{ "_id": "6ac3e15f34f9a32edea2315e", "Package": "tbepreport", "Title": "Compile and Visualize Ecosystem Report Card Indicators for Tampa\nBay", "Version": "1.0.0", "Authors@R": "person(given = \"Marcus\",\nfamily = \"Beck\",\nrole = c(\"aut\", \"cre\"),\nemail = \"mbeck@tbep.org\",\ncomment = c(ORCID = \"0000-0002-4996-0059\")\n)", "Description": "Functions to calculate, combine, and visualize water\nquality, sediment, fish/wildlife, and habitat indicators as bay\nsegment \"report card\" scores for the Tampa Bay Estuary Program.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "LazyData": "true", "LazyDataCompression": "xz", "URL": "", "BugReports": "https://github.com/tbep-tech/tbepreport/issues", "SystemRequirements": "GDAL (>= 2.0.0)", "Remotes": [ "tbep-tech/tbeptools" ], "Config/testthat/edition": "3", "VignetteBuilder": "quarto", "Config/pak/sysreqs": "libabsl-dev libcairo2-dev cmake libfontconfig1-dev\nlibfreetype6-dev libfribidi-dev libgdal-dev gdal-bin\nlibgeos-dev make libharfbuzz-dev libicu-dev libjpeg-dev\nlibpng-dev libtiff-dev libuv1-dev libwebp-dev libxml2-dev\nlibssl-dev libproj-dev libsqlite3-dev libudunits2-dev\nlibx11-dev", "Repository": "https://tbep-tech.r-universe.dev", "Date/Publication": "2026-08-21 12:17:40 UTC", "RemoteUrl": "https://github.com/tbep-tech/tbepreport", "RemoteRef": "HEAD", "RemoteSha": "c09fdfe065672fbddd51c544bd3f13714908384e", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-05 17:02:45 UTC", "User": "root" }, "Author": "Marcus Beck [aut, cre] (ORCID: )", "Maintainer": "Marcus Beck ", "_user": "tbep-tech", "_type": "src", "_file": "tbepreport_1.0.0.tar.gz", "_fileid": "https://r2.ropensci.org/a88ff7ab1490ae5b603b7b4278a39b5d46313fe8b9867fc0f077e1585204f0e5", "_filesize": 3340437, "_sha256": "a88ff7ab1490ae5b603b7b4278a39b5d46313fe8b9867fc0f077e1585204f0e5", "_expires": "2027-01-13T17:41:48.000Z", "_created": "2026-10-05T17:02:45.000Z", "_published": "2026-10-05T17:41:51.357Z", "_jobs": [ { "job": 111883102278, "time": 286, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "11360492283" }, { "job": 111883102575, "time": 288, "config": "linux-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "11360890774" }, { "job": 111883102157, "time": 266, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "11361918089" }, { "job": 111883102093, "time": 286, "config": "macos-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "11361958212" }, { "job": 111879267957, "time": 532, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11360057292" }, { "job": 111883102144, "time": 156, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11359319414" }, { "job": 111883103009, "time": 282, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "ERROR", "artifact": "11360019097" }, { "job": 111883102306, "time": 268, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "11359319687" }, { "job": 111883102421, "time": 264, "config": "windows-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "11359929234" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/tbep-tech/actions/runs/37344359262", "_status": "success", "_upstream": "https://github.com/tbep-tech/tbepreport", "_commit": { "id": "c09fdfe065672fbddd51c544bd3f13714908384e", "author": "fawda123 ", "committer": "fawda123 ", "message": "minor vignette language tweak\n", "time": 1787314660 }, "_maintainer": { "name": "Marcus Beck", "email": "mbeck@tbep.org", "login": "fawda123", "description": "Scientist with the Tampa Bay Estuary Program", "uuid": 