Read

Download and import data

read_chkdate()

Compare date of local xlsx file with the same file on the server

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_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_importwq()

Load local water quality file

read_transect()

Import JSON seagrass transect data from Water Atlas

Analyze

Analyze and summarize data

anlz_attain()

Get attainment categories

anlz_attainsite()

Get site attainments

anlz_avedat()

Estimate annual means

anlz_avedatsite()

Estimate annual means by site

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_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

Visualize

Plot and map 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_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_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_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

Data

Supplementary data sets

benthicdata

Benthic data for the Tampa Bay Benthic Index current as of 10222020

epcdata

All bay data as of 02092021

fimdata

FIM data for Tampa Bay Nekton Index current as of 04242020

fimstations

Spatial data object of FIM stations including Tampa Bay segments

iwrraw

FDEP IWR run 56

seagrass

Seagrass coverage by year

stations

Bay stations by segment

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

transect

Seagrass transect data for Tampa Bay current as of 11202020

trnlns

Seagrass transect locations

trnpts

Seagrass transect starting locations

Other

Other functions not defined by the concepts above

bsmap

Terrain basemap

targets

Bay segment targets

tbniref

Reference conditions for Tampa Bay Nekton Index metrics

tbnispp

Reference table for Tampa Bay Nekton Index species classifications

tidaltargets

Tidal creek nitrogen targets