{ "_id": "6a2148c9cd65a98ecbd2bed3", "Package": "epiviz", "Title": "Data Visualisation Functions for Epidemiological Data Science\nProducts", "Version": "0.1.2", "Authors@R": "c(person(given=\"Harshana\", family=\"Liyanage\", email=\"harshana.liyanage@ukhsa.gov.uk\", role = c(\"aut\",\"cre\"),\ncomment = c(ORCID = \"0000-0001-9738-6349\")),\nperson(given=\"James\", family=\"Duke\", email=\"james.duke@ukhsa.gov.uk\", role = c(\"aut\")),\nperson(given=\"Alex\", family=\"Bhattacharya\", email=\"alex.bhattacharya@ukhsa.gov.uk\", role = c(\"aut\"),\ncomment = c(ORCID = \"0000-0003-3000-2771\")),\nperson(given=\"Liam\", family=\"Fitzpatrick\", email=\"liam.fitzpatrick@ukhsa.gov.uk\", role = c(\"aut\")),\nperson(given=\"James\", family=\"Leatherland\", email=\"james.leatherland@ukhsa.gov.uk\", role = c(\"aut\")),\nperson(given=\"Jordan\", family=\"Worth\", email=\"jordan.worth@ukhsa.gov.uk\", role = c(\"aut\")),\nperson(given=\"Emma\", family=\"Parker\", email=\"emma.k.parker@ukhsa.gov.uk\", role = c(\"aut\")),\nperson(given=\"Jade\", family=\"Talbot\", email=\"Jade.Talbot@ukhsa.gov.uk\", role = c(\"ctb\"),\ncomment = c(ORCID = \"0000-0001-6460-5170\")),\nperson(given=\"Karen\", family=\"Crawford\", email=\"Karen.Crawford@ukhsa.gov.uk\", role = c(\"ctb\")),\nperson(given=\"Frederick\", family=\"Sloots\", email=\"Frederick.Sloots@ukhsa.gov.uk\", role = c(\"ctb\")),\nperson(given=\"Charlie\", family=\"Turner\", email=\"Charlie.Turner@ukhsa.gov.uk\", role = c(\"ctb\"))\n)", "Description": "Tools for making epidemiological reporting easier with\nconsistent static and dynamic charts and maps. Builds on\n'ggplot2' for static visualizations as described in Wickham\n(2016) and 'plotly' for\ninteractive visualizations as described in Sievert (2020)\n.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "LazyData": "true", "LazyDataCompression": "xz", "Config/testthat/edition": "3", "VignetteBuilder": "knitr", "URL": "https://github.com/ukhsa-collaboration/epiviz", "BugReports": "https://github.com/ukhsa-collaboration/epiviz/issues", "Repository": "https://ukhsa-collaboration.r-universe.dev", "Date/Publication": "2026-02-28 18:12:39 UTC", "RemoteUrl": "https://github.com/ukhsa-collaboration/epiviz", "RemoteRef": "HEAD", "RemoteSha": "2f820bb9313326024659e2f68f7bfed07832e789", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-04 09:38:36 UTC", "User": "root" }, "Author": "Harshana Liyanage [aut, cre] (ORCID:\n),\nJames Duke [aut],\nAlex Bhattacharya [aut] (ORCID:\n),\nLiam Fitzpatrick [aut],\nJames Leatherland [aut],\nJordan Worth [aut],\nEmma Parker [aut],\nJade Talbot [ctb] (ORCID: ),\nKaren Crawford [ctb],\nFrederick Sloots [ctb],\nCharlie Turner [ctb]", "Maintainer": "Harshana Liyanage ", "MD5sum": "fb01e52b23301851d2c3ccc7d5814362", "_user": "ukhsa-collaboration", "_type": "src", "_file": "epiviz_0.1.2.tar.gz", "_fileid": "45f2a37899b1feb72a62e569f2a2195b8e566be5a8e68fcda84bb4a3940b941b", "_filesize": 5642518, "_sha256": "45f2a37899b1feb72a62e569f2a2195b8e566be5a8e68fcda84bb4a3940b941b", "_created": "2026-06-04T09:38:36.000Z", "_published": "2026-06-04T09:43:37.455Z", "_distro": "noble", "_jobs": [ { "job": 79491542467, "time": 225, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7408198853" }, { "job": 79491542606, "time": 214, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7408194382" }, { "job": 79491542494, "time": 147, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7408169562" }, { "job": 79491542502, "time": 182, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7408182530" }, { "job": 79490826967, "time": 253, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7408116277" }, { "job": 79491542459, "time": 169, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7408177365" }, { "job": 