ], "rows": 7, "table": false, "tojson": true }, { "name": "targets", "title": "Bay segment targets", "object": "targets", "class": [ "data.frame" ], "fields": [ "bay_segment", "name", "chla_target", "chla_smallex", "chla_thresh", "la_target", "la_smallex", "la_thresh" ], "rows": 9, "table": true, "tojson": true }, { "name": "tbniref", "title": "Reference conditions for Tampa Bay Nekton Index metrics", "object": "tbniref", "class": [ "grouped_df", "tbl_df", "tbl", "data.frame" ], "fields": [ "bay_segment", "Season", "NumTaxa_P5", "NumTaxa_P95", 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"name": "tbsegdetailbcbs", "title": "Spatial data object of detailed Tampa Bay segments, Boca Ciega Bay as southern portion", "object": "tbsegdetailbcbs", "class": [ "sf", "data.frame" ], "fields": [ "long_name", "bay_segment", "geometry" ], "rows": 7, "table": false, "tojson": true }, { "name": "tbseglines", "title": "Spatial data object of lines defining major Tampa Bay segments", "object": "tbseglines", "class": [ "sf", "data.frame" ], "fields": [ "Id", "geometry" ], "rows": 3, "table": true, "tojson": true }, { "name": "tbsegshed", "title": "Spatial data object of Tampa Bay segments plus watersheds", "object": "tbsegshed", "class": [ "sf", "data.frame" ], "fields": [ "long_name", "bay_segment", "geometry" ], "rows": 7, "table": false, "tojson": true }, { "name": "tbshed", "title": "Spatial data object of Tampa Bay watershed", "object": "tbshed", "class": [ "sf", "data.frame" ], "fields": [ "Acres", "geometry" ], "rows": 1, "table": false, "tojson": true }, { "name": "tidalcreeks", "title": "Spatial data object of tidal creeks in Impaired Waters Rule, Run 67", "object": "tidalcreeks", "class": [ "sf", "data.frame" ], "fields": [ "id", "name", "JEI", "wbid", "class", "Creek_Length_m", "geometry" ], "rows": 623, "table": false, "tojson": true }, { "name": "tidaltargets", "title": "Tidal creek nitrogen targets", "object": "tidaltargets", "class": [ "data.frame" ], "fields": [ "region", "prioritize", "investigate", "caution" ], "rows": 2, "table": true, "tojson": true }, { "name": "transect", "title": "Seagrass transect data for Tampa Bay current as of 12052025", "object": "transect", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "Crew", "MonitoringAgency", "Date", "Transect", "Site", "Depth", "Savspecies", "SeagrassEdge", "var", "aveval", "sdval" ], "rows": 164724, "table": true, "tojson": true }, { "name": "trnlns", "title": "Seagrass transect locations", "object": "trnlns", "class": [ "sf", "data.frame" ], "fields": [ "OBJECTID", "Site", "Shape_Leng", "MonAgency", "ActiveYN", "Comments", "bearing", "bay_segment", "geometry" ], "rows": 66, "table": true, "tojson": true }, { "name": "trnpts", "title": "Seagrass transect starting locations", "object": "trnpts", "class": [ "sf", "data.frame" ], "fields": [ "SEGMENT", "TRANSECT", "TRAN_ID", "Metermark", "ID", "LAT_DD", "LONG_DD", "MonAgency", "STATUS", "Comments", "bay_segment", "geometry" ], "rows": 66, "table": true, "tojson": true } ], "_help": [ { "page": "acres", "title": "Tampa Bay intertidal and supratidal land use and cover", "concept": [ "data" ], "topics": [ "acres" ] }, { "page": "ambispp", "title": "AMBI species group assignments for Tampa Bay benthic taxa", "concept": [ "data" ], "topics": [ "ambispp" ] }, { "page": "anlz_ambimed", "title": "Get annual medians of AMBI scores by bay segment", "concept": [ "analyze" ], "topics": [ "anlz_ambimed" ] }, { "page": "anlz_ambiscr", "title": "Get AMBI scores for benthic stations", "concept": [ "analyze" ], "topics": [ "anlz_ambiscr" ] }, { "page": "anlz_attain", "title": "Get attainment categories", "concept": [ "analyze" ], "topics": [ "anlz_attain" ] }, { "page": "anlz_attainsite", "title": "Get site attainments", "concept": [ "analyze" ], "topics": [ "anlz_attainsite" ] }, { "page": "anlz_avedat", "title": "Estimate annual means", "concept": [ "analyze" ], "topics": [ "anlz_avedat" ] }, { "page": "anlz_avedatsite", "title": "Estimate annual means by site", "concept": [ "analyze" ], "topics": [ "anlz_avedatsite" ] }, { "page": "anlz_enteromap", "title": "Assign threshold categories to Enterococcus data", "topics": [ "anlz_enteromap" ] }, { "page": "anlz_fibmap", "title": "Assign threshold categories to Fecal Indicator Bacteria (FIB) data", "concept": [ "anlz" ], "topics": [ "anlz_fibmap" ] }, { "page": "anlz_fibmatrix", "title": "Analyze Fecal Indicator Bacteria categories over time by station or bay segment", "concept": [ "show" ], "topics": [ "anlz_fibmatrix" ] }, { "page": "anlz_fibwetdry", "title": "Identify Fecal Indicator Bacteria samples as coming from a 'wet' or 'dry' time period", "topics": [ "anlz_fibwetdry" ] }, { "page": "anlz_hmpreport", "title": "Evaluate Habitat Master Plan progress for report card", "concept": [ "analyze" ], "topics": [ "anlz_hmpreport" ] }, { "page": "anlz_hydroload", "title": "Estimate hydrological estimates and adjustment factors for bay segments", "concept": [ "analyze" ], "topics": [ "anlz_hydroload" ] }, { "page": "anlz_iwrraw", "title": "Format raw IWR data", "concept": [ "analyze" ], "topics": [ "anlz_iwrraw" ] }, { "page": "anlz_refs", "title": "Convert references csv to bib", "concept": [ "analyze" ], "topics": [ "anlz_refs" ] }, { "page": "anlz_sedimentaddtot", "title": "Add contaminant totals to sediment data", "concept": [ "anlz" ], "topics": [ "anlz_sedimentaddtot" ] }, { "page": "anlz_sedimentave", "title": "Get average concentrations for a sediment parameter by bay segment", "concept": [ "anlz" ], "topics": [ "anlz_sedimentave" ] }, { "page": "anlz_sedimentpel", "title": "Get sediment PEL ratios at stations in Tampa Bay", "concept": [ "anlz" ], "topics": [ "anlz_sedimentpel" ] }, { "page": "anlz_sedimentpelave", "title": "Get average concentrations for a sediment parameter by bay segment", "concept": [ "anlz" ], "topics": [ "anlz_sedimentpelave" ] }, { "page": "anlz_splitdata", "title": "Analyze time series data split by date within years", "concept": [ "analyze" ], "topics": [ "anlz_splitdata" ] }, { "page": "anlz_splitstorms", "title": "Analyze storm data split by date within years", "concept": [ "analyze" ], "topics": [ "anlz_splitstorms" ] }, { "page": "anlz_tbbimed", "title": "Get annual medians of Tampa Bay Benthic Index scores by bay segment", "concept": [ "analyze" ], "topics": [ "anlz_tbbimed" ] }, { "page": "anlz_tbbiscr", "title": "Get Tampa Bay Benthic Index scores", "concept": [ "analyze" ], "topics": [ "anlz_tbbiscr" ] }, { "page": "anlz_tbniave", "title": "Get annual averages of Tampa Bay Nekton Index scores by bay segment", "concept": [ "analyze" ], "topics": [ "anlz_tbniave" ] }, { "page": "anlz_tbnimet", "title": "Get all raw metrics for Tampa Bay Nekton Index", "concept": [ "analyze" ], "topics": [ "anlz_tbnimet" ] }, { "page": "anlz_tbniscr", "title": "Get