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

library(climniche)

case_path <- system.file("extdata/mediterranean_anchovy", package = "climniche")
range_summary <- read.csv(
  file.path(case_path, "anchovy_climniche_time_range_summary.csv")
)
departure_summary <- read.csv(
  file.path(case_path, "anchovy_climniche_time_departure_summary.csv")
)
change_rate <- read.csv(
  file.path(case_path, "anchovy_climniche_time_change_rate.csv")
)

## ----series-fit, eval = FALSE-------------------------------------------------
# projection_years <- c(2030, 2050, 2070, 2090)
# 
# future_series <- list(
#   ssp245_2030 = climate_2030,
#   ssp245_2050 = climate_2050,
#   ssp245_2070 = climate_2070,
#   ssp245_2090 = climate_2090
# )
# 
# # Project each period into the same fitted climatic niche.
# series <- fit_climniche_series(
#   current = current_climate,
#   future = future_series,
#   time = projection_years,
#   scenario = "SSP2-4.5",
#   occupied = anchovy_suitability,
#   occupied_threshold = sdm_threshold,
#   domain = mediterranean_sea_mask,
#   sensitivity = climatic_weights
# )

## ----range-code, eval = FALSE-------------------------------------------------
# range_summary <- climniche_range_summary(
#   series,
#   scope = "current",
#   area_weight = TRUE
# )
# 
# subset(
#   range_summary,
#   select = c(
#     time,
#     exposed_fraction,
#     conditional_relative_exceedance,
#     range_wide_relative_exceedance
#   )
# )

## ----range-table, echo = FALSE------------------------------------------------
range_table <- data.frame(
  `Projection year` = range_summary[["time"]],
  `Weighted boundary exceedance fraction` = paste0(
    round(100 * range_summary[["exposed_fraction"]], 1),
    "%"
  ),
  `Conditional relative Niche Boundary Exceedance` = paste0(
    round(100 * range_summary[["conditional_relative_exceedance"]], 1),
    "%"
  ),
  `Range mean relative Niche Boundary Exceedance` = paste0(
    round(100 * range_summary[["range_wide_relative_exceedance"]], 1),
    "%"
  ),
  check.names = FALSE
)

knitr::kable(range_table, row.names = FALSE)

## ----range-figure-code, eval = FALSE------------------------------------------
# extent_plot <- plot_climniche_time(
#   series,
#   metric = "exposed_fraction",
#   scope = "current",
#   area_weight = TRUE,
#   show_models = FALSE
# )
# 
# conditional_plot <- plot_climniche_time(
#   series,
#   metric = "conditional_relative_exceedance",
#   scope = "current",
#   area_weight = TRUE,
#   show_models = FALSE
# )
# 
# range_plot <- plot_climniche_time(
#   series,
#   metric = "range_wide_relative_exceedance",
#   scope = "current",
#   area_weight = TRUE,
#   show_models = FALSE
# )
# 
# patchwork::wrap_plots(
#   extent_plot,
#   conditional_plot,
#   range_plot,
#   nrow = 1
# )

## ----range-figure-output, echo = FALSE, out.width = "100%"--------------------
knitr::include_graphics("figures/anchovy-climniche-through-time.png")

## ----departure-code, eval = FALSE---------------------------------------------
# departure <- climniche_departure(
#   series,
#   scope = "current"
# )
# 
# rate <- climniche_change_rate(
#   series,
#   metric = "range_wide_relative_exceedance",
#   scope = "current",
#   area_weight = TRUE
# )

## ----departure-summary, echo = FALSE------------------------------------------
departure_table <- data.frame(
  `Boundary exceedance fraction` = paste0(
    round(
      100 * departure_summary[["proportion_with_boundary_exceedance"]],
      1
    ),
    "%"
  ),
  `Median first exceedance` =
    departure_summary[["median_first_boundary_exceedance"]],
  `Mean projection fraction` = paste0(
    round(
      100 * departure_summary[[
        "mean_boundary_exceedance_projection_fraction"
      ]],
      1
    ),
    "%"
  ),
  check.names = FALSE
)

knitr::kable(departure_table, row.names = FALSE)

## ----departure-map-code, eval = FALSE-----------------------------------------
# onset_map <- plot_climniche_departure_map(
#   series,
#   metric = "first_boundary_exceedance",
#   scope = "current",
#   scenario = "SSP2-4.5",
#   study_region = mediterranean_boundary,
#   degree_labels = "hemisphere"
# )
# 
# frequency_map <- plot_climniche_departure_map(
#   series,
#   metric = "boundary_exceedance_projection_fraction",
#   scope = "current",
#   scenario = "SSP2-4.5",
#   study_region = mediterranean_boundary,
#   degree_labels = "hemisphere"
# )
# 
# patchwork::wrap_plots(onset_map, frequency_map, nrow = 1)

## ----departure-map-output, echo = FALSE, out.width = "100%"-------------------
knitr::include_graphics("figures/anchovy-climniche-time-maps.png")

## ----rate-table, echo = FALSE-------------------------------------------------
rate_row <- subset(
  change_rate,
  metric == "range_wide_relative_exceedance"
)
rate_table <- data.frame(
  `Interval start` = rate_row[["interval_start"]],
  `Interval end` = rate_row[["interval_end"]],
  `Increase in range mean relative exceedance` = paste0(
    round(100 * rate_row[["maximum_interval_increase"]], 1),
    " percentage points"
  ),
  check.names = FALSE
)

knitr::kable(rate_table, row.names = FALSE)

## ----series-report, eval = FALSE----------------------------------------------
# series_report <- climniche_series_report(
#   series,
#   species = "European anchovy",
#   scope = "current",
#   area_weight = TRUE
# )
# 
# series_report
# write_climniche_series_report(
#   series_report,
#   "anchovy-exposure-through-time.md"
# )