Package index • tbeptools

Read data

Functions for reading data.

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 Portal

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 use

read_importfib(): Load local water quality file for Fecal Indicator Bacteria (FIB)

read_importfim(): Load local FIM data for the Tampa Bay Nekton Index

read_importphyto(): Load local phytoplankton cell count file

read_importrain(): Download daily precip data and summarise by station catchment

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_transect(): Import JSON seagrass transect data from Water Atlas

Analyze data

Functions for analyzing data.

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) data

anlz_fibmatrix(): Analyze Fecal Indicator Bacteria categories over time by station or bay segment

anlz_fibwetdry(): Identify Fecal Indicator Bacteria samples as coming from a 'wet' or 'dry' time period

anlz_hmpreport(): Evaluate Habitat Master Plan progress for report card

anlz_hydroload(): Estimate hydrological estimates and adjustment factors for bay segments

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 segment

anlz_sedimentpel(): Get sediment PEL ratios at stations in Tampa Bay

anlz_sedimentpelave(): Get average concentrations for a sediment parameter by bay segment

anlz_tbbimed(): Get annual medians of Tampa Bay Benthic Index scores by bay segment

anlz_tbbiscr(): Get Tampa Bay Benthic Index scores

anlz_tbniave(): Get annual averages of Tampa Bay Nekton Index scores by bay segment

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 segments and year

anlz_transectavespp(): Get annual averages of seagrass frequency occurrence by bay segments, year, and species

anlz_transectocc(): Get seagrass average abundance and occurrence across transects

anlz_yrattain(): Get attainment categories for a chosen year

Show data

Functions for plotting data.

show_annualassess(): Create a table for the annual management outcome assessments

show_boxplot(): Plot monthly chlorophyll or light attenuation values for a segment

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, and location

show_fibmatmap(): Map Fecal Indicator Bacteria matrix results by year

show_fibmatrix(): Plot a matrix of Fecal Indicator Bacteria categories over time by station or bay segment

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 reasonable assurance period

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 exceedances by segment

show_segplotly(): Plot chlorophyll and secchi data together with matrix outcomes

show_sitemap(): Map site attainment categories for a selected year

show_sitesegmap(): Map site and bay segment attainment categories for a selected year

show_tbbimatrix(): Plot a matrix of Tampa Bay Benthic Index scores over time by bay segment

show_tbnimatrix(): Plot a matrix of Tampa Bay Nekton Index scores over time by bay segment

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 across bay segments

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 a segment

show_transect(): Plot results for a seagrass transect by time and location

show_transectavespp(): Show annual averages of seagrass frequency occurrence by bay segments, year, and species

show_transectmatrix(): Show matrix of seagrass frequency occurrence by bay segments and year

show_transectsum(): Plot frequency occurrence for a seagrass transect by time for all species

show_wqmatrix(): Create a colorized table for chlorophyll or light attenuation exceedances

Internal datasets

Supporting datasets used by the other functions.

acres: Tampa Bay intertidal and supratidal land use and cover

benthicdata: Benthic data for the Tampa Bay Benthic Index current as of 20241212

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 20241212

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

Utility functions

Utility functions used by other functions.

util_fibicons(): Return leaflet icon set for FIB maps

util_fiblevs(): A list of Fecal Indicator Bacteria (FIB) factor levels and labels

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 Water Quality Portal