Man pages for tbep-tech/tbeptools
Data and Indicators for the Tampa Bay Estuary Program
| acres | Tampa Bay intertidal and supratidal land use and cover |
| anlz_attain | Get attainment categories |
| anlz_attainsite | Get site attainments |
| anlz_avedat | Estimate annual means |
| anlz_avedatsite | Estimate annual means by site |
| anlz_enteromap | Assign threshold categories to Enterococcus data |
| anlz_fibmap | Assign threshold categories to Fecal Indicator Bacteria (FIB)... |
| anlz_fibmatrix | Analyze Fecal Indicator Bacteria categories over time by... |
| anlz_fibwetdry | Identify Fecal Indicator Bacteria samples as coming from a... |
| anlz_hmpreport | Evaluate Habitat Master Plan progress for report card |
| anlz_hydroload | Estimate hydrological estimates and adjustment factors for... |
| anlz_iwrraw | Format raw IWR data |
| anlz_refs | Convert references csv to bib |
| anlz_sedimentaddtot | Add contaminant totals to sediment data |
| anlz_sedimentave | Get average concentrations for a sediment parameter by bay... |
| anlz_sedimentpel | Get sediment PEL ratios at stations in Tampa Bay |
| anlz_sedimentpelave | Get average concentrations for a sediment parameter by bay... |
| anlz_splitdata | Analyze time series data split by date within years |
| anlz_splitstorms | Analyze storm data split by date within years |
| anlz_tbbimed | Get annual medians of Tampa Bay Benthic Index scores by bay... |
| anlz_tbbiscr | Get Tampa Bay Benthic Index scores |
| anlz_tbniave | Get annual averages of Tampa Bay Nekton Index scores by bay... |
| anlz_tbnimet | Get all raw metrics for Tampa Bay Nekton Index |
| anlz_tbniscr | Get Tampa Bay Nekton Index scores |
| anlz_tdlcrk | Estimate tidal creek report card scores |
| anlz_tdlcrkindic | Analyze tidal creek water quality indicators |
| anlz_transectave | Get annual averages of seagrass frequency occurrence by bay... |
| anlz_transectavespp | Get annual averages of seagrass frequency occurrence by bay... |
| anlz_transectocc | Get seagrass average abundance and occurrence across... |
| anlz_yrattain | Get attainment categories for a chosen year |
| benthicdata | Benthic data for the Tampa Bay Benthic Index current as of... |
| bsmap | Terrain basemap |
| catchpixels | Catchments and radar pixels (for precip) of selected... |
| catchprecip | Daily precip by catchment for selected Enterococcus stations |
| enterodata | Enterococcus data from 53 key Enterococcus stations since... |
| epcdata | All bay data as of 20250210 |
| fibdata | All Fecal Indicator Bacteria (FIB) data as of 20250321 |
| fimdata | FIM data for Tampa Bay Nekton Index current as of 07092024 |
| fimstations | Spatial data object of FIM stations including Tampa Bay... |
| hcesdfibdata | Hillsborough County Environmental Services Division (ESD) FIB... |
| hmptrgs | Habitat Master Plan targets and goals |
| iwrraw | FDEP IWR run 66 |
| mancofibdata | Manatee County FIB data as of 20250211 |
| pascofibdata | Pasco County FIB data as of 20250304 |
| phytodata | Phytoplankton data current as of 10312024 |
| polcofibdata | Polk County FIB data as of 20250304 |
| read_dlcurrent | Download latest file from epchc.org |
| read_formbenthic | Format benthic data for the Tampa Bay Benthic Index |
| read_formfib | Format Fecal Indicator Bacteria (FIB) data |
| read_formfim | Format FIM data for the Tampa Bay Nekton Index |
| read_formphyto | Format phytoplankton data |
| read_formsediment | Format sediment data |
| read_formtransect | Format seagrass transect data from Water Atlas |
| read_formwq | Format water quality data |
| read_formwqp | Format data and station metadata from the Water Quality... |
| read_importbenthic | Download and import benthic data for Tampa Bay |
| read_importentero | Download Enterococcus data from the Water Quality Portal |
| read_importepc | Download and/or import local water quality file for internal... |
| read_importfib | Load local water quality file for Fecal Indicator Bacteria... |
| read_importfim | Load local FIM data for the Tampa Bay Nekton Index |
| read_importphyto | Load local phytoplankton cell count file |
| read_importprism | Import PRISM daily weather data |
| read_importrain | Download daily precip data and summarise by station catchment |
| read_importrainmany | Run 'read_importrain' for multiple years |
| read_importsealevels | Import monthly sea levels by station from NOAA Tides and... |
| read_importsediment | Download and import sediment data for Tampa Bay |
| read_importwq | Load local water quality file |
| read_importwqp | Import data from the Water Quality Portal |
| read_prism_rasters | Read PRISM raster layers into data frame |
| read_transect | Import JSON seagrass transect data from Water Atlas |
| seagrass | Seagrass coverage by year |
