Package: tbepreport 1.0.0

Marcus Beck

tbepreport: Compile and Visualize Ecosystem Report Card Indicators for Tampa Bay

Functions to calculate, combine, and visualize water quality, sediment, fish/wildlife, and habitat indicators as bay segment "report card" scores for the Tampa Bay Estuary Program.

Authors:Marcus Beck [aut, cre]

tbepreport_1.0.0.tar.gz
tbepreport_1.0.0.zip(r-4.7-any)tbepreport_1.0.0.zip(r-4.6-any)tbepreport_1.0.0.zip(r-4.5-any)
tbepreport_1.0.0.tgz(r-4.6-any)tbepreport_1.0.0.tgz(r-4.5-any)
tbepreport_1.0.0.tar.gz(r-4.7-any)tbepreport_1.0.0.tar.gz(r-4.6-any)
tbepreport_1.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
tbepreport/json (API)

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

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

Datasets:
  • aoi_shp - Area of interest boundary for non-native species occurrence data
  • bayseg_shp - Bay segment boundaries for non-native species occurrence data
  • sgsegest - Seagrass coverage estimates by bay segment and year

On CRAN:

Conda:

reportingtampa-baytbepquarto

3.78 score 26 exports 120 dependencies

Last updated from:c09fdfe065. Checks:6 NOTE, 2 OK, 1 ERROR. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develNOTE286
source / vignettesOK532
linux-releaseNOTE288
macos-releaseNOTE286
macos-oldrelNOTE266
windows-develERROR282
windows-releaseNOTE264
windows-oldrelNOTE268
wasm-releaseOK156

Exports:anlz_categoryanlz_fw_nonnative_abundanceanlz_fw_nonnative_obsanlz_fw_nonnative_richnessanlz_fw_tbnianlz_hab_seagrass_coverageanlz_hab_seagrass_transectanlz_indicatorsanlz_scoreanlz_sed_peltelanlz_sed_tbbianlz_wq_attainanlz_wq_fibanlz_wq_loadanlz_wq_threshanlz_wq_tidalcreeksplot_categoryplot_scoreplot_trendutil_fw_fetch_fimutil_fw_fetch_nasutil_fw_nonnative_areasutil_fw_nonnative_longutil_outcomeutil_percentileutil_rdataload

Dependencies:askpassbase64encbitbit64bslibcachemcellrangerclassclassIntclicliprcpp11crayoncrosstalkcurldata.tabledataRetrievalDBIdigestdplyre1071evaluatefarverfastmapflextablefontawesomefontBitstreamVerafontLiberationfontquiverfsgdtoolsgenericsggplot2ggrepelgluegtableherehighrhmshtmltoolshtmlwidgetshttrhttr2isobandjquerylibjsonliteKernSmoothknitrlabelinglaterlatticelazyevalleafletleaflet.providerslifecyclelubridatemagrittrmemoisemimeofficeropensslotelpatchworkpillarpkgconfigplotlypngprettyunitsprogresspromisesproxypurrrR6raggrappdirsrasterRColorBrewerRcppreactablereactRreadrreadxlrematchrlangrmarkdownrprojrootrvests2S7sassscalesselectrsfspstringistringrsyssystemfontstbeptoolsterratextshapingtibbletidyrtidyselecttimechangetinytextzdbunitsutf8uuidvctrsviridisLitevroomwhiskerwithrwkxfunxml2yamlzip

scoring
Water Quality | Targets | Chlorophyll and Light Thresholds | Nutrient and Hydrologic Loading | Tidal Creeks | Fecal Indicator Bacteria | Sediment | Contaminants | Benthic Index | Fish and Wildlife | Nekton Index | Non-natives | Habitat | Seagrass Transects | Seagrass Coverage | Scoring | Continuous Example | Sediment Contaminants Example | Benthic Index Example | Smooth vs. Hard Threshold Example | Combining Scores | Visualizing Scores
Rendered fromscoring.qmdusingquarto::html

Last update: 2026-08-21
Started: 2026-08-09

trends
Setup | Comparing Bay Segments | Trends | 2024 Snapshot by Bay Segment | How Scoring Decisions Affect Results | Nekton Index: Breakpoint Window vs. Full Range | Threshold Scoring: Smooth vs. Hard Cutoff | Category Weights
Rendered fromtrends.qmdusingquarto::html

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

tbepreport
Compute Indicators | Combine Scores | Visualize
Rendered fromtbepreport.qmdusingquarto::html

Last update: 2026-08-18
Started: 2026-08-07

Readme and manuals

Help Manual

Help pageTopics
Combine indicators into a single score by bay segment and yearanlz_category
Non-native species abundance outcome by bay segment and yearanlz_fw_nonnative_abundance
Non-native species occurrence points, clipped and assigned to a bay segmentanlz_fw_nonnative_obs
Non-native species richness outcome by bay segment and yearanlz_fw_nonnative_richness
Tampa Bay Nekton Index (TBNI) outcome by bay segment and yearanlz_fw_tbni
Seagrass coverage outcome by bay segment and yearanlz_hab_seagrass_coverage
Seagrass transect frequency of occurrence outcome by bay segment and yearanlz_hab_seagrass_transect
Stack indicator outcomes into one long-format tableanlz_indicators
Overall bay segment score across all four indicator categoriesanlz_score
Sediment quality (PEL/TEL) outcome by bay segment and yearanlz_sed_peltel
Benthic index (TBBI) outcome by bay segment and yearanlz_sed_tbbi
Water quality attainment outcome by bay segment and yearanlz_wq_attain
Fecal indicator bacteria (FIB) outcome by bay segment and yearanlz_wq_fib
Nutrient loading outcome by bay segment, year, and indicatoranlz_wq_load
Water quality threshold attainment outcome by bay segment, year, and variableanlz_wq_thresh
Tidal creek condition outcome by bay segment and yearanlz_wq_tidalcreeks
Area of interest boundary for non-native species occurrence dataaoi_shp
Bay segment boundaries for non-native species occurrence databayseg_shp
Sunburst plot of indicator outcomes for one category, bay segment, and yearplot_category
Sunburst plot of indicator, category, and overall outcomes for one bay segment and yearplot_score
Faceted trend plot of indicator, category, and overall outcomes over timeplot_trend
Seagrass coverage estimates by bay segment and yearsgsegest
Fetch the Tampa Bay FIM species datasetutil_fw_fetch_fim
Fetch USGS NAS non-native species occurrences for a set of HUC8 watershedsutil_fw_fetch_nas
Bay segment and AOI areas for non-native species density calculationsutil_fw_nonnative_areas
Reshape a non-native metric's wide year-by-segment table to long formatutil_fw_nonnative_long
Convert raw indicator values to a 0-1 outcome scoreutil_outcome
Convert a wide data frame of values to percentiles by mean and standard deviationutil_percentile
Load an RData file from a URLutil_rdataload