Package: tbeptools 3.0.0.9004

Marcus Beck

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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tbeptools.pdf |tbeptools.html✨
tbeptools/json (API)

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

Peer review:

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

Datasets:
  • acres - Tampa Bay intertidal and supratidal land use and cover
  • benthicdata - Benthic data for the Tampa Bay Benthic Index current as of 03132024
  • bsmap - Terrain basemap
  • catchpixels - Catchments and radar pixels (for precip) of selected Enterococcus stations
  • catchprecip - Daily precip by catchment for selected Enterococcus stations
  • enterodata - Enterococcus data from 53 key Enterococcus stations since 1995
  • epcdata - All bay data as of 20240201
  • fibdata - All Fecal Indicator Bacteria (FIB) data as of 20240814
  • fimdata - FIM data for Tampa Bay Nekton Index current as of 07092024
  • fimstations - Spatial data object of FIM stations including Tampa Bay segments
  • hmptrgs - Habitat Master Plan targets and goals
  • iwrraw - FDEP IWR run 65
  • mancofibdata - Manatee County FIB data as of 20241011
  • phytodata - Phytoplankton data current as of 10312024
  • seagrass - Seagrass coverage by year
  • sedimentdata - Sediment data for the Tampa Bay current as of 12142023
  • 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
  • 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
  • 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 65
  • 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

On CRAN:

data-analysistampa-baytbepwater-quality

7.67 score 7 stars 137 scripts 91 exports 128 dependencies

Last updated 18 days agofrom:57a2315611. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 03 2024
R-4.5-winNOTENov 03 2024
R-4.5-linuxNOTENov 03 2024
R-4.4-winNOTENov 03 2024
R-4.4-macNOTENov 03 2024
R-4.3-winNOTENov 03 2024
R-4.3-macNOTENov 03 2024

Exports:anlz_attainanlz_attainsiteanlz_avedatanlz_avedatsiteanlz_enteromapanlz_fibmapanlz_fibmatrixanlz_fibwetdryanlz_hmpreportanlz_hydroloadanlz_iwrrawanlz_refsanlz_sedimentaddtotanlz_sedimentaveanlz_sedimentpelanlz_sedimentpelaveanlz_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_importsedimentread_importwqread_importwqpread_transectshow_annualassessshow_boxplotshow_compplotshow_enteromapshow_fibmapshow_fibmatmapshow_fibmatrixshow_hmpreportshow_matrixshow_matrixplotlyshow_ratabshow_reactableshow_seagrasscoverageshow_sedimentalratioshow_sedimentaveshow_sedimentmapshow_sedimentpelaveshow_sedimentpelaveplotlyshow_sedimentpelmapshow_segmatrixshow_segplotlyshow_sitemapshow_sitesegmapshow_tbbimatrixshow_tbnimatrixshow_tbniscrshow_tbniscrallshow_tbniscrplotlyshow_tdlcrkshow_tdlcrkindicshow_tdlcrkindiccdfshow_tdlcrklineshow_tdlcrkmatrixshow_tdlcrkradarshow_thrplotshow_transectshow_transectavesppshow_transectmatrixshow_transectsumshow_wqmatrixutil_fibiconsutil_fiblevsutil_htmlutil_maputil_orgin

Dependencies:askpassbase64encbitbit64bslibcachemcellrangerclassclassIntclicliprcolorspacecpp11crayoncrosstalkcrulcurldata.tabledataRetrievalDBIdigestdplyre1071evaluatefansifarverfastmapflextablefontawesomefontBitstreamVerafontLiberationfontquiverfsgdtoolsgenericsgeonamesggplot2gluegridExtragtablehighrhmshoardrhtmltoolshtmlwidgetshttpcodehttrisdparserisobandjquerylibjsonliteKernSmoothknitrlabelinglaterlatticelazyevalleafletleaflet.providerslifecyclelubridatemagrittrMASSMatrixmemoisemgcvmimemunsellnlmeofficeropensslpatchworkpillarpkgconfigplotlypngprettyunitsprogresspromisesproxypurrrR6raggrappdirsrasterRColorBrewerRcppreactablereactRreadrreadxlrematchrjsonrlangrmarkdownrnoaas2sassscalessfspstringistringrsyssystemfontsterratextshapingtibbletidyrtidyselecttimechangetinytextriebeardtzdbunitsurltoolsutf8uuidvctrsviridisLitevroomwithrwkxfunXMLxml2yamlzip

Fecal Indicator Bacteria

Rendered fromfib.Rmdusingknitr::rmarkdownon Nov 03 2024.

Last update: 2024-10-22
Started: 2023-07-03

Habitat Master Plan

Rendered fromhabitatmasterplan.Rmdusingknitr::rmarkdownon Nov 03 2024.

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

Seagrass Transect Data

Rendered fromseagrasstransect.Rmdusingknitr::rmarkdownon Nov 03 2024.

Last update: 2024-11-03
Started: 2020-07-21

Tampa Bay Benthic Index

Rendered fromtbbi.Rmdusingknitr::rmarkdownon Nov 03 2024.

Last update: 2023-12-14
Started: 2020-08-21

Tampa Bay Nekton Index

Rendered fromtbni.Rmdusingknitr::rmarkdownon Nov 03 2024.

Last update: 2023-02-17
Started: 2020-04-24

Tidal Creek Assessment

Rendered fromtidalcreeks.Rmdusingknitr::rmarkdownon Nov 03 2024.

Last update: 2024-03-20
Started: 2019-12-31

Water Quality Data

Rendered fromintro.Rmdusingknitr::rmarkdownon Nov 03 2024.

Last update: 2024-10-28
Started: 2019-07-09

Readme and manuals

Help Manual

Help pageTopics
Tampa Bay intertidal and supratidal land use and coveracres
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
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 03132024benthicdata
Terrain basemapbsmap
Catchments and radar pixels (for precip) of selected Enterococcus stationscatchpixels
Daily precip by catchment for selected Enterococcus stationscatchprecip
Enterococcus data from 53 key Enterococcus stations since 1995enterodata
All bay data as of 20240201epcdata
All Fecal Indicator Bacteria (FIB) data as of 20240814fibdata
FIM data for Tampa Bay Nekton Index current as of 07092024fimdata
Spatial data object of FIM stations including Tampa Bay segmentsfimstations
Habitat Master Plan targets and goalshmptrgs
FDEP IWR run 65iwrraw
Manatee County FIB data as of 20241011mancofibdata
Phytoplankton data current as of 10312024phytodata
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
Download daily precip data and summarise by station catchmentread_importrain
Download and import sediment data for Tampa Bayread_importsediment
Load local water quality fileread_importwq
Import data from the Water Quality Portalread_importwqp
Import JSON seagrass transect data from Water Atlasread_transect
Seagrass coverage by yearseagrass
Sediment data for the Tampa Bay current as of 12142023sedimentdata
Seagrass management areas for Tampa Baysgmanagement
Seagrass segment reporting boundaries for southwest Floridasgseg
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
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
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 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 65tidalcreeks
Tidal creek nitrogen targetstidaltargets
Seagrass transect data for Tampa Bay current as of 11032024transect
Seagrass transect locationstrnlns
Seagrass transect starting locationstrnpts
Return leaflet icon set for FIB mapsutil_fibicons
A list of Fecal Indicator Bacteria (FIB) factor levels and labelsutil_fiblevs
Convert character string to html classutil_html
Create an empty leaflet map from sf inpututil_map
Get organization name from organization identifier in USEPA Water Quality Portalutil_orgin