{
  "_id": "69d4c2a410581d1350db9ec9",
  "Package": "ggsurveillance",
  "Title": "Tools for Outbreak Investigation/Infectious Disease Surveillance",
  "Version": "0.5.2",
  "Authors@R": "person(\"Alexander\", \"Bartel\", , \"alexander.bartel@fu-berlin.de\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-1280-6138\"))",
  "Description": "Create epicurves, epigantt charts, and diverging bar\ncharts using 'ggplot2'. Prepare data for visualisation or other\nreporting for infectious disease surveillance and outbreak\ninvestigation (time series data).  Includes tidy functions to\nsolve date based transformations for common reporting tasks,\nlike (A) seasonal date alignment for respiratory disease\nsurveillance, (B) date-based case binning based on specified\ntime intervals like isoweek, epiweek, month and more, (C)\nautomated detection and marking of the new year based on the\ndate/datetime axis of the 'ggplot2', (D) labelling of the last\nvalue of a time-series.  An introduction on how to use\nepicurves can be found on the US CDC website (2012,\n<https://www.cdc.gov/training/quicklearns/epimode/index.html>).",
  "License": "GPL (>= 3)",
  "URL": "https://ggsurveillance.biostats.dev,\nhttps://github.com/biostats-dev/ggsurveillance",
  "BugReports": "https://github.com/biostats-dev/ggsurveillance/issues",
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  "RoxygenNote": "7.3.3",
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  "Repository": "https://r-multiverse.r-universe.dev",
  "Date/Publication": "2025-11-27 14:33:38 UTC",
  "RemoteUrl": "https://github.com/biostats-dev/ggsurveillance",
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  "Packaged": {
    "Date": "2026-04-07 08:27:20 UTC",
    "User": "root"
  },
  "Author": "Alexander Bartel [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-1280-6138>)",
  "Maintainer": "Alexander Bartel <alexander.bartel@fu-berlin.de>",
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      "package": "Hmisc",
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    {
      "package": "knitr",
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    {
      "package": "outbreaks",
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    {
      "package": "plotly",
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    },
    {
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    },
    {
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    },
    {
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      "date": "2025-07-02"
    },
    {
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  "_topics": [
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    "infectious-disease-surveillance",
    "infectious-diseases",
    "outbreaks"
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  "_contributors": [
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    "name": "R-multiverse",
    "description": "A community-curated collection of R package releases, powered by R-universe"
  },
  "_downloads": {
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    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/ggsurveillance"
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  "_devurl": "https://github.com/biostats-dev/ggsurveillance",
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  "_rbuild": "4.5.3",
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    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/ggsurveillance.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
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  "_homeurl": "https://github.com/biostats-dev/ggsurveillance",
  "_realowner": "biostats-dev",
  "_cranurl": true,
  "_releases": [
    {
      "version": "0.1.1",
      "date": "2025-01-31"
    },
    {
      "version": "0.1.2",
      "date": "2025-02-11"
    },
    {
      "version": "0.2.0",
      "date": "2025-03-02"
    },
    {
      "version": "0.3.0",
      "date": "2025-04-11"
    },
    {
      "version": "0.4.0",
      "date": "2025-05-09"
    },
    {
      "version": "0.5.0",
      "date": "2025-07-01"
    },
    {
      "version": "0.5.1",
      "date": "2025-07-02"
    },
    {
      "version": "0.5.2",
      "date": "2025-11-27"
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  ],
  "_exports": [
    "align_and_bin_dates_seasonal",
    "align_dates_seasonal",
    "bin_by_date",
    "create_agegroups",
    "expand_counts",
    "geom_area_diverging",
    "geom_bar_diverging",
    "geom_col_range",
    "geom_epicurve",
    "geom_epicurve_point",
    "geom_epicurve_text",
    "geom_epigantt",
    "geom_hline_year",
    "geom_label_last_value",
    "geom_label_last_value_repel",
    "geom_text_last_value",
    "geom_text_last_value_repel",
    "geom_vline_year",
    "geometric_mean",
    "guide_axis_nested_date",
    "label_date",
    "label_date_short",
    "label_power10",
    "label_skip",
    "scale_x_cases_5er",
    "scale_x_continuous_diverging",
    "scale_x_discrete_reverse",
    "scale_y_cases_5er",
    "scale_y_continuous_diverging",
    "scale_y_discrete_reverse",
    "stat_bin_date",
    "stat_date_count",
    "stat_diverging",
    "stat_last_value",
    "StatBinDate",
    "StatDateCount",
    "StatEpicurve",
    "StatLastValue",
    "StatLastValueRepel",
    "theme_mod_disable_legend",
    "theme_mod_legend_bottom",
    "theme_mod_legend_left",
    "theme_mod_legend_position",
    "theme_mod_legend_right",
    "theme_mod_legend_top",
    "theme_mod_remove_legend_title",
    "theme_mod_remove_minor_grid",
    "theme_mod_remove_minor_grid_x",
    "theme_mod_remove_minor_grid_y",
    "theme_mod_remove_panel_grid",
    "theme_mod_rotate_x_axis_labels",
    "theme_mod_rotate_x_axis_labels_30",
    "theme_mod_rotate_x_axis_labels_45",
    "theme_mod_rotate_x_axis_labels_60",
    "theme_mod_rotate_x_axis_labels_90",
    "theme_mod_rotate_y_axis_labels",
    "uncount"
  ],
  "_datasets": [
    {
      "name": "influenza_germany",
      "title": "German Influenza (FLU) Surveillance data",
      "object": "influenza_germany",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "ReportingWeek",
        "AgeGroup",
        "Cases",
        "Incidence"
      ],
      "rows": 1037,
      "table": true,
      "tojson": true
    },
    {
      "name": "linelist_hospital_outbreak",
      "title": "Line list of a fictional hospital outbreak (Data)",
      "object": "linelist_hospital_outbreak",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "Patient",
        "ward_name_1",
        "ward_start_of_stay_1",
        "ward_end_of_stay_1",
        "ward_name_2",
        "ward_start_of_stay_2",
        "ward_end_of_stay_2",
        "pathogen_detection_1",
        "pathogen_detection_2"
      ],
      "rows": 8,
      "table": true,
      "tojson": true
    },
    {
      "name": "population_german_states",
      "title": "Population of the German states (2023)",
      "object": "population_german_states",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "reporting_date",
        "state",
        "sex",
        "age",
        "n"
      ],
      "rows": 2912,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "align_dates_seasonal",
      "title": "Align dates for seasonal comparison",
      "topics": [
        "align_and_bin_dates_seasonal",
        "align_dates_seasonal"
      ]
    },
    {
      "page": "bin_by_date",
      "title": "Aggregate data by time periods",
      "topics": [
        "bin_by_date"
      ]
    },
    {
      "page": "create_agegroups",
      "title": "Create Age Groups from Numeric Values",
      "topics": [
        "create_agegroups"
      ]
    },
    {
      "page": "geom_bar_diverging",
      "title": "Create diverging bar charts, diverging area charts or other plots for opposing categorical data.",
      "topics": [
        "geom_area_diverging",
        "geom_bar_diverging",
        "stat_diverging"
      ]
    },
    {
      "page": "geom_col_range",
      "title": "Create a ranged bar chart",
      "topics": [
        "geom_col_range"
      ]
    },
    {
      "page": "geom_epicurve",
      "title": "Create an epidemic curve plot or bin/count observations by date periods",
      "topics": [
        "geom_epicurve",
        "geom_epicurve_point",
        "geom_epicurve_text",
        "StatBinDate",
        "StatDateCount",
        "StatEpicurve",
        "stat_bin_date",
        "stat_date_count"
      ]
    },
    {
      "page": "geom_epigantt",
      "title": "Epi Gantt Chart: Visualize Epidemiological Time Intervals",
      "topics": [
        "geom_epigantt"
      ]
    },
    {
      "page": "stat_last_value",
      "title": "Add labels or points to the last value of a line chart",
      "topics": [
        "geom_label_last_value",
        "geom_label_last_value, stat_last_value",
        "geom_label_last_value_repel",
        "geom_text_last_value",
        "geom_text_last_value_repel",
        "StatLastValue",
        "StatLastValueRepel",
        "stat_last_value"
      ]
    },
    {
      "page": "geom_vline_year",
      "title": "Automatically create lines at the turn of every year",
      "topics": [
        "geom_hline_year",
        "geom_vline_year"
      ]
    },
    {
      "page": "geometric_mean",
      "title": "Compute a Geometric Mean",
      "topics": [
        "geometric_mean"
      ]
    },
    {
      "page": "guide_axis_nested_date",
      "title": "Nested axis guide for date scales",
      "topics": [
        "guide_axis_nested_date"
      ]
    },
    {
      "page": "influenza_germany",
      "title": "German Influenza (FLU) Surveillance data",
      "topics": [
        "influenza_germany"
      ]
    },
    {
      "page": "label_date",
      "title": "Date labeller",
      "topics": [
        "label_date",
        "label_date_short"
      ]
    },
    {
      "page": "label_power10",
      "title": "Format numbers as power-of-10 R expressions",
      "topics": [
        "label_power10"
      ]
    },
    {
      "page": "label_skip",
      "title": "Skip labels on an axis",
      "topics": [
        "label_skip"
      ]
    },
    {
      "page": "linelist_hospital_outbreak",
      "title": "Line list of a fictional hospital outbreak (Data)",
      "topics": [
        "linelist_hospital_outbreak"
      ]
    },
    {
      "page": "population_german_states",
      "title": "Population of the German states (2023)",
      "topics": [
        "population_german_states"
      ]
    },
    {
      "page": "scale_continuous_diverging",
      "title": "Diverging continuous scales for diverging bar charts with symmetrical limits",
      "topics": [
        "scale_continuous_diverging",
        "scale_x_continuous_diverging",
        "scale_y_continuous_diverging"
      ]
    },
    {
      "page": "scale_y_cases_5er",
      "title": "Continuous x-axis and y-axis scale for (case) counts",
      "topics": [
        "scale_x_cases_5er",
        "scale_y_cases_5er"
      ]
    },
    {
      "page": "scale_y_discrete_reverse",
      "title": "Reversed discrete scale for 'ggplot2'",
      "topics": [
        "scale_x_discrete_reverse",
        "scale_y_discrete_reverse"
      ]
    },
    {
      "page": "theme_mod_disable_legend",
      "title": "Quickly adjust the legend position",
      "topics": [
        "theme_mod_disable_legend",
        "theme_mod_disable_legend, theme_mod_legend_position",
        "theme_mod_legend_bottom",
        "theme_mod_legend_left",
        "theme_mod_legend_position",
        "theme_mod_legend_right",
        "theme_mod_legend_top",
        "theme_mod_remove_legend_title"
      ]
    },
    {
      "page": "theme_mod_remove_minor_grid",
      "title": "Quickly remove the minor lines of the panel grid",
      "topics": [
        "theme_mod_remove_minor_grid",
        "theme_mod_remove_minor_grid_x",
        "theme_mod_remove_minor_grid_y",
        "theme_mod_remove_panel_grid"
      ]
    },
    {
      "page": "theme_mod_rotate_axis_labels",
      "title": "Rotate axis labels",
      "topics": [
        "theme_mod_rotate_axis_labels",
        "theme_mod_rotate_x_axis_labels",
        "theme_mod_rotate_x_axis_labels_30",
        "theme_mod_rotate_x_axis_labels_45",
        "theme_mod_rotate_x_axis_labels_60",
        "theme_mod_rotate_x_axis_labels_90",
        "theme_mod_rotate_y_axis_labels"
      ]
    },
    {
      "page": "uncount",
      "title": "Duplicate rows according to a weighting variable",
      "topics": [
        "expand_counts",
        "uncount",
        "uncount, expand_counts"
      ]
    }
  ],
  "_pkglogo": "https://github.com/biostats-dev/ggsurveillance/raw/0.5.2/man/figures/logo.svg",
  "_readme": "https://github.com/biostats-dev/ggsurveillance/raw/0.5.2/README.md",
  "_rundeps": [
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    "cpp11",
    "dplyr",
    "farver",
    "forcats",
    "generics",
    "ggplot2",
    "glue",
    "gtable",
    "isoband",
    "ISOweek",
    "labeling",
    "legendry",
    "lifecycle",
    "lubridate",
    "magrittr",
    "pillar",
    "pkgconfig",
    "purrr",
    "R6",
    "RColorBrewer",
    "rlang",
    "S7",
    "scales",
    "stringi",
    "stringr",
    "tibble",
    "tidyr",
    "tidyselect",
    "timechange",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr"
  ],
  "_vignettes": [
    {
      "source": "Epicurves_with_ggsurveillance.Rmd",
      "filename": "Epicurves_with_ggsurveillance.html",
      "title": "EpiCurves: epicurves in ggplot with ggsurveillance",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Epi Curve examples",
        "Ebola Outbreak in Kikwit, Democratic Republic of the Congo 1995",
        "SARS Outbreak in Canada 2003",
        "Influenza Data from Germany 2020-2025",
        "Extra"
      ],
      "created": "2025-01-25 15:01:41",
      "modified": "2025-02-02 20:25:56",
      "commits": 9
    },
    {
      "source": "Epigantt_with_ggsurveillance.Rmd",
      "filename": "Epigantt_with_ggsurveillance.html",
      "title": "EpiGantt: epigantt charts in ggplot with ggsurveillance",
      "engine": "knitr::rmarkdown",
      "headings": [
        "EpiGantt examples",
        "Start with the Line List",
        "Transform the Line List into long format for ggplot",
        "Plot the Epigantt chart",
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