Package index • ggsurveillance

Epidemic Curves

Functions for creating and styling epidemic curves

geom_epicurve() stat_bin_date() stat_date_count() geom_epicurve_text() geom_epicurve_point(): Create an epidemic curve plot or bin/count observations by date periods
scale_y_cases_5er() scale_x_cases_5er(): Continuous x-axis and y-axis scale for (case) counts
geom_vline_year() geom_hline_year(): Automatically create lines at the turn of every year
label_date() label_date_short(): Date labeller
guide_axis_nested_date(): Nested axis guide for date scales

Functions for diverging plots for population pyramids, likert scales, etc.

geom_bar_diverging() geom_area_diverging() stat_diverging(): Create diverging bar charts, diverging area charts or other plots for opposing categorical data.
scale_x_continuous_diverging() scale_y_continuous_diverging(): Diverging continuous scales for diverging bar charts with symmetrical limits
scale_y_discrete_reverse() scale_x_discrete_reverse(): Reversed discrete scale for 'ggplot2'

Functions for binning cases by date intervalls and aligning and comparing data across seasons

bin_by_date(): Aggregate data by time periods
align_dates_seasonal() align_and_bin_dates_seasonal(): Align dates for seasonal comparison

Functions for EpiGantt Charts

geom_epigantt(): Epi Gantt Chart: Visualize Epidemiological Time Intervals
scale_y_discrete_reverse() scale_x_discrete_reverse(): Reversed discrete scale for 'ggplot2'

Various functions helper functions for common epi tasks

create_agegroups(): Create Age Groups from Numeric Values
geometric_mean(): Compute a Geometric Mean
uncount() expand_counts(): Duplicate rows according to a weighting variable

Included datasets for examples and demonstrations

influenza_germany: German Influenza (FLU) Surveillance data
linelist_hospital_outbreak: Line list of a fictional hospital outbreak (Data)
population_german_states: Population of the German states (2023)

Geoms and Stats in this package

geom_bar_diverging() geom_area_diverging() stat_diverging(): Create diverging bar charts, diverging area charts or other plots for opposing categorical data.
geom_col_range(): Create a ranged bar chart
geom_epicurve() stat_bin_date() stat_date_count() geom_epicurve_text() geom_epicurve_point(): Create an epidemic curve plot or bin/count observations by date periods
geom_epigantt(): Epi Gantt Chart: Visualize Epidemiological Time Intervals
geom_vline_year() geom_hline_year(): Automatically create lines at the turn of every year
stat_last_value() geom_label_last_value() geom_text_last_value() geom_label_last_value_repel() geom_text_last_value_repel(): Add labels or points to the last value of a line chart

ggplot2 scales and guides in this package

scale_x_continuous_diverging() scale_y_continuous_diverging(): Diverging continuous scales for diverging bar charts with symmetrical limits
scale_y_cases_5er() scale_x_cases_5er(): Continuous x-axis and y-axis scale for (case) counts
scale_y_discrete_reverse() scale_x_discrete_reverse(): Reversed discrete scale for 'ggplot2'
guide_axis_nested_date(): Nested axis guide for date scales

Functions for formatting labels and annotations

Functions for customizing plot appearance

theme_mod_disable_legend() theme_mod_legend_position() theme_mod_legend_top() theme_mod_legend_bottom() theme_mod_legend_left() theme_mod_legend_right() theme_mod_remove_legend_title(): Quickly adjust the legend position
theme_mod_remove_minor_grid() theme_mod_remove_minor_grid_y() theme_mod_remove_minor_grid_x() theme_mod_remove_panel_grid(): Quickly remove the minor lines of the panel grid
theme_mod_rotate_x_axis_labels() theme_mod_rotate_x_axis_labels_90() theme_mod_rotate_x_axis_labels_45() theme_mod_rotate_x_axis_labels_30() theme_mod_rotate_x_axis_labels_60() theme_mod_rotate_y_axis_labels(): Rotate axis labels