79491542497, "time": 199, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7408188942" }, { "job": 79491542601, "time": 195, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7408187487" }, { "job": 79491542487, "time": 175, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7408180015" } ], "_buildurl": "https://github.com/r-universe/ukhsa-collaboration/actions/runs/26943562808", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/ukhsa-collaboration/epiviz", "_commit": { "id": "2f820bb9313326024659e2f68f7bfed07832e789", "author": "Harshana Liyanage <148277171+harshana-ukhsa@users.noreply.github.com>", "committer": "GitHub ", "message": "Merge pull request #8 from ukhsa-collaboration/crancomments-feb\n\nCran comments addressed", "time": 1772302359 }, "_maintainer": { "name": "Harshana Liyanage", "email": "harshana.liyanage@ukhsa.gov.uk", "login": "harshana-ukhsa", "description": "", "uuid": 148277171, "orcid": "0000-0001-9738-6349" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "grDevices", "role": "Imports" }, { "package": "assertthat", "role": "Imports" }, { "package": "classInt", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "RColorBrewer", "role": "Imports" }, { "package": "plotly", "role": "Imports" }, { "package": "sf", "role": "Imports" }, { "package": "leaflet", "role": "Imports" }, { "package": "htmltools", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "scales", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "lubridate", "role": "Imports" }, { "package": "ISOweek", "role": "Imports" }, { "package": "forcats", "role": "Imports" }, { "package": "slider", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "ellmer", "role": "Imports" }, { "package": "jsonlite", "role": "Imports" }, { "package": "lifecycle", "role": "Imports" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "mockery", "role": "Suggests" }, { "package": "withr", "role": "Suggests" }, { "package": "yarrr", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "shiny", "role": "Suggests" } ], "_owner": "ukhsa-collaboration", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-29", "n": 1 }, { "week": "2025-40", "n": 2 }, { "week": "2025-42", "n": 13 }, { "week": "2025-43", "n": 7 }, { "week": "2025-44", "n": 15 }, { "week": "2026-02", "n": 2 }, { "week": "2026-09", "n": 1 } ], "_tags": [ { "name": "v0.1.0", "date": "2025-10-23" }, { "name": "v0.1.1", "date": "2025-10-29" }, { "name": "v0.1.1-cran", "date": "2025-10-31" } ], "_stars": 4, "_contributors": [ { "user": "harshanal", "count": 225, "uuid": 270178 }, { "user": "jamesbduke", "count": 95, "uuid": 171152303 }, { "user": "harshana-ukhsa", "count": 72, "uuid": 148277171 } ], "_userbio": { "uuid": 116561398, "type": "organization", "name": "ukhsa-collaboration" }, "_downloads": { "count": 565, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/epiviz" }, "_devurl": "https://github.com/ukhsa-collaboration/epiviz", "_searchresults": 43, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/epiviz.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/ukhsa-collaboration/epiviz", "_realowner": "ukhsa-collaboration", "_cranurl": true, "_releases": [ { "version": "0.1.2", "date": "2026-03-05" } ], "_exports": [ "age_sex_pyramid", "col_chart", "epi_curve", "epi_map", "line_chart", "llm_interpret", "point_chart" ], "_datasets": [ { "name": "lab_data", "title": "Synthetic Lab Data for EpiViz functions", "object": "lab_data", "class": [ "data.frame" ], "fields": [ "date_of_birth", "sex", "organism_species_name", "specimen_date", "lab_code", "local_authority_name", "local_authority_code", "region" ], "rows": 32560, "table": true, "tojson": true }, { "name": "London_LA_boundaries_2023", "title": "Local Authority Districts (May 