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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_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_importbenthic()
Download and import benthic data for Tampa Bay
read_importfim()
Load local FIM data for the Tampa Bay Nekton Index
read_importphyto()
Load local phytoplankton cell count file
read_importsediment()
Download and import sediment data for Tampa Bay
read_importwq()
Load local water quality file
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_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_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_boxplot()
Plot monthly chlorophyll or light attenuation values for a segment
show_compplot()
Make a bar plot for transect training group comparisons
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_reactable()
Create reactable table from matrix data
show_seagrasscoverage()
Create a barplot of seagrass coverage over time in Tampa Bay
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_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 12092022
bsmap
Terrain basemap
epcdata
All bay data as of 12132022
fimdata
FIM data for Tampa Bay Nekton Index current as of 12122022
fimstations
Spatial data object of FIM stations including Tampa Bay segments
hmptrgs
Habitat Master Plan targets and goals
iwrraw
FDEP IWR run 61
phytodata
Phytoplankton data current as of 05192022
seagrass
Seagrass coverage by year
sedimentdata
Sediment data for the Tampa Bay current as of 01062023
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
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
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
tidaltargets
Tidal creek nitrogen targets
transect
Seagrass transect data for Tampa Bay current as of 12122022
trnlns
Seagrass transect locations
trnpts
Seagrass transect starting locations