Tampa Bay Nekton Index scores", "concept": [ "analyze" ], "topics": [ "anlz_tbniscr" ] }, { "page": "anlz_tdlcrk", "title": "Estimate tidal creek report card scores", "concept": [ "analyze" ], "topics": [ "anlz_tdlcrk" ] }, { "page": "anlz_tdlcrkindic", "title": "Analyze tidal creek water quality indicators", "concept": [ "analyze" ], "topics": [ "anlz_tdlcrkindic" ] }, { "page": "anlz_transectave", "title": "Get annual averages of seagrass frequency occurrence by bay segments and year", "concept": [ "analyze" ], "topics": [ "anlz_transectave" ] }, { "page": "anlz_transectavespp", "title": "Get annual averages of seagrass frequency occurrence by bay segments, year, and species", "concept": [ "analyze" ], "topics": [ "anlz_transectavespp" ] }, { "page": "anlz_transectocc", "title": "Get seagrass average abundance and occurrence across transects", "concept": [ "analyze" ], "topics": [ "anlz_transectocc" ] }, { "page": "anlz_yrattain", "title": "Get attainment categories for a chosen year", "concept": [ "analyze" ], "topics": [ "anlz_yrattain" ] }, { "page": "benthicdata", "title": "Benthic data for the Tampa Bay Benthic Index current as of 20251225", "concept": [ "data" ], "topics": [ "benthicdata" ] }, { "page": "bsmap", "title": "Terrain basemap", "topics": [ "bsmap" ] }, { "page": "catchpixels", "title": "Catchments and radar pixels (for precip) of selected Enterococcus stations", "topics": [ "catchpixels" ] }, { "page": "catchprecip", "title": "Daily precip by catchment for selected Enterococcus stations", "topics": [ "catchprecip" ] }, { "page": "dbasin", "title": "Spatial data object of minor subbasins (dbasins) in the Tampa Bay watershed", "concept": [ "data" ], "topics": [ "dbasin" ] }, { "page": "enterodata", "title": "Enterococcus data from 53 key Enterococcus stations since 1995", "topics": [ "enterodata" ] }, { "page": "epcdata", "title": "All bay data as of 20260203", "concept": [ "data" ], "topics": [ "epcdata" ] }, { "page": "fibdata", "title": "All Fecal Indicator Bacteria (FIB) data as of 20260302", "concept": [ "data" ], "topics": [ "fibdata" ] }, { "page": "fimdata", "title": "FIM data for Tampa Bay Nekton Index current as of 09032025", "concept": [ "data" ], "topics": [ "fimdata" ] }, { "page": "fimstations", "title": "Spatial data object of FIM stations including Tampa Bay segments", "concept": [ "data" ], "topics": [ "fimstations" ] }, { "page": "hcesdfibdata", "title": "Hillsborough County Environmental Services Division (ESD) FIB data as of 20260302", "concept": [ "data" ], "topics": [ "hcesdfibdata" ] }, { "page": "hmptrgs", "title": "Habitat Master Plan targets and goals", "concept": [ "data" ], "topics": [ "hmptrgs" ] }, { "page": "iwrraw", "title": "FDEP IWR run 67", "concept": [ "data" ], "topics": [ "iwrraw" ] }, { "page": "mancofibdata", "title": "Manatee County FIB data as of 20260302", "concept": [ "data" ], "topics": [ "mancofibdata" ] }, { "page": "pascofibdata", "title": "Pasco County FIB data as of 20260302", "concept": [ "data" ], "topics": [ "pascofibdata" ] }, { "page": "phytodata", "title": "Phytoplankton data current as of 20260204", "concept": [ "data" ], "topics": [ "phytodata" ] }, { "page": "polcofibdata", "title": "Polk County FIB data as of 20260302", "concept": [ "data" ], "topics": [ "polcofibdata" ] }, { "page": "read_dlcurrent", "title": "Download latest file from epchc.org", "concept": [ "read" ], "topics": [ "read_dlcurrent" ] }, { "page": "read_formbenthic", "title": "Format benthic data for the Tampa Bay Benthic Index", "concept": [ "read" ], "topics": [ "read_formbenthic" ] }, { "page": "read_formfib", "title": "Format Fecal Indicator Bacteria (FIB) data", "concept": [ "read" ], "topics": [ "read_formfib" ] }, { "page": "read_formfim", "title": "Format FIM data for the Tampa Bay Nekton Index", "concept": [ "read" ], "topics": [ "read_formfim" ] }, { "page": "read_formphyto", "title": "Format phytoplankton data", "concept": [ "read" ], "topics": [ "read_formphyto" ] }, { "page": "read_formsediment", "title": "Format sediment data", "concept": [ "read" ], "topics": [ "read_formsediment" ] }, { "page": "read_formtransect", "title": "Format seagrass transect data from Water Atlas", "concept": [ "read" ], "topics": [ "read_formtransect" ] }, { "page": "read_formwq", "title": "Format water quality data", "concept": [ "read" ], "topics": [ "read_formwq" ] }, { "page": "read_formwqp", "title": "Format data and station metadata from the Water Quality Portal", "concept": [ "read" ], "topics": [ "read_formwqp" ] }, { "page": "read_importbenthic", "title": "Download and import benthic data for Tampa Bay", "concept": [ "read" ], "topics": [ "read_importbenthic" ] }, { "page": "read_importentero", "title": "Download Enterococcus data from the Water Quality Portal", "topics": [ "read_importentero" ] }, { "page": "read_importepc", "title": "Download and/or import local water quality file for internal use", "concept": [ "read" ], "topics": [ "read_importepc" ] }, { "page": "read_importfib", "title": "Load local water quality file for Fecal Indicator Bacteria (FIB)", "concept": [ "read" ], "topics": [ "read_importfib" ] }, { "page": "read_importfim", "title": "Load local FIM data for the Tampa Bay Nekton Index", "concept": [ "read" ], "topics": [ "read_importfim" ] }, { "page": "read_importphyto", "title": "Load local phytoplankton cell count file", "concept": [ "read" ], "topics": [ "read_importphyto" ] }, { "page": "read_importprism", "title": "Import PRISM daily weather data", "concept": [ "read" ], "topics": [ "read_importprism" ] }, { "page": "read_importrain", "title": "Download daily precip data and summarise by station catchment", "topics": [ "read_importrain" ] }, { "page": "read_importrainmany", "title": "Run 'read_importrain' for multiple years", "topics": [ "read_importrainmany" ] }, { "page": "read_importsealevels", "title": "Import monthly sea levels by station from NOAA Tides and Currents", "concept": [ "read" ], "topics": [ "read_importsealevels" ] }, { "page": "read_importsediment", "title": "Download and import sediment data for Tampa Bay", "concept": [ "read" ], "topics": [ "read_importsediment" ] }, { "page": "read_importwq", "title": "Load local water quality file", "concept": [ "read" ], "topics": [ "read_importwq" ] }, { "page": "read_importwqp", "title": "Import data from the Water Quality Portal", "concept": [ "read" ], "topics": [ "read_importwqp" ] }, { "page": "read_importwqwa", "title": "Import data from the Water Atlas API", "topics": [ "read_importwqwa" ] }, { "page": "read_importwqwin", "title": "Retrieve water quality data from the Florida Department of Environmental Protection's Watershed Information Network (WIN)", "topics": [ "read_importwqwin" ] }, { "page": "read_prism_rasters", "title": "Read PRISM raster layers into data frame", "concept": [ "read" ], "topics": [ "read_prism_rasters" ] }, { "page": "read_transect", "title": "Import JSON seagrass transect data from Water Atlas", "concept": [ "read" ], "topics": [ "read_transect" ] }, { "page": "seagrass", "title": "Seagrass coverage by year", "concept": [ "data" ], "topics": [ "seagrass" ] }, { "page": "sealevelstations", "title": "Sea level stations in Tampa Bay", "concept": [ "data" ], "topics": [ "sealevelstations" ] }, { "page": "sedimentdata", "title": "Sediment data for the Tampa Bay current as of 20251210", "concept": [ "data" ], "topics": [ "sedimentdata" ] }, { "page": "sgmanagement", "title": "Seagrass management areas for Tampa Bay", "concept": [ "data" ], "topics": [ "sgmanagement" ] }, { "page": "sgseg", "title": "Seagrass segment reporting boundaries for southwest Florida", "concept": [ "data" ], "topics": [ "sgseg" ] }, { "page": "show_ambimatrix", "title": "Plot a matrix of AMBI scores over time by bay segment", "concept": [ "show" ], "topics": [ "show_ambimatrix" ] }, { "page": "show_ambitab", "title": "Create a summary table of AMBI category percentages by bay segment", "concept": [ "show" ], "topics": [ "show_ambitab" ] }, { "page": "show_ambitrend", "title": "Plot mean AMBI scores over time by bay segment", "concept": [ "show" ], "topics": [ "show_ambitrend" ] }, { "page": "show_annualassess", "title": "Create a table for the annual management outcome assessments", "concept": [ "show" ], "topics": [ "show_annualassess" ] }, { "page": "show_boxplot", "title": "Plot monthly chlorophyll or light attenuation values for a segment", "concept": [ "show" ], "topics": [ "show_boxplot" ] }, { "page": "show_compplot", "title": "Make a bar plot for transect training group comparisons", "concept": [ "show" ], "topics": [ "show_compplot" ] }, { "page": "show_enteromap", "title": "Map Enterococcus results by month, year, and location", "concept": [ "show" ], "topics": [ "show_enteromap" ] }, { "page": "show_fibmap", "title": "Map Fecal Indicator Bacteria (FIB) results by month, year, and location", "concept": [ "show" ], "topics": [ "show_fibmap" ] }, { "page": "show_fibmatmap", "title": "Map Fecal Indicator Bacteria matrix results by year", "concept": [ "show" ], "topics": [ "show_fibmatmap" ] }, { "page": "show_fibmatrix", "title": "Plot a matrix of Fecal Indicator Bacteria categories over time by station or bay segment", "concept": [ "show" ], "topics": [ "show_fibmatrix" ] }, { "page": "show_hmpreport", "title": "Show Habitat Master Plan progress report card", "concept": [ "show" ], "topics": [ "show_hmpreport" ] }, { "page": "show_matrix", "title": "Create a colorized table for indicator reporting", "concept": [ "show" ], "topics": [ "show_matrix" ] }, { "page": "show_matrixplotly", "title": "Creates a plotly matrix from any matrix function input", "concept": [ "show" ], "topics": [ "show_matrixplotly" ] }, { "page": "show_ratab", "title": "Create a bay segment assessment table for the 2022-2026 reasonable assurance period", "concept": [ "show" ], "topics": [ "show_ratab" ] }, { "page": "show_reactable", "title": "Create reactable table from matrix data", "concept": [ "show" ], "topics": [ "show_reactable" ] }, { "page": "show_seagrasscoverage", "title": "Create a barplot of seagrass coverage over time in Tampa Bay", "concept": [ "show" ], "topics": [ "show_seagrasscoverage" ] }, { "page": "show_sedimentalratio", "title": "Plot metal concentrations against