## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.align = "center",
  warning = FALSE,
  message = FALSE
)

## ----setup, results='hide', message=FALSE-------------------------------------
# Load GHRexplore
library(GHRexplore)

# Other necessary libraries for the vignette
library(dplyr)
library(sf)

## ----load data----------------------------------------------------------------
data("dengue_MS")
glimpse(dengue_MS)

## ----load boundaries----------------------------------------------------------
data("map_MS")
glimpse(map_MS)

## ----IDE palettes, fig.width=6, fig.height=5----------------------------------
GHR_palettes()

## ----ts1, fig.width=7, fig.height=3.5-----------------------------------------
plot_timeseries(
  dengue_MS,
  var = "tmin",
  type = "cov",
  var_label = "Minimum temp.",
  time = "date",
  unit = "micro_code"
)

## ----ts2, fig.width=7, fig.height=6-------------------------------------------
plot_timeseries(
  dengue_MS,
  var = "tmin",
  type = "cov",
  var_label = "Minimum temp.",
  time = "date",
  unit = "micro_code",
  facet = TRUE
)

## ----ts3, fig.width=7, fig.height=3.5-----------------------------------------
plot_timeseries(
  dengue_MS,
  var = "tmin",
  type = "cov",
  var_label = "Minimum temp.",
  time = "date",
  unit = "micro_code",
  highlight = "50001",
  title = "Micro code 50001"
)

## ----ts4, fig.width=7, fig.height=3.5-----------------------------------------
plot_timeseries(
  dengue_MS,
  var = "tmin",
  type = "cov",
  var_label = "Minimum temp.",
  time = "date",
  unit = "micro_code",
  aggregate_space = "meso_code"
)

## ----ts5, fig.width=7, fig.height=3.5-----------------------------------------
plot_timeseries(
  dengue_MS,
  var = "dengue_cases",
  type = "counts",
  time = "date",
  unit = "micro_code",
  aggregate_space = "meso_code",
  transform = "log10p1"
)

## ----ts6, fig.width=7, fig.height=3.5-----------------------------------------
plot_timeseries(
  dengue_MS,
  var = "dengue_cases",
  type = "inc",
  pop = "population",
  time = "date",
  unit = "micro_code",
  aggregate_space = "meso_code",
  pt = 1000,
  transform = "log10p1"
)

## ----ts2-1, fig.width=7, fig.height=5-----------------------------------------
plot_timeseries2(
  dengue_MS,
  var = c("tmax", "pdsi"),
  type = c("cov", "cov"),
  time = "date",
  unit = "micro_code",
  align = "mean"
)

## ----ts2-2, fig.width=7, fig.height=5-----------------------------------------
plot_timeseries2(
  dengue_MS,
  var = c("tmax", "pdsi"),
  type = c("cov", "cov"),
  time = "date",
  unit = "micro_code",
  aggregate_space = "meso_code",
  palette = c("tomato", "royalblue"),
  var_label = c("Maximum temp.", "PDSI"),
  align = "mean"
)

## ----ts2-3, fig.width=7, fig.height=5-----------------------------------------
plot_timeseries2(
  dengue_MS,
  var = c("dengue_cases", "pdsi"),
  type = c("inc", "cov"),
  pop = "population",
  time = "date",
  unit = "micro_code",
  aggregate_space = "meso_code"
)

## ----ts2-4, fig.width=7, fig.height=5-----------------------------------------
plot_timeseries2(
  dengue_MS,
  var = c("dengue_cases", "pdsi"),
  type = c("counts", "cov"),
  time = "date",
  unit = "micro_code",
  aggregate_space = "meso_code"
)

## ----heatmap1, fig.width=7, fig.height=6--------------------------------------
plot_heatmap(
  dengue_MS,
  var = "pdsi",
  type = "cov",
  var_label = "PDSI",
  time = "date",
  unit = "micro_code",
  aggregate_space = "meso_code",
  palette = "-Vik",
  centering = 0
)

## ----heatmap2, fig.width=7, fig.height=6--------------------------------------
plot_heatmap(
  dengue_MS,
  var = "dengue_cases",
  type = "inc",
  pop = "population",
  time = "date",
  unit = "micro_code",
  aggregate_space = "meso_code",
  title = "Monthly Incidence",
  transform = "log10p1"
)

## ----seasonality, fig.width=7, fig.height=5-----------------------------------
plot_seasonality(
  dengue_MS,
  var = "tmin",
  var_label = "Minimum temperature",
  type = "cov",
  time = "date",
  unit = "micro_code",
  aggregate_space = "meso_code"
)

## ----map1, fig.width=4, fig.height=3------------------------------------------
plot_map(
  data = dengue_MS,
  var = "urban",
  time = "date",
  type = "cov",
  unit = "micro_code",
  map = map_MS,
  map_unit = "code",
  aggregate_time = "all",
  var_label = "Urbanicity",
  palette = "-Heat"
)

