GHRexplore (version 0.2.1)

plot_seasonality: Seasonality plot

Description

Plots yearly time series of covariates, case counts, or incidence rates to explore seasonality patterns.

Usage

plot_seasonality(
  data,
  var,
  time,
  type = "cov",
  pop = NULL,
  pt = 1e+05,
  area = NULL,
  aggregate_space = NULL,
  aggregate_time = "month",
  aggregate_space_fun = "mean",
  aggregate_time_fun = "mean",
  transform = "identity",
  title = NULL,
  var_label = NULL,
  ylab = NULL,
  xlab = NULL,
  free_y_scale = FALSE,
  palette = "IDE1"
)

Value

A ggplot2 seasonality plot.

Arguments

data

Data frame containing equally spaced (daily, weekly, monthly) covariate or disease case observations for one or multiple locations.

var

Name of the column identifying the variable to be plotted.

time

Name of the variable that identifies the temporal dimension of the data frame. Its values must be in date format ("yyyy-mm-dd") representing the day of observation for daily data, the first day of the week for weekly, or the first day of the month for monthly observations.

type

Character that specifies the type of variable in var. Possible values include 'cov' (covariate, default), 'counts' (case counts), and 'inc' (case incidence). If type='inc', pop is required.

pop

Character identifying the variable name for population. Only needed if type='inc'.

pt

Scale of the person-time (default 100,000) for incidence rates.

area

Name of variable that identifies the different locations (e.g., areal units) for which a time series is available.

aggregate_space

Name of variable used to define spatial aggregation groups.

aggregate_time

Temporal scale used to perform temporal aggregation. Options are: "week" (ISO 8601), "month", "year".

aggregate_space_fun

Character indicating the function to be used in the aggregation over space for type="cov". Options are "mean" (default), "median", "sum". For case counts and incidence, "sum" is always applied.

aggregate_time_fun

Character indicating the function to be used in the aggregation over time for type="cov". Options are "mean" (default), "median", "sum". For case counts and incidence, "sum" is always applied.

transform

Character, defaults to "identity" (i.e., no transformation). Transforms the y-axis for better visualization. Useful options include "log10p1" log10(x+1) for case counts and incidence with 0s, or any of the in-built ggplot2 options such as "log10" log10(x), "log1p" log(x+1), and "sqrt" sqrt(x) (check all possible options using ?scale_y_continuous).

title

Optional title of the plot.

var_label

Character with a custom name for the case or covariate variable.

ylab

Label for the y-axis.

xlab

Label for the x-axis.

free_y_scale

If TRUE, the y-axis scale is free in each facet.

palette

GHR, RColorBrewer or colorspace palette. Use "-" before the palette name (e.g., "-Reds") to reverse it.

Examples

# Load data
data("dengue_MS")

# Seasonality plot of a covariate with space aggregation
plot_seasonality(dengue_MS,
                 var = "tmax",
                 time = "date",
                 var_label = "Max temp.",
                 type = "cov",
                 area = "micro_code",
                 aggregate_space = "region_code") 

# Plot case counts (log scale) with space aggregation
 plot_seasonality(dengue_MS,
                  var = "dengue_cases",
                  time = "date",  
                  type = "counts",
                  area = "micro_code",
                  aggregate_space = "meso_code",
                  transform = "log10p1",
                  var_label = "Monthly Dengue Cases", 
                  xlab = "Month", 
                  ylab = "Number of cases",
                  free_y_scale = TRUE)
                  
# Seasonality plot of incidence
plot_seasonality(dengue_MS,
                 var = "dengue_cases",
                 time = "date",    
                 type = "inc",
                 pop = "population",
                 area = "micro_code",
                 pt = 1000, 
                 title = "Monthly Dengue Incidence",
                 palette = "Reds")