2023) Boundaries for London BGC", "object": "London_LA_boundaries_2023", "class": [ "sf", "tbl_df", "tbl", "data.frame" ], "fields": [ "FID", "LAD23CD", "LAD23NM", "LAD23NMW", "BNG_E", "BNG_N", "LONG", "LAT", "GlobalID", "SHAPE_Length", "SHAPE_Area", "geometry" ], "rows": 33, "table": false, "tojson": true }, { "name": "PHEC_boundaries_2016", "title": "PHEC (Dec 2016) Generalised Clipped Boundaries in England", "object": "PHEC_boundaries_2016", "class": [ "sf", "tbl_df", "tbl", "data.frame" ], "fields": [ "OBJECTID", "phec16cd", "phec16nm", "bng_e", "bng_n", "long", "lat", "GlobalID", "SHAPE_Length", "SHAPE_Area", "geometry" ], "rows": 9, "table": false, "tojson": true }, { "name": "UK_boundaries_2023", "title": "Countries (December 2023) Boundaries UK BUC", "object": "UK_boundaries_2023", "class": [ "sf", "tbl_df", "tbl", "data.frame" ], "fields": [ "FID", "CTRY23CD", "CTRY23NM", "CTRY23NMW", "BNG_E", "BNG_N", "LONG", "LAT", "GlobalID", "SHAPE_Length", "SHAPE_Area", "geometry" ], "rows": 4, "table": false, "tojson": true } ], "_help": [ { "page": "age_sex_pyramid", "title": "Age-Sex Pyramid", "topics": [ "age_sex_pyramid" ] }, { "page": "col_chart", "title": "Column chart", "topics": [ "col_chart" ] }, { "page": "epi_curve", "title": "Epi Curve", "topics": [ "epi_curve" ] }, { "page": "epi_map", "title": "Epi Map", "topics": [ "epi_map" ] }, { "page": "lab_data", "title": "Synthetic Lab Data for EpiViz functions", "topics": [ "lab_data" ] }, { "page": "line_chart", "title": "Line Chart", "topics": [ "line_chart" ] }, { "page": "llm_interpret", "title": "Interpret Epidemiological Data or Visualisations using LLMs", "topics": [ "llm_interpret" ] }, { "page": "point_chart", "title": "Point Chart", "topics": [ "point_chart" ] } ], "_pkglogo": "https://github.com/ukhsa-collaboration/epiviz/raw/HEAD/man/figures/logo.png", "_readme": "https://github.com/ukhsa-collaboration/epiviz/raw/HEAD/README.md", "_rundeps": [ "askpass", "assertthat", "base64enc", "bslib", "cachem", "class", "classInt", "cli", "coro", "cpp11", "crosstalk", "curl", "data.table", "DBI", "digest", "dplyr", "e1071", "ellmer", "evaluate", "farver", "fastmap", "fontawesome", "forcats", "fs", "generics", "ggplot2", "glue", "gtable", "highr", "htmltools", "htmlwidgets", "httr", "httr2", "isoband", "ISOweek", "jquerylib", "jsonlite", "KernSmooth", "knitr", "labeling", "later", "lattice", "lazyeval", "leaflet", "leaflet.providers", "lifecycle", "lubridate", "magrittr", "MASS", "memoise", "mime", "openssl", "otel", "pillar", "pkgconfig", "plotly", "png", "promises", "proxy", "purrr", "R6", "rappdirs", "raster", "RColorBrewer", "Rcpp", "rlang", "rmarkdown", "s2", "S7", "sass", "scales", "sf", "slider", "sp", "stringi", "stringr", "sys", "terra", "tibble", "tidyr", "tidyselect", "timechange", "tinytex", "units", "utf8", "vctrs", "viridisLite", "warp", "withr", "wk", "xfun", "yaml" ], "_vignettes": [ { "source": "age-sex-pyramid.Rmd", "filename": "age-sex-pyramid.html", "title": "Age-sex pyramids", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Prerequisites", "Example 1: Static pyramid from line-list data", "Prepare the line-list data", "Plot the static pyramid", "Example 2: Interactive grouped pyramid with confidence intervals", "Aggregate counts and calculate confidence intervals", "Plot the interactive grouped pyramid", "Tips for age-sex pyramids" ], "created": "2025-10-16 18:15:43", "modified": "2025-10-16 18:15:43", "commits": 1 }, { "source": "col-chart.Rmd", "filename": "col-chart.html", "title": "Column charts", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Prerequisites", "Example 1: Basic single-series column chart", "Prepare the data", "Create the basic column chart", "Example 2: Grouped stacked column chart", "Create the grouped stacked chart", "Example 3: Column chart with bar labels", "Create the chart with bar labels", "Example 4: Interactive column chart with case boxes", "Prepare data for case boxes", "Create the interactive chart with case boxes", "Example 5: Column chart with threshold lines", "Create the chart with threshold lines", "Example 6: Time-series column chart", "Prepare the time-series data", "Create the time-series column chart", "Tips for column charts" ], "created": "2025-10-16 18:15:43", "modified": "2025-10-16 18:15:43", "commits": 1 }, { "source": "epi-curve.Rmd", "filename": "epi-curve.html", "title": "Epi curves", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Prerequisites", "Example 1: Basic epi curve with rolling average", "Create the basic epi curve", "Example 2: Grouped epi curve with stacked bars", "Create the grouped epi curve", "Example 3: Daily epi curve with case boxes and cumulative line", "Create the detailed daily epi curve", "Example 4: Pre-aggregated data with rolling and cumulative lines", "Prepare pre-aggregated data", "Create the pre-aggregated epi curve", "Example 5: Interactive grouped epi curve", "Create the interactive grouped epi curve", "Tips for epi curves" ], "created": "2025-10-16 18:15:43", "modified": "2025-10-30 12:47:26", "commits": 3 }, { "source": "epi-map.Rmd", "filename": "epi-map.html", "title": "Epidemiological maps", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Prerequisites", "Example 1: Static map with un-merged shapefile", "Prepare the data", "Create the static map with un-merged shapefile", "Example 2: Static map with pre-merged shapefile", "Prepare the pre-merged data", "Create the static map with pre-merged data", "Example 3: Static map with border shapefile", "Create the map with border shapefile", "Example 4: Interactive map with un-merged shapefile", "Create the interactive map", "Example 5: Interactive map with border shapefile and area labels", "Create the interactive map with borders and labels", "Tips for epidemiological maps" ], "created": "2025-10-16 18:15:43", "modified": "2025-10-16 19:23:11", "commits": 2 }, { "source": "getting-started.Rmd", "filename": "getting-started.html", "title": "Getting started with epiviz", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Prerequisites", "The lab_data dataset", "Example 1: Regional distribution of detections", "Prepare the data", "Create the visualization", "Example 2: Temporal trends in detections", "Tips for getting started", "Next steps" ], "created": "2025-10-16 18:15:43", "modified": "2025-10-16 18:15:43", "commits": 1 }, { "source": "line-chart.Rmd", "filename": "line-chart.html", "title": "Line charts", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Prerequisites", "Example 1: Single time series without grouping", "Prepare the data", "Create the single time series line chart", "Example 2: Multiple time series with grouping", "Prepare the grouped data", "Create the multiple time series line chart", "Example 3: Interactive multiple time series", "Create the interactive line chart", "Example 4: Custom styled line chart with enhanced formatting", "Prepare data for enhanced styling", "Create the enhanced line chart", "Tips for line charts" ], "created": "2025-10-16 18:15:43", "modified": "2025-10-30 12:47:26", "commits": 3 }, { "source": "llm-interpret.Rmd", "filename": "llm-interpret.html", "title": "LLM-assisted epidemiological narrative", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Prerequisites", "Environment Setup", "Required Environment Variables", "Verify Setup", "Example 1: Interpreting an epidemic curve", "Prepare the data and create a visualization", "Interpret the visualisation", "Example 2: Custom interpretation with