## ----map2, fig.width=6, fig.height=5------------------------------------------
plot_map(
  dengue_MS,
  var = "dengue_cases",
  type = "inc",
  pop = "population",
  pt = 1000,
  time = "date",
  unit = "micro_code",
  map = map_MS,
  map_unit = "code",
  aggregate_time = "year",
  bins = 5,
  bins_method = "quantile",
  palette = "-Rocket"
)

## ----map3, fig.width=4, fig.height=3------------------------------------------
plot_map(
  data = dengue_MS,
  var = "biome_name",
  type = "cov",
  time = "date",
  unit = "micro_code",
  aggregate_time = "all",
  map = map_MS,
  map_unit = "code",
  var_label = "Biome"
)

## ----biv1, fig.width=6, fig.height=4------------------------------------------
plot_bivariate(
  dengue_MS,
  var = c("tmax", "pdsi"),
  var_label = c("Max. temp", "PDSI"),
  unit = "meso_code"
)

## ----biv2, fig.width=7, fig.height=5------------------------------------------
plot_bivariate(
  dengue_MS,
  var = c("tmax", "pdsi"),
  var_label = c("Max. temp", "PDSI"),
  unit = "meso_code",
  facet = TRUE,
  free_x_scale = TRUE,
  free_y_scale = TRUE
)

## ----biv3, fig.width=6, fig.height=4------------------------------------------
plot_bivariate(
  dengue_MS,
  var = c("biome_name", "tmax"),
  var_label = c("Biome", "Max. temp"),
  unit = "meso_code"
)

## ----corr1, fig.width=6, fig.height=5-----------------------------------------
plot_correlation(
  dengue_MS,
  var = c(
    "dengue_cases",
    "pop_density",
    "tmax",
    "tmin",
    "pdsi",
    "urban",
    "water_network",
    "water_shortage"
  )
)

## ----corr2, fig.width=6, fig.height=5-----------------------------------------
plot_correlation(
  dengue_MS,
  var = c(
    "dengue_cases",
    "pop_density",
    "tmax",
    "tmin",
    "pdsi",
    "urban",
    "water_network",
    "water_shortage"
  ),
  method = "spearman",
  plot_type = c("number", "raster"),
  palette = "RdBu"
)

## ----croscorr1, fig.width=7, fig.height=4-------------------------------------
plot_crosscorrelation(
  data = dengue_MS,
  var = c("dengue_cases", "tmax"),
  type = c("inc", "cov"),
  pop = "population",
  time = "date",
  unit = "micro_name",
  lags = 0:6
)

## ----croscorr2, fig.width=6, fig.height=5-------------------------------------
plot_crosscorrelation(
  data = dengue_MS,
  var = c("dengue_cases", "tmax"),
  type = c("inc", "cov"),
  pop = "population",
  time = "date",
  unit = "micro_name",
  method = "spearman",
  aggregate_space = "meso_name",
  facet = TRUE,
  title = "Cross-correlation for meso areas",
  palette = "navy",
  lags = 0:6
)

## ----anim1, eval = FALSE------------------------------------------------------
# animate_map(
#   data = dengue_MS[dengue_MS$year %in% 2002:2004, ],
#   var = "tmin",
#   time = "date",
#   unit = "micro_code",
#   map = map_MS,
#   map_unit = "code",
#   type = "cov",
#   palette = "Blue-Red 3",
#   out_width = 400,
#   out_height = 300,
#   filename = "tmin.gif"
# )

## ----anim2, eval = FALSE------------------------------------------------------
# animate_map(
#   data = dengue_MS[dengue_MS$year %in% 2006:2007, ],
#   var = "dengue_cases",
#   pop = "population",
#   time = "date",
#   unit = "micro_code",
#   map = map_MS,
#   map_unit = "code",
#   type = "counts",
#   fps = 2,
#   ts_include = TRUE,
#   transform = "log10p1",
#   out_width = 500,
#   out_height = 500,
#   ts_color = "#453975",
#   filename = "counts.gif",
# )

## ----compare, fig.width=7, fig.height=6---------------------------------------
plot_compare(
  plot_function = plot_timeseries,
  data = dengue_MS,
  var = c("pdsi", "dengue_cases"),
  type = c("cov", "inc"),
  var_lab = c("PDSI", "Dengue Incidence"),
  pop = "population",
  time = "date",
  unit = "micro_code",
  aggregate_space = "meso_code",
  ncol = 1,
  combine_legend = TRUE
)

## ----compare2, fig.width=7, fig.height=9--------------------------------------
plot_compare(
  plot_function = plot_heatmap,
  data = dengue_MS,
  var = c("pdsi", "dengue_cases"),
  type = c("cov", "inc"),
  var_lab = c("PDSI", "Incidence"),
  palette = c("Purp", "Reds"),
  pop = "population",
  time = "date",
  unit = "micro_code",
  aggregate_space = "meso_code",
  ncol = 1
)