| sealevelstations | Sea level stations in Tampa Bay |
| sedimentdata | Sediment data for the Tampa Bay current as of 20241212 |
| sgmanagement | Seagrass management areas for Tampa Bay |
| sgseg | Seagrass segment reporting boundaries for southwest Florida |
| show_annualassess | Create a table for the annual management outcome assessments |
| show_boxplot | Plot monthly chlorophyll or light attenuation values for a... |
| show_compplot | Make a bar plot for transect training group comparisons |
| show_enteromap | Map Enterococcus results by month, year, and location |
| show_fibmap | Map Fecal Indicator Bacteria (FIB) results by month, year,... |
| show_fibmatmap | Map Fecal Indicator Bacteria matrix results by year |
| show_fibmatrix | Plot a matrix of Fecal Indicator Bacteria categories over... |
| show_hmpreport | Show Habitat Master Plan progress report card |
| show_matrix | Create a colorized table for indicator reporting |
| show_matrixplotly | Creates a plotly matrix from any matrix function input |
| show_ratab | Create a bay segment assessment table for the 2022-2026... |
| show_reactable | Create reactable table from matrix data |
| show_seagrasscoverage | Create a barplot of seagrass coverage over time in Tampa Bay |
| show_sedimentalratio | Plot metal concentrations against aluminum |
| show_sedimentave | Plot sediment concentration averages by bay segment |
| show_sedimentmap | Make a map for sediment contaminants at stations in Tampa Bay |
| show_sedimentpelave | Plot summary of PEL averages by bay segment |
| show_sedimentpelaveplotly | Creates a plotly object for average PEL plots |
| show_sedimentpelmap | Make a map for sediment PEL ratios at stations in Tampa Bay |
| show_segmatrix | Create a colorized table for water quality outcomes and... |
| show_segplotly | Plot chlorophyll and secchi data together with matrix... |
| show_sitemap | Map site attainment categories for a selected year |
| show_sitesegmap | Map site and bay segment attainment categories for a selected... |
| show_splitbarplot | Show a Split Bar Plot with Error Bars |
| show_tbbimatrix | Plot a matrix of Tampa Bay Benthic Index scores over time by... |
| show_tbnimatrix | Plot a matrix of Tampa Bay Nekton Index scores over time by... |
| show_tbniscr | Plot Tampa Bay Nekton Index scores over time by bay segment |
| show_tbniscrall | Plot Tampa Bay Nekton Index scores over time as average... |
| show_tbniscrplotly | Creates a plotly object for TBNI score plots |
| show_tdlcrk | Make a map for tidal creek report card |
| show_tdlcrkindic | Plotly barplots of tidal creek context indicators |
| show_tdlcrkindiccdf | Plotly empirical CDF plots of tidal creek context indicators |
| show_tdlcrkline | Add a line or annotation to a plotly graph |
| show_tdlcrkmatrix | Plot the tidal creek report card matrix |
| show_tdlcrkradar | Radar plots for tidal creek indicators |
| show_thrplot | Plot annual water quality values, targets, and thresholds for... |
| show_transect | Plot results for a seagrass transect by time and location |
| show_transectavespp | Show annual averages of seagrass frequency occurrence by bay... |
| show_transectmatrix | Show matrix of seagrass frequency occurrence by bay segments... |
| show_transectsum | Plot frequency occurrence for a seagrass transect by time for... |
| show_wqmatrix | Create a colorized table for chlorophyll or light attenuation... |
| stations | Bay stations by segment |
| subtacres | Tampa Bay subtidal cover |
| swfwmdtbseg | Spatial data object of SWFWMD Tampa Bay segments |
| targets | Bay segment targets |
| tbniref | Reference conditions for Tampa Bay Nekton Index metrics |
| tbnispp | Reference table for Tampa Bay Nekton Index species... |
| tbseg | Spatial data object of Tampa Bay segments |
| tbsegdetail | Spatial data object of detailed Tampa Bay segments |
| tbseglines | Spatial data object of lines defining major Tampa Bay... |
| tbsegshed | Spatial data object of Tampa Bay segments plus watersheds |
| tbshed | Spatial data object of Tampa Bay watershed |
| tidalcreeks | Spatial data object of tidal creeks in Impaired Waters Rule,... |
| tidaltargets | Tidal creek nitrogen targets |
| transect | Seagrass transect data for Tampa Bay current as of 11032024 |
| trnlns | Seagrass transect locations |
| trnpts | Seagrass transect starting locations |
| util_fibicons | Return leaflet icon set for FIB maps |
| util_fiblevs | A list of Fecal Indicator Bacteria (FIB) factor levels and... |
| util_frmyrrng | Format a Vector of Years into a Concise Range |
| util_html | Convert character string to html class |
| util_map | Create an empty leaflet map from sf input |
| util_orgin | Get organization name from organization identifier in USEPA... |
