analysis/maizuru_analysis.R

In ha0ye/portalDS: Compute Dynamic Stability for Rodents at Portal

library(portalDS)
library(dplyr)
data(maizuru_block)

#### run using Maizuru Bay fish community ----
if (FALSE) {
  maizuru_time_series <- plot_time_series(maizuru_block) +
    scale_x_date(
      limits = as.Date(c("2005-03-01", "2011-01-01")),
      date_breaks = "1 year", date_labels = "%Y", expand = c(0.01, 0)
    ) +
    scale_color_viridis_d() +
    guides(color = FALSE)
  ggsave(here::here("figures/maizuru_time_series.pdf"),
    maizuru_time_series,
    width = 9, height = 4.5
  )

  ## plot network ----
  my_graph <- results$ccm_links %>%
    filter(lib_column != target_column) %>%
    arrange(target_column) %>%
    select(target_column, lib_column) %>%
    graph_from_data_frame(vertices = levels(.$target_column))

  palette <- viridis(length(V(my_graph)))
  names(palette) <- as_ids(V(my_graph))

  my_graph <- create_layout(my_graph, layout = layout)

  maizuru_network <- ggraph(my_graph) +
    geom_edge_fan(
      edge_width = 1, start_cap = circle(0.3, "inches"),
      end_cap = circle(0.3, "inches"),
      arrow = arrow(
        angle = 20, type = "closed",
        length = unit(0.15, "inches")
      )
    ) +
    geom_node_circle(aes(r = 0.08, fill = name)) +
    theme_graph(
      foreground = "black", fg_text_colour = "white",
      background = "transparent"
    ) +
    coord_fixed() +
    theme(
      text = element_text(family = "Helvetica"),
      panel.border = element_rect(color = NA, fill = NA)
    ) +
    scale_fill_manual(values = palette) +
    guides(fill = guide_legend(title = "Species"))
  ggsave(here::here("figures/maizuru_network.pdf"),
    maizuru_network,
    width = 8, height = 6
  )

  ## plot subset of time series ----
  sp_list <- c("Rudarius.ercodes", "Trachurus.japonicus")
  palette <- viridis(NCOL(block) - 1)[match(sp_list, sort(colnames(select(block, -censusdate))))]
  maizuru_time_series_subset <-
    select(block, c("censusdate", sp_list)) %>%
    plot_time_series() +
    scale_x_date(
      limits = as.Date(c("2005-03-01", "2011-01-01")),
      date_breaks = "1 year", date_labels = "%Y", expand = c(0.01, 0)
    ) +
    scale_color_manual(values = palette) +
    guides(color = FALSE) +
    facet_wrap(~species, ncol = 1)

  ggsave(here::here("figures/maizuru_time_series_subset.pdf"),
    maizuru_time_series_subset,
    width = 9, height = 5
  )

  ## plot subset of network ----
  existing_graph <- my_graph # save old graph layout

  my_graph <- results$ccm_links %>%
    filter(lib_column != target_column) %>%
    arrange(target_column) %>%
    select(target_column, lib_column) %>%
    filter(target_column %in% sp_list, lib_column %in% sp_list) %>%
    graph_from_data_frame()

  my_graph <- create_layout(my_graph, layout = layout)
  idx <- match(my_graph$name, existing_graph$name)
  my_graph$x <- existing_graph$x[idx]
  my_graph$y <- existing_graph$y[idx]

  maizuru_network_subset <- ggraph(my_graph) +
    geom_edge_fan(
      edge_width = 1, start_cap = circle(0.3, "inches"),
      end_cap = circle(0.3, "inches"),
      arrow = arrow(
        angle = 20, type = "closed",
        length = unit(0.15, "inches")
      )
    ) +
    geom_node_circle(aes(r = 0.08, fill = name)) +
    theme_graph(
      foreground = "black", fg_text_colour = "white",
      background = "transparent"
    ) +
    coord_fixed() +
    theme(
      text = element_text(family = "Helