Package: ggsurveillance 0.1.2
ggsurveillance: Tools for Outbreak Investigation/Infectious Disease Surveillance
Create epicurves or epigantt charts in 'ggplot2'. Prepare data for visualisation or other reporting for infectious disease surveillance and outbreak investigation. Includes tidy functions to solve date based transformations for common reporting tasks, like (A) seasonal date alignment for respiratory disease surveillance, (B) date-based case binning based on specified time intervals like isoweek, epiweek, month and more, (C) automated detection and marking of the new year based on the date/datetime axis of the 'ggplot2'. An introduction on how to use epicurves can be found on the US CDC website (2012, <https://www.cdc.gov/training/quicklearns/epimode/index.html>).
Authors:
ggsurveillance_0.1.2.tar.gz
ggsurveillance_0.1.2.zip(r-4.5)ggsurveillance_0.1.2.zip(r-4.4)ggsurveillance_0.1.2.zip(r-4.3)
ggsurveillance_0.1.2.tgz(r-4.5-any)ggsurveillance_0.1.2.tgz(r-4.4-any)ggsurveillance_0.1.2.tgz(r-4.3-any)
ggsurveillance_0.1.2.tar.gz(r-4.5-noble)ggsurveillance_0.1.2.tar.gz(r-4.4-noble)
ggsurveillance_0.1.2.tgz(r-4.4-emscripten)ggsurveillance_0.1.2.tgz(r-4.3-emscripten)
ggsurveillance.pdf |ggsurveillance.html✨
ggsurveillance/json (API)
NEWS
# Install 'ggsurveillance' in R: |
install.packages('ggsurveillance', repos = c('https://biostats-dev.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/biostats-dev/ggsurveillance/issues
Pkgdown site:https://ggsurveillance.biostats.dev
- influenza_germany - Germany Influenza (FLU) Surveillance data
epidemiologyinfectious-disease-surveillanceinfectious-diseasesoutbreaks
Last updated 9 days agofrom:a63d97fc79. Checks:8 OK. Indexed: yes.
Target | Result | Latest binary |
---|---|---|
Doc / Vignettes | OK | Feb 11 2025 |
R-4.5-win | OK | Feb 11 2025 |
R-4.5-mac | OK | Feb 11 2025 |
R-4.5-linux | OK | Feb 11 2025 |
R-4.4-win | OK | Feb 11 2025 |
R-4.4-mac | OK | Feb 11 2025 |
R-4.3-win | OK | Feb 11 2025 |
R-4.3-mac | OK | Feb 11 2025 |
Exports:align_and_bin_dates_seasonalalign_dates_seasonalcreate_agegroupsexpand_countsgeom_epicurvegeom_epiganttgeom_hline_yeargeom_vline_yeargeometric_meanscale_x_cases_5erscale_y_cases_5erstat_bin_datestat_date_countStatBinDateStatDateCountStatEpicurveuncount
Dependencies:anytimeBHclicolorspacecpp11dplyrellipsisfansifarverforcatsgenericsggplot2gluegtableisobandISOweeklabelinglatticelifecyclelubridatemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigpurrrR6RColorBrewerRcpprlangscalesstringistringrtibbletidyrtidyselecttimechangetsibbleutf8vctrsviridisLitewithr
EpiCurves: epicurves in ggplot with ggsurveillance
Rendered fromEpicurves_with_ggsurveillance.Rmd
usingknitr::rmarkdown
on Feb 11 2025.Last update: 2025-02-02
Started: 2025-01-25
EpiGantt: epigantt charts in ggplot with ggsurveillance
Rendered fromEpigantt_with_ggsurveillance.Rmd
usingknitr::rmarkdown
on Feb 11 2025.Last update: 2025-02-02
Started: 2025-01-25
Seasonal Plots: Align case data for seasonal analysis
Rendered fromalign_dates_seasonal.Rmd
usingknitr::rmarkdown
on Feb 11 2025.Last update: 2025-02-02
Started: 2025-01-25
Readme and manuals
Help Manual
Help page | Topics |
---|---|
Align dates for seasonal comparison | align_and_bin_dates_seasonal align_dates_seasonal |
Create Age Groups from Numeric Values | create_agegroups |
Create an epidemic curve plot or bin/count observations by date periods | geom_epicurve StatBinDate StatDateCount StatEpicurve stat_bin_date stat_date_count |
Epi Gantt Chart: Visualize Epidemiological Time Intervals | geom_epigantt |
Automatically create lines at the turn of every year | geom_hline_year geom_vline_year |
Compute a Geometric Mean | geometric_mean |
Germany Influenza (FLU) Surveillance data | influenza_germany |
Continuous x-axis and y-axis scale for (case) counts | scale_x_cases_5er scale_y_cases_5er |
Duplicate rows according to a weighting variable | expand_counts uncount |