specific focus", "Interpret with custom epidemiological focus", "Tips for LLM interpretation", "Troubleshooting", "Common Issues" ], "created": "2025-10-16 18:15:43", "modified": "2025-10-30 12:47:26", "commits": 3 }, { "source": "point-chart.Rmd", "filename": "point-chart.html", "title": "Point charts", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Prerequisites", "Example 1: Basic point chart", "Prepare the data", "Create the basic point chart", "Example 2: Interactive point chart", "Create the interactive point chart", "Example 3: Grouped point chart with confidence ribbons", "Prepare grouped data with confidence intervals", "Create the grouped point chart with confidence ribbons", "Example 4: Point chart with threshold lines", "Create the point chart with threshold lines", "Example 5: Interactive grouped point chart with all features", "Create the comprehensive interactive point chart", "Tips for point charts" ], "created": "2025-10-16 18:15:43", "modified": "2025-10-30 12:47:26", "commits": 3 } ], "_score": 6.983716473913749, "_indexed": true, "_nocasepkg": "epiviz", "_universes": [ "ukhsa-collaboration", "harshana-ukhsa" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.1.2", "date": "2026-06-04T09:41:45.000Z", "distro": "noble", "commit": "2f820bb9313326024659e2f68f7bfed07832e789", "fileid": "e36e21830c5bcda44d1211eed74e8cbe68fad09d193975ca5c27e7c3c3e725fc", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ukhsa-collaboration/actions/runs/26943562808" }, { "r": "4.6.0", "os": "linux", "version": "0.1.2", "date": "2026-06-04T09:41:38.000Z", "distro": "noble", "commit": "2f820bb9313326024659e2f68f7bfed07832e789", "fileid": "3aa77bd03ebbcdc48ab8683e41f4d90c05a8cfe3c299103ed92652bc11ab49df", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ukhsa-collaboration/actions/runs/26943562808" }, { "r": "4.5.3", "os": "mac", "version": "0.1.2", "date": "2026-06-04T09:40:57.000Z", "commit": "2f820bb9313326024659e2f68f7bfed07832e789", "fileid": "81c8f72eb09573d1a121bc4820ec2f20f68641e02ed745eacf2b29614224a97b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ukhsa-collaboration/actions/runs/26943562808" }, { "r": "4.6.0", "os": "mac", "version": "0.1.2", "date": "2026-06-04T09:41:10.000Z", "commit": "2f820bb9313326024659e2f68f7bfed07832e789", "fileid": "76bee26fc6fc1d920c4b5b3c35856ac31f248d6c94ad5c5c4be879044695b842", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ukhsa-collaboration/actions/runs/26943562808" }, { "r": "4.6.0", "os": "wasm", "version": "0.1.2", "date": "2026-06-04T09:42:12.000Z", "commit": "2f820bb9313326024659e2f68f7bfed07832e789", "fileid": "1c6282bf08140697aa327a1278bbbf1c3ce8de40012b61243c2ca410c47c2b51", "status": "success", "buildurl": "https://github.com/r-universe/ukhsa-collaboration/actions/runs/26943562808" }, { "r": "4.7.0", "os": "win", "version": "0.1.2", "date": "2026-06-04T09:40:56.000Z", "commit": "2f820bb9313326024659e2f68f7bfed07832e789", "fileid": "48e093e8597b30f822062b04299b0a5e21e9b1080085d9601c16e21a13144f3f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ukhsa-collaboration/actions/runs/26943562808" }, { "r": "4.5.3", "os": "win", "version": "0.1.2", "date": "2026-06-04T09:40:49.000Z", "commit": "2f820bb9313326024659e2f68f7bfed07832e789", "fileid": "3e07af74d1cf0aeeb9e0012cb90e1341412738d742d35aaeb33472408ef8cad3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ukhsa-collaboration/actions/runs/26943562808" }, { "r": "4.6.0", "os": "win", "version": "0.1.2", "date": "2026-06-04T09:40:36.000Z", "commit": "2f820bb9313326024659e2f68f7bfed07832e789", "fileid": "d3e9447ef2491d2dab11abdadc549586eb8db8f5cb6e24c0c94667d4e1d3d3bb", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ukhsa-collaboration/actions/runs/26943562808" } ] }