3086881, "orcid": "0000-0002-4996-0059" }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.2", "role": "Depends" }, { "package": "tbeptools", "role": "Depends" }, { "package": "dplyr", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "ggrepel", "role": "Imports" }, { "package": "here", "role": "Imports" }, { "package": "jsonlite", "role": "Imports" }, { "package": "plotly", "role": "Imports" }, { "package": "purrr", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "scales", "role": "Imports" }, { "package": "sf", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "tibble", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "tools", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "mockery", "role": "Suggests" }, { "package": "patchwork", "role": "Suggests" }, { "package": "quarto", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "tbep-tech", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-31", "n": 1 }, { "week": "2026-32", "n": 18 }, { "week": "2026-33", "n": 10 }, { "week": "2026-34", "n": 17 } ], "_tags": [ { "name": "v1.0.0", "date": "2026-08-18" } ], "_topics": [ "reporting", "tampa-bay", "tbep", "quarto" ], "_stars": 0, "_contributors": [ { "user": "fawda123", "count": 46, "uuid": 3086881 } ], "_userbio": { "uuid": 49565964, "type": "organization", "name": "Tampa Bay Estuary Program", "followers": 35, "description": "Tampa Bay Estuary Program is an independent, special district of the State of Florida, and 1 of 28 national estuary programs administered by the USEPA." }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/tbepreport" }, "_devurl": "https://github.com/tbep-tech/tbepreport", "_searchresults": 0, "_quarto": true, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "extra/tbepreport.html", "LICENSE" ], "_cranurl": false, "_exports": [ "anlz_category", "anlz_fw_nonnative_abundance", "anlz_fw_nonnative_obs", "anlz_fw_nonnative_richness", "anlz_fw_tbni", "anlz_hab_seagrass_coverage", "anlz_hab_seagrass_transect", "anlz_indicators", "anlz_score", "anlz_sed_peltel", "anlz_sed_tbbi", "anlz_wq_attain", "anlz_wq_fib", "anlz_wq_load", "anlz_wq_thresh", "anlz_wq_tidalcreeks", "plot_category", "plot_score", "plot_trend", "util_fw_fetch_fim", "util_fw_fetch_nas", "util_fw_nonnative_areas", "util_fw_nonnative_long", "util_outcome", "util_percentile", "util_rdataload" ], "_datasets": [ { "name": "aoi_shp", "title": "Area of interest boundary for non-native species occurrence data", "object": "aoi_shp", "class": [ "sf", "data.frame" ], "fields": [ "BAY_SEG", "area_ac", "geometry" ], "rows": 1, "table": false, "tojson": true }, { "name": "bayseg_shp", "title": "Bay segment boundaries for non-native species occurrence data", "object": "bayseg_shp", "class": [ "sf", "data.frame" ], "fields": [ "BAY_SEG", "BAY_SEG_GP", "BAY_GP_ABB", "area_ac", "geometry" ], "rows": 7, "table": false, "tojson": true }, { "name": "sgsegest", "title": "Seagrass coverage estimates by bay segment and year", "object": "sgsegest", "class": [ "data.frame" ], "fields": [ "segment", "acres", "year" ], "rows": 126, "table": true, "tojson": true } ], "_help": [ { "page": "anlz_category", "title": "Combine indicators into a single score by bay segment and year", "topics": [ "anlz_category" ] }, { "page": "anlz_fw_nonnative_abundance", "title": "Non-native species abundance outcome by bay segment and year", "topics": [ "anlz_fw_nonnative_abundance" ] }, { "page": "anlz_fw_nonnative_obs", "title": "Non-native species occurrence points, clipped and assigned to a bay segment", "topics": [ "anlz_fw_nonnative_obs" ] }, { "page": "anlz_fw_nonnative_richness", "title": "Non-native species richness outcome by bay segment and year", "topics": [ "anlz_fw_nonnative_richness" ] }, { "page": "anlz_fw_tbni", "title": "Tampa Bay Nekton Index (TBNI) outcome by bay segment and year", "topics": [ "anlz_fw_tbni" ] }, { "page": "anlz_hab_seagrass_coverage", "title": "Seagrass coverage outcome by bay segment and year", "topics": [ "anlz_hab_seagrass_coverage" ] }, { "page": "anlz_hab_seagrass_transect", "title": "Seagrass transect frequency of occurrence outcome by bay segment and year", "topics": [ "anlz_hab_seagrass_transect" ] }, { "page": "anlz_indicators", "title": "Stack indicator outcomes into one long-format table", "topics": [ "anlz_indicators" ] }, { "page": "anlz_score", "title": "Overall bay segment score across all four indicator categories", "topics": [ "anlz_score" ] }, { "page": "anlz_sed_peltel", "title": "Sediment quality (PEL/TEL) outcome by bay segment and year", "topics": [ "anlz_sed_peltel" ] }, { "page": "anlz_sed_tbbi", "title": "Benthic index (TBBI) outcome by bay segment and year", "topics": [ "anlz_sed_tbbi" ] }, { "page": "anlz_wq_attain", "title": "Water quality attainment outcome by bay segment and year", "topics": [ "anlz_wq_attain" ] }, { "page": "anlz_wq_fib", "title": "Fecal indicator bacteria (FIB) outcome by bay segment and year", "topics": [ "anlz_wq_fib" ] }, { "page": "anlz_wq_load", "title": "Nutrient loading outcome by bay segment, year, and indicator", "topics": [ "anlz_wq_load" ] }, { "page": "anlz_wq_thresh", "title": "Water quality threshold attainment outcome by bay segment, year, and variable", "topics": [ "anlz_wq_thresh" ] }, { "page": "anlz_wq_tidalcreeks", "title": "Tidal creek condition outcome by bay segment and year", "topics": [ "anlz_wq_tidalcreeks" ] }, { "page": "aoi_shp", "title": "Area of interest boundary for non-native species occurrence data", "topics": [ "aoi_shp" ] }, { "page": "bayseg_shp", "title": "Bay segment boundaries for non-native species occurrence data", "topics": [ "bayseg_shp" ] }, { "page": "plot_category", "title": "Sunburst plot of indicator outcomes for one category, bay segment, and year", "topics": [ "plot_category" ] }, { "page": "plot_score", "title": "Sunburst plot of indicator, category, and overall outcomes for one bay segment and year", "topics": [ "plot_score" ] }, { "page": "plot_trend", "title": "Faceted trend plot of indicator, category, and overall outcomes over time", "topics": [ "plot_trend" ] }, { "page": "sgsegest", "title": "Seagrass coverage estimates by bay segment and year", "topics": [ "sgsegest" ] }, { "page": "util_fw_fetch_fim", "title": "Fetch the Tampa Bay FIM species dataset", "topics": [ "util_fw_fetch_fim" ] }, { "page": "util_fw_fetch_nas", "title": "Fetch USGS NAS non-native species occurrences for a set of HUC8 watersheds", "topics": [ "util_fw_fetch_nas" ] }, { "page": "util_fw_nonnative_areas", "title": "Bay segment and AOI areas for non-native species density calculations", "topics": [ "util_fw_nonnative_areas" ] }, { "page": "util_fw_nonnative_long", "title": "Reshape a non-native metric's wide year-by-segment table to long format", "topics": [ "util_fw_nonnative_long" ] }, { "page": "util_outcome", "title": "Convert raw indicator values to a 0-1 outcome score", "topics": [ "util_outcome" ] }, { "page": "util_percentile", "title": "Convert a wide data frame of values to percentiles by mean and standard deviation", "topics": [ "util_percentile" ] }, { "page": "util_rdataload", "title": "Load an RData file from a URL", "topics": [ "util_rdataload" ] } ], "_pkglogo": "https://github.com/tbep-tech/tbepreport/raw/HEAD/man/figures/logo.png", "_readme": "https://github.com/tbep-tech/tbepreport/raw/HEAD/README.md", "_rundeps": [ "askpass", "base64enc", "bit", "bit64", "bslib", "cachem", "cellranger", "class", "classInt", "cli", "clipr", "cpp11", "crayon", "crosstalk", "curl", "data.table", "dataRetrieval", "DBI", "digest", "dplyr", "e1071", "evaluate", "farver", "fastmap", "flextable", "fontawesome", "fontBitstreamVera", "fontLiberation", "fontquiver", "fs", "gdtools", "generics", "ggplot2", "ggrepel", "glue", "gtable", "here", "highr", "hms", "htmltools", "htmlwidgets", "httr", "httr2", "isoband", "jquerylib", "jsonlite", "KernSmooth", "knitr", "labeling", "later", "lattice", "lazyeval", "leaflet", "leaflet.providers", "lifecycle", "lubridate", "magrittr", "memoise", "mime", "officer", "openssl", "otel", "patchwork", "pillar", "pkgconfig", "plotly", "png", "prettyunits", "progress", "promises", "proxy", "purrr", "R6", "ragg", "rappdirs", "raster", "RColorBrewer", "Rcpp", "reactable", "reactR", "readr", "readxl", "rematch", "rlang", "rmarkdown", "rprojroot", "rvest", "s2", "S7", "sass", "scales", "selectr", "sf", "sp", "stringi", "stringr", "sys", "systemfonts", "tbeptools", "terra", "textshaping", "tibble", "tidyr", "tidyselect", "timechange", "tinytex", "tzdb", "units", "utf8", "uuid", "vctrs", "viridisLite", "vroom", "whisker", "withr", "wk", "xfun", "xml2", "yaml", "zip" ], "_vignettes": [ { "source": "scoring.qmd", "filename": "scoring.html", "title": "scoring", "engine": "quarto::html", "headings": [ "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" ], "created": "2026-08-09 18:40:15", "modified": "2026-08-21 12:17:40", "commits": 18 }, { "source": "tbepreport.qmd", "filename": "tbepreport.html", "title": "tbepreport", "engine": "quarto::html", "headings": [ "Compute Indicators", "Combine Scores", "Visualize" ], "created": "2026-08-07 13:11:02", "modified": "2026-08-18 13:10:35", "commits": 4 }, { "source": "trends.qmd", "filename": "trends.html", "title": "trends", "engine": "quarto::html", "headings": [ "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" ], "created": "2026-08-18 21:35:50", "modified": "2026-08-21 12:17:40", "commits": 6 } ], "_score": 3.778151250383644, "_indexed": true, "_nocasepkg": "tbepreport", "_universes": [ "tbep-tech", "fawda123" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.0.0", "date": "2026-10-05T17:05:43.000Z", "distro": "resolute", "commit": "c09fdfe065672fbddd51c544bd3f13714908384e", "fileid": "https://r2.ropensci.org/2750a47ac591ea910f9c3cdd2517f427729ae29ea4af1767b065ed8011a366f5", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/tbep-tech/actions/runs/37344359262" }, { "r": "4.6.1", "os": "linux", "version": "1.0.0", "date": "2026-10-05T17:05:38.000Z", "distro": "resolute", "commit": "c09fdfe065672fbddd51c544bd3f13714908384e", "fileid": "https://r2.ropensci.org/7d33d52b3bb4068358cd664f6f3352df5aad3d8002f077faa0ceee9d089e5591", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/tbep-tech/actions/runs/37344359262" }, { "r": "4.5.3", "os": "mac", "version": "1.0.0", "date": "2026-10-05T17:39:15.000Z", "commit": "c09fdfe065672fbddd51c544bd3f13714908384e", "fileid": "https://r2.ropensci.org/dc4e01253f3481924682192025e622ffdb8cd4bf78fe90200853e0d4181bb6d6", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/tbep-tech/actions/runs/37344359262" }, { "r": "4.6.1", "os": "mac", "version": "1.0.0", "date": "2026-10-05T17:36:30.000Z", "commit": "c09fdfe065672fbddd51c544bd3f13714908384e", "fileid": "https://r2.ropensci.org/f85b722b8b8d283b6134a1db597432246b1111557366bd8976afb84169382e8e", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/tbep-tech/actions/runs/37344359262" }, { "r": "4.6.0", "os": "wasm", "version": "1.0.0", "date": "2026-10-05T17:05:57.000Z", "commit": "c09fdfe065672fbddd51c544bd3f13714908384e", "fileid": "https://r2.ropensci.org/ec4d3847b0f0d919caed4eed4653c77bd601d4c9125f688443d8acd3e528fb0f", "status": "success", "buildurl": "https://github.com/r-universe/tbep-tech/actions/runs/37344359262" }, { "r": "4.7.0", "os": "win", "version": "1.0.0", "date": "2026-10-05T17:05:12.000Z", "commit": "c09fdfe065672fbddd51c544bd3f13714908384e", "fileid": "https://r2.ropensci.org/91638dfe64b83a576a30c5b88ed17227b941f5ecb6cfee5d1cf8edc62bf7ed14", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/tbep-tech/actions/runs/37344359262" }, { "r": "4.5.3", "os": "win", "version": "1.0.0", "date": "2026-10-05T17:05:05.000Z", "commit": "c09fdfe065672fbddd51c544bd3f13714908384e", "fileid": "https://r2.ropensci.org/80d65c44be01b1d7eb9512a14e6dad1c4c10cd14ddba2c947784838123bacc2e", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/tbep-tech/actions/runs/37344359262" }, { "r": "4.6.1", "os": "win", "version": "1.0.0", "date": "2026-10-05T17:04:58.000Z", "commit": "c09fdfe065672fbddd51c544bd3f13714908384e", "fileid": "https://r2.ropensci.org/3fe4a22b8e8d638e412068d046599f8b6da548f3c95209731609b0dc15f9e7dc", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/tbep-tech/actions/runs/37344359262" } ] }