aluminum", "topics": [ "show_sedimentalratio" ] }, { "page": "show_sedimentave", "title": "Plot sediment concentration averages by bay segment", "concept": [ "show" ], "topics": [ "show_sedimentave" ] }, { "page": "show_sedimentmap", "title": "Make a map for sediment contaminants at stations in Tampa Bay", "concept": [ "show" ], "topics": [ "show_sedimentmap" ] }, { "page": "show_sedimentpelave", "title": "Plot summary of PEL averages by bay segment", "concept": [ "show" ], "topics": [ "show_sedimentpelave" ] }, { "page": "show_sedimentpelaveplotly", "title": "Creates a plotly object for average PEL plots", "concept": [ "show" ], "topics": [ "show_sedimentpelaveplotly" ] }, { "page": "show_sedimentpelmap", "title": "Make a map for sediment PEL ratios at stations in Tampa Bay", "concept": [ "show" ], "topics": [ "show_sedimentpelmap" ] }, { "page": "show_segmatrix", "title": "Create a colorized table for water quality outcomes and exceedances by segment", "concept": [ "show" ], "topics": [ "show_segmatrix" ] }, { "page": "show_segplotly", "title": "Plot chlorophyll and secchi data together with matrix outcomes", "concept": [ "show" ], "topics": [ "show_segplotly" ] }, { "page": "show_sitemap", "title": "Map site attainment categories for a selected year", "concept": [ "show" ], "topics": [ "show_sitemap" ] }, { "page": "show_sitesegmap", "title": "Map site and bay segment attainment categories for a selected year", "concept": [ "show" ], "topics": [ "show_sitesegmap" ] }, { "page": "show_splitbarplot", "title": "Show a Split Bar Plot with Error Bars", "concept": [ "show" ], "topics": [ "show_splitbarplot" ] }, { "page": "show_tbbimatrix", "title": "Plot a matrix of Tampa Bay Benthic Index scores over time by bay segment", "concept": [ "show" ], "topics": [ "show_tbbimatrix" ] }, { "page": "show_tbnimatrix", "title": "Plot a matrix of Tampa Bay Nekton Index scores over time by bay segment", "concept": [ "show" ], "topics": [ "show_tbnimatrix" ] }, { "page": "show_tbniscr", "title": "Plot Tampa Bay Nekton Index scores over time by bay segment", "concept": [ "show" ], "topics": [ "show_tbniscr" ] }, { "page": "show_tbniscrall", "title": "Plot Tampa Bay Nekton Index scores over time as average across bay segments", "concept": [ "show" ], "topics": [ "show_tbniscrall" ] }, { "page": "show_tbniscrplotly", "title": "Creates a plotly object for TBNI score plots", "concept": [ "show" ], "topics": [ "show_tbniscrplotly" ] }, { "page": "show_tdlcrk", "title": "Make a map for tidal creek report card", "concept": [ "show" ], "topics": [ "show_tdlcrk" ] }, { "page": "show_tdlcrkindic", "title": "Plotly barplots of tidal creek context indicators", "concept": [ "show" ], "topics": [ "show_tdlcrkindic" ] }, { "page": "show_tdlcrkindiccdf", "title": "Plotly empirical CDF plots of tidal creek context indicators", "concept": [ "show" ], "topics": [ "show_tdlcrkindiccdf" ] }, { "page": "show_tdlcrkline", "title": "Add a line or annotation to a plotly graph", "concept": [ "show" ], "topics": [ "show_tdlcrkline" ] }, { "page": "show_tdlcrkmatrix", "title": "Plot the tidal creek report card matrix", "concept": [ "show" ], "topics": [ "show_tdlcrkmatrix" ] }, { "page": "show_tdlcrkradar", "title": "Radar plots for tidal creek indicators", "concept": [ "show" ], "topics": [ "show_tdlcrkradar" ] }, { "page": "show_thrplot", "title": "Plot 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