## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.width = 10,
  fig.height = 6
)

## ----setup--------------------------------------------------------------------
library(ervissexplore)
library(ggplot2)

## ----plot-positivity, eval=FALSE----------------------------------------------
# data <- get_sentineltests_positivity(
#   date_min = as.Date("2024-01-01"),
#   date_max = as.Date("2024-06-30"),
#   pathogen = "SARS-CoV-2",
#   countries = c("France", "Germany")
# )
# 
# plot_erviss_positivity(data, date_breaks = "1 month")

## ----plot-variants, eval=FALSE------------------------------------------------
# data <- get_erviss_variants(
#   date_min = as.Date("2025-06-01"),
#   date_max = as.Date("2025-12-31"),
#   variant = c("XFG"),
#   countries = c("France", "Belgium")
# )
# 
# plot_erviss_variants(data, date_breaks = "1 month")

## ----plot-ili, eval=FALSE-----------------------------------------------------
# data <- get_ili_ari_rates(
#   date_min = as.Date("2024-01-01"),
#   date_max = as.Date("2024-12-31"),
#   indicator = "ILIconsultationrate",
#   countries = c("France")
# )
# 
# plot_ili_ari_rates(data, date_breaks = "1 month")

## ----plot-sari-rates, eval=FALSE----------------------------------------------
# data <- get_sari_rates(
#   date_min = as.Date("2024-01-01"),
#   date_max = as.Date("2024-12-31"),
#   countries = c("Belgium")
# )
# 
# plot_sari_rates(data, date_breaks = "1 month")

## ----plot-sari-positivity, eval=FALSE-----------------------------------------
# data <- get_sari_positivity(
#   date_min = as.Date("2025-01-01"),
#   date_max = as.Date("2025-12-31"),
#   pathogen = "Influenza",
#   indicator = "positivity",
#   countries = c("Belgium")
# )
# 
# plot_sari_positivity(data, date_breaks = "1 month")

## ----plot-severity, eval=FALSE------------------------------------------------
# data <- get_nonsentinel_severity(
#   date_min = as.Date("2024-01-01"),
#   date_max = as.Date("2024-12-31"),
#   pathogen = "SARS-CoV-2",
#   indicator = "hospitaladmissions",
#   countries = c("EU/EEA"),
#   age = "total"
# )
# 
# plot_nonsentinel_severity(data, date_breaks = "1 month")

## ----plot-nonsentinel-tests, eval=FALSE---------------------------------------
# data <- get_nonsentinel_tests(
#   date_min = as.Date("2024-01-01"),
#   date_max = as.Date("2024-12-31"),
#   pathogen = "Influenza",
#   indicator = "detections",
#   countries = c("France", "Germany")
# )
# 
# plot_nonsentinel_tests(data, date_breaks = "1 month")

## ----quick-plot, eval=FALSE---------------------------------------------------
# # One-liner for ILI rates
# quick_plot_ili_ari_rates(
#   date_min = as.Date("2024-01-01"),
#   date_max = as.Date("2024-12-31"),
#   indicator = "ILIconsultationrate",
#   countries = c("France"),
#   date_breaks = "1 month"
# )

## ----quick-plot-generic, eval=FALSE-------------------------------------------
# quick_plot_erviss_data(
#   type = "nonsentinel_severity",
#   date_min = as.Date("2024-01-01"),
#   date_max = as.Date("2024-12-31"),
#   pathogen = "SARS-CoV-2",
#   indicator = "hospitaladmissions",
#   countries = c("France", "Spain"),
#   date_breaks = "1 month"
# )

## ----generic-plot, eval=FALSE-------------------------------------------------
# data <- get_erviss_data(
#   type = "sari_rates",
#   date_min = as.Date("2025-01-01"),
#   date_max = as.Date("2025-12-31"),
#   countries = "Spain"
# )
# 
# plot_erviss_data(data, type = "sari_rates", date_breaks = "1 month")

## ----generic-plot-positivity, eval=FALSE--------------------------------------
# data <- get_erviss_data(
#   type = "positivity",
#   date_min = as.Date("2024-01-01"),
#   date_max = as.Date("2024-06-30"),
#   pathogen = "SARS-CoV-2",
#   countries = "EU/EEA",
#   indicator = "positivity"
# )
# 
# plot_erviss_data(data, type = "positivity")

## ----custom-theme, eval=FALSE-------------------------------------------------
# data <- get_sentineltests_positivity(
#   date_min = as.Date("2024-01-01"),
#   date_max = as.Date("2024-06-30"),
#   pathogen = "SARS-CoV-2",
#   countries = c("France", "Germany")
# )
# 
# plot_erviss_positivity(data) +
#   theme_bw() +
#   theme(
#     legend.position = "top",
#     strip.background = element_rect(fill = "steelblue"),
#     strip.text = element_text(color = "white", face = "bold")
#   )

## ----custom-axes, eval=FALSE--------------------------------------------------
# plot_erviss_positivity(data) +
#   scale_x_date(
#     date_breaks = "1 month",
#     date_labels = "%d/%m/%Y"
#   ) +
#   scale_y_continuous(
#     limits = c(0, 50),
#     breaks = seq(0, 50, 10)
#   ) +
#   ylab("Positivity (%)")

## ----custom-title, eval=FALSE-------------------------------------------------
# plot_erviss_positivity(data) +
#   labs(
#     title = "My custom title",
#     subtitle = "SARS-CoV-2 positivity in France and Germany",
#     caption = "Source: ERVISS / EU-ECDC"
#   )

## ----custom-colors, eval=FALSE------------------------------------------------
# data <- get_ili_ari_rates(
#   date_min = as.Date("2024-01-01"),
#   date_max = as.Date("2024-12-31"),
#   indicator = "ILIconsultationrate",
#   countries = "France"
# )
# 
# plot_ili_ari_rates(data) +
#   scale_colour_brewer(palette = "Set1", name = "Age group")

## ----custom-full, eval=FALSE--------------------------------------------------
# data <- get_nonsentinel_severity(
#   date_min = as.Date("2024-01-01"),
#   date_max = as.Date("2024-12-31"),
#   pathogen = "SARS-CoV-2",
#   indicator = c("hospitaladmissions", "ICUadmissions"),
#   age = "total",
#   countries = c("France", "Spain")
# )
# 
# ggplot(data, aes(x = date, y = value, fill = indicator)) +
#   geom_col(position = "dodge") +
#   facet_wrap(~countryname, scales = "free_y") +
#   scale_fill_manual(
#     values = c("hospitaladmissions" = "#E69F00", "ICUadmissions" = "#D55E00"),
#     labels = c("Hospital admissions", "ICU admissions"),
#     name = ""
#   ) +
#   labs(
#     title = "SARS-CoV-2 severity indicators",
#     x = NULL,
#     y = "Count",
#     caption = "Source: ERVISS / EU-ECDC"
#   ) +
#   theme_minimal() +
#   theme(legend.position = "top")

## ----custom-heatmap, eval=FALSE-----------------------------------------------
# data <- get_ili_ari_rates(
#   date_min = as.Date("2024-01-01"),
#   date_max = as.Date("2024-12-31"),
#   indicator = "ILIconsultationrate",
#   age = "total",
#   countries = c("Spain", "Austria", "Greece")
# )
# 
# ggplot(data, aes(x = date, y = countryname, fill = value)) +
#   geom_tile() +
#   scale_fill_viridis_c(name = "ILI rate") +
#   scale_x_date(date_breaks = "1 month", date_labels = "%b") +
#   labs(title = "ILI consultation rates across Europe", x = NULL, y = NULL) +
#   theme_minimal() +
#   theme(axis.text.x = element_text(angle = 45, hjust = 1))