Package: tbeptools 3.1.0.9028

tbeptools: Data and Indicators for the Tampa Bay Estuary Program

Several functions are provided for working with Tampa Bay Estuary Program data and indicators, including the water quality report card, tidal creek assessments, Tampa Bay Nekton Index, Tampa Bay Benthic Index, seagrass transect data, habitat report card, and fecal indicator bacteria. Additional functions are provided for miscellaneous tasks, such as reference library curation.

Authors:Marcus Beck [aut, cre], Meagan Schrandt [aut], Mike Wessel [aut], Ed Sherwood [aut], Gary Raulerson [aut], Adhokshaja Achar Budihal Prasad [aut], Benjamin Best [aut], Kim Cressman [aut]

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manual.pdf |manual.html✨
card.svg |card.png
tbeptools/json (API)

# Install 'tbeptools' in R:
install.packages('tbeptools', repos = c('https://fawda123.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/tbep-tech/tbeptools/issues

Datasets:
  • acres - Tampa Bay intertidal and supratidal land use and cover
  • ambispp - AMBI species group assignments for Tampa Bay benthic taxa
  • benthicdata - Benthic data for the Tampa Bay Benthic Index current as of 20251225
  • bsmap - Terrain basemap
  • catchpixels - Catchments and radar pixels (for precip) of selected Enterococcus stations
  • catchprecip - Daily precip by catchment for selected Enterococcus stations
  • dbasin - Spatial data object of minor subbasins (dbasins) in the Tampa Bay watershed
  • enterodata - Enterococcus data from 53 key Enterococcus stations since 1995
  • epcdata - All bay data as of 20260203
  • fibdata - All Fecal Indicator Bacteria (FIB) data as of 20260302
  • fimdata - FIM data for Tampa Bay Nekton Index current as of 09032025
  • fimstations - Spatial data object of FIM stations including Tampa Bay segments
  • hcesdfibdata - Hillsborough County Environmental Services Division (ESD) FIB data as of 20260302
  • hmptrgs - Habitat Master Plan targets and goals
  • iwrraw - FDEP IWR run 67
  • mancofibdata - Manatee County FIB data as of 20260302
  • pascofibdata - Pasco County FIB data as of 20260302
  • phytodata - Phytoplankton data current as of 20260204
  • polcofibdata - Polk County FIB data as of 20260302
  • seagrass - Seagrass coverage by year
  • sealevelstations - Sea level stations in Tampa Bay
  • sedimentdata - Sediment data for the Tampa Bay current as of 20251210
  • sgmanagement - Seagrass management areas for Tampa Bay
  • sgseg - Seagrass segment reporting boundaries for southwest Florida
  • stations - Bay stations by segment
  • subtacres - Tampa Bay subtidal cover
  • swfwmdtbseg - Spatial data object of SWFWMD Tampa Bay segments
  • swfwmdtbseg2024 - Spatial data object of SWFWMD Tampa Bay segments, 2024
  • targets - Bay segment targets
  • tbniref - Reference conditions for Tampa Bay Nekton Index metrics
  • tbnispp - Reference table for Tampa Bay Nekton Index species classifications
  • tbseg - Spatial data object of Tampa Bay segments
  • tbsegdetail - Spatial data object of detailed Tampa Bay segments
  • tbsegdetailbcbs - Spatial data object of detailed Tampa Bay segments, Boca Ciega Bay as southern portion
  • tbseglines - Spatial data object of lines defining major Tampa Bay segments
  • 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, Run 67
  • tidaltargets - Tidal creek nitrogen targets
  • transect - Seagrass transect data for Tampa Bay current as of 12052025
  • trnlns - Seagrass transect locations
  • trnpts - Seagrass transect starting locations

On CRAN:

Conda:

data-analysistampa-baytbepwater-quality

8.01 score 9 stars 1 packages 144 scripts 110 exports 117 dependencies

Last updated from:5869099529. Checks:7 NOTE, 2 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-x86_64NOTE781
source / vignettesOK537
linux-release-x86_64NOTE777
macos-release-arm64NOTE673
macos-oldrel-arm64NOTE627
windows-develNOTE786
windows-releaseNOTE782
windows-oldrelNOTE792
wasm-releaseOK200

Exports:anlz_ambimedanlz_ambiscranlz_attainanlz_attainsiteanlz_avedatanlz_avedatsiteanlz_enteromapanlz_fibmapanlz_fibmatrixanlz_fibwetdryanlz_hmpreportanlz_hydroloadanlz_iwrrawanlz_refsanlz_sedimentaddtotanlz_sedimentaveanlz_sedimentpelanlz_sedimentpelaveanlz_splitdataanlz_splitstormsanlz_tbbimedanlz_tbbiscranlz_tbniaveanlz_tbnimetanlz_tbniscranlz_tdlcrkanlz_tdlcrkindicanlz_transectaveanlz_transectavesppanlz_transectoccanlz_yrattainread_dlcurrentread_formbenthicread_formfibread_formfimread_formphytoread_formsedimentread_formtransectread_formwqread_formwqpread_importbenthicread_importenteroread_importepcread_importfibread_importfimread_importphytoread_importprismread_importrainmanyread_importsealevelsread_importsedimentread_importwqread_importwqpread_importwqwaread_importwqwinread_prism_rastersread_transectshow_ambimatrixshow_ambitabshow_ambitrendshow_annualassessshow_boxplotshow_compplotshow_enteromapshow_fibmapshow_fibmatmapshow_fibmatrixshow_hmpreportshow_matrixshow_matrixplotlyshow_ratabshow_reactableshow_seagrasscoverageshow_sedimentalratioshow_sedimentaveshow_sedimentmapshow_sedimentpelaveshow_sedimentpelaveplotlyshow_sedimentpelmapshow_segmatrixshow_segplotlyshow_sitemapshow_sitesegmapshow_splitbarplotshow_tbbimatrixshow_tbnimatrixshow_tbniscrshow_tbniscrallshow_tbniscrplotlyshow_tdlcrkshow_tdlcrkindicshow_tdlcrkindiccdfshow_tdlcrklineshow_tdlcrkmatrixshow_tdlcrkradarshow_thrplotshow_transectshow_transectavesppshow_transectmatrixshow_transectsumshow_wqmatrixutil_datesequtil_fibiconsutil_fiblevsutil_frmyrrngutil_htmlutil_importwqwautil_importwqwinutil_maputil_orginutil_rain

Dependencies:askpassbase64encbitbit64bslibcachemcellrangerclassclassIntclicliprcpp11crayoncrosstalkcurldata.tabledataRetrievalDBIdigestdplyre1071evaluatefarverfastmapflextablefontawesomefontBitstreamVerafontLiberationfontquiverfsgdtoolsgenericsggplot2gluegtablehighrhmshtmltoolshtmlwidgetshttrhttr2isobandjquerylibjsonliteKernSmoothknitrlabelinglaterlatticelazyevalleafletleaflet.providerslifecyclelubridatemagrittrMASSmemoisemimeofficeropensslotelpatchworkpillarpkgconfigplotlypngprettyunitsprogresspromisesproxypurrrR6raggrappdirsrasterRColorBrewerRcppreactablereactRreadrreadxlrematchrlangrmarkdownrvests2S7sassscalesselectrsfspstringistringrsyssystemfontsterratextshapingtibbletidyrtidyselecttimechangetinytextzdbunitsutf8uuidvctrsviridisLitevroomwhiskerwithrwkxfunxml2yamlzip

Fecal Indicator Bacteria

Rendered fromfib.Rmdusingknitr::rmarkdownon May 19 2026.

Last update: 2026-03-02
Started: 2023-07-03

Habitat Master Plan

Rendered fromhabitatmasterplan.Rmdusingknitr::rmarkdownon May 19 2026.

Last update: 2024-06-10
Started: 2022-11-19

Seagrass Transect Data

Rendered fromseagrasstransect.Rmdusingknitr::rmarkdownon May 19 2026.

Last update: 2025-10-29
Started: 2020-07-21

Tampa Bay Benthic Index

Rendered fromtbbi.Rmdusingknitr::rmarkdownon May 19 2026.

Last update: 2026-05-18
Started: 2020-08-21

Tampa Bay Nekton Index

Rendered fromtbni.Rmdusingknitr::rmarkdownon May 19 2026.

Last update: 2025-07-14
Started: 2020-04-24

Tidal Creek Assessment

Rendered fromtidalcreeks.Rmdusingknitr::rmarkdownon May 19 2026.

Last update: 2026-01-29
Started: 2019-12-31

Water Quality Data

Rendered fromintro.Rmdusingknitr::rmarkdownon May 19 2026.

Last update: 2026-03-02
Started: 2019-07-09

Readme and manuals

Help Manual

Help pageTopics
Tampa Bay intertidal and supratidal land use and coveracres
AMBI species group assignments for Tampa Bay benthic taxaambispp
Get annual medians of AMBI scores by bay segmentanlz_ambimed
Get AMBI scores for benthic stationsanlz_ambiscr
Get attainment categoriesanlz_attain
Get site attainmentsanlz_attainsite
Estimate annual meansanlz_avedat
Estimate annual means by siteanlz_avedatsite
Assign threshold categories to Enterococcus dataanlz_enteromap
Assign threshold categories to Fecal Indicator Bacteria (FIB) dataanlz_fibmap
Analyze Fecal Indicator Bacteria categories over time by station or bay segmentanlz_fibmatrix
Identify Fecal Indicator Bacteria samples as coming from a 'wet' or 'dry' time periodanlz_fibwetdry
Evaluate Habitat Master Plan progress for report cardanlz_hmpreport
Estimate hydrological estimates and adjustment factors for bay segmentsanlz_hydroload
Format raw IWR dataanlz_iwrraw
Convert references csv to bibanlz_refs
Add contaminant totals to sediment dataanlz_sedimentaddtot
Get average concentrations for a sediment parameter by bay segmentanlz_sedimentave
Get sediment PEL ratios at stations in Tampa Bayanlz_sedimentpel
Get average concentrations for a sediment parameter by bay segmentanlz_sedimentpelave
Analyze time series data split by date within yearsanlz_splitdata
Analyze storm data split by date within yearsanlz_splitstorms
Get annual medians of Tampa Bay Benthic Index scores by bay segmentanlz_tbbimed
Get Tampa Bay Benthic Index scoresanlz_tbbiscr
Get annual averages of Tampa Bay Nekton Index scores by bay segmentanlz_tbniave
Get all raw metrics for Tampa Bay Nekton Indexanlz_tbnimet
Get Tampa Bay Nekton Index scoresanlz_tbniscr
Estimate tidal creek report card scoresanlz_tdlcrk
Analyze tidal creek water quality indicatorsanlz_tdlcrkindic
Get annual averages of seagrass frequency occurrence by bay segments and yearanlz_transectave
Get annual averages of seagrass frequency occurrence by bay segments, year, and speciesanlz_transectavespp
Get seagrass average abundance and occurrence across transectsanlz_transectocc
Get attainment categories for a chosen yearanlz_yrattain
Benthic data for the Tampa Bay Benthic Index current as of 20251225benthicdata
Terrain basemapbsmap
Catchments and radar pixels (for precip) of selected Enterococcus stationscatchpixels
Daily precip by catchment for selected Enterococcus stationscatchprecip
Spatial data object of minor subbasins (dbasins) in the Tampa Bay watersheddbasin
Enterococcus data from 53 key Enterococcus stations since 1995enterodata
All bay data as of 20260203epcdata
All Fecal Indicator Bacteria (FIB) data as of 20260302fibdata
FIM data for Tampa Bay Nekton Index current as of 09032025fimdata
Spatial data object of FIM stations including Tampa Bay segmentsfimstations
Hillsborough County Environmental Services Division (ESD) FIB data as of 20260302hcesdfibdata
Habitat Master Plan targets and goalshmptrgs
FDEP IWR run 67iwrraw
Manatee County FIB data as of 20260302mancofibdata
Pasco County FIB data as of 20260302pascofibdata
Phytoplankton data current as of 20260204phytodata
Polk County FIB data as of 20260302polcofibdata
Download latest file from epchc.orgread_dlcurrent
Format benthic data for the Tampa Bay Benthic Indexread_formbenthic
Format Fecal Indicator Bacteria (FIB) dataread_formfib
Format FIM data for the Tampa Bay Nekton Indexread_formfim
Format phytoplankton dataread_formphyto
Format sediment dataread_formsediment
Format seagrass transect data from Water Atlasread_formtransect
Format water quality dataread_formwq
Format data and station metadata from the Water Quality Portalread_formwqp
Download and import benthic data for Tampa Bayread_importbenthic
Download Enterococcus data from the Water Quality Portalread_importentero
Download and/or import local water quality file for internal useread_importepc
Load local water quality file for Fecal Indicator Bacteria (FIB)read_importfib
Load local FIM data for the Tampa Bay Nekton Indexread_importfim
Load local phytoplankton cell count fileread_importphyto
Import PRISM daily weather dataread_importprism
Download daily precip data and summarise by station catchmentread_importrain
Run 'read_importrain' for multiple yearsread_importrainmany
Import monthly sea levels by station from NOAA Tides and Currentsread_importsealevels
Download and import sediment data for Tampa Bayread_importsediment
Load local water quality fileread_importwq
Import data from the Water Quality Portalread_importwqp
Import data from the Water Atlas APIread_importwqwa
Retrieve water quality data from the Florida Department of Environmental Protection's Watershed Information Network (WIN)read_importwqwin
Read PRISM raster layers into data frameread_prism_rasters
Import JSON seagrass transect data from Water Atlasread_transect
Seagrass coverage by yearseagrass
Sea level stations in Tampa Baysealevelstations
Sediment data for the Tampa Bay current as of 20251210sedimentdata
Seagrass management areas for Tampa Baysgmanagement
Seagrass segment reporting boundaries for southwest Floridasgseg
Plot a matrix of AMBI scores over time by bay segmentshow_ambimatrix
Create a summary table of AMBI category percentages by bay segmentshow_ambitab
Plot mean AMBI scores over time by bay segmentshow_ambitrend
Create a table for the annual management outcome assessmentsshow_annualassess
Plot monthly chlorophyll or light attenuation values for a segmentshow_boxplot
Make a bar plot for transect training group comparisonsshow_compplot
Map Enterococcus results by month, year, and locationshow_enteromap
Map Fecal Indicator Bacteria (FIB) results by month, year, and locationshow_fibmap
Map Fecal Indicator Bacteria matrix results by yearshow_fibmatmap
Plot a matrix of Fecal Indicator Bacteria categories over time by station or bay segmentshow_fibmatrix
Show Habitat Master Plan progress report cardshow_hmpreport
Create a colorized table for indicator reportingshow_matrix
Creates a plotly matrix from any matrix function inputshow_matrixplotly
Create a bay segment assessment table for the 2022-2026 reasonable assurance periodshow_ratab
Create reactable table from matrix datashow_reactable
Create a barplot of seagrass coverage over time in Tampa Bayshow_seagrasscoverage
Plot metal concentrations against aluminumshow_sedimentalratio
Plot sediment concentration averages by bay segmentshow_sedimentave
Make a map for sediment contaminants at stations in Tampa Bayshow_sedimentmap
Plot summary of PEL averages by bay segmentshow_sedimentpelave
Creates a plotly object for average PEL plotsshow_sedimentpelaveplotly
Make a map for sediment PEL ratios at stations in Tampa Bayshow_sedimentpelmap
Create a colorized table for water quality outcomes and exceedances by segmentshow_segmatrix
Plot chlorophyll and secchi data together with matrix outcomesshow_segplotly
Map site attainment categories for a selected yearshow_sitemap
Map site and bay segment attainment categories for a selected yearshow_sitesegmap
Show a Split Bar Plot with Error Barsshow_splitbarplot
Plot a matrix of Tampa Bay Benthic Index scores over time by bay segmentshow_tbbimatrix
Plot a matrix of Tampa Bay Nekton Index scores over time by bay segmentshow_tbnimatrix
Plot Tampa Bay Nekton Index scores over time by bay segmentshow_tbniscr
Plot Tampa Bay Nekton Index scores over time as average across bay segmentsshow_tbniscrall
Creates a plotly object for TBNI score plotsshow_tbniscrplotly
Make a map for tidal creek report cardshow_tdlcrk
Plotly barplots of tidal creek context indicatorsshow_tdlcrkindic
Plotly empirical CDF plots of tidal creek context indicatorsshow_tdlcrkindiccdf
Add a line or annotation to a plotly graphshow_tdlcrkline
Plot the tidal creek report card matrixshow_tdlcrkmatrix
Radar plots for tidal creek indicatorsshow_tdlcrkradar
Plot annual water quality values, targets, and thresholds for a segmentshow_thrplot
Plot results for a seagrass transect by time and locationshow_transect
Show annual averages of seagrass frequency occurrence by bay segments, year, and speciesshow_transectavespp
Show matrix of seagrass frequency occurrence by bay segments and yearshow_transectmatrix
Plot frequency occurrence for a seagrass transect by time for all speciesshow_transectsum
Create a colorized table for chlorophyll or light attenuation exceedancesshow_wqmatrix
Bay stations by segmentstations
Tampa Bay subtidal coversubtacres
Spatial data object of SWFWMD Tampa Bay segmentsswfwmdtbseg
Spatial data object of SWFWMD Tampa Bay segments, 2024swfwmdtbseg2024
Bay segment targetstargets
Reference conditions for Tampa Bay Nekton Index metricstbniref
Reference table for Tampa Bay Nekton Index species classificationstbnispp
Spatial data object of Tampa Bay segmentstbseg
Spatial data object of detailed Tampa Bay segmentstbsegdetail
Spatial data object of detailed Tampa Bay segments, Boca Ciega Bay as southern portiontbsegdetailbcbs
Spatial data object of lines defining major Tampa Bay segmentstbseglines
Spatial data object of Tampa Bay segments plus watershedstbsegshed
Spatial data object of Tampa Bay watershedtbshed
Spatial data object of tidal creeks in Impaired Waters Rule, Run 67tidalcreeks
Tidal creek nitrogen targetstidaltargets
Seagrass transect data for Tampa Bay current as of 12052025transect
Seagrass transect locationstrnlns
Seagrass transect starting locationstrnpts
Generate a two-column data frame of datesutil_dateseq
Return leaflet icon set for FIB mapsutil_fibicons
A list of Fecal Indicator Bacteria (FIB) factor levels and labelsutil_fiblevs
Format a Vector of Years into a Concise Rangeutil_frmyrrng
Convert character string to html classutil_html
Retrieve metadata from the Water Atlas APIutil_importwqwa
Utility function to retrieve water quality data from the Florida Department of Environmental Protection's Watershed Information Network (WIN)util_importwqwin
Create an empty leaflet map from sf inpututil_map
Get organization name from organization identifier in USEPA Water Quality Portalutil_orgin
Get rainfall data at NOAA NCDC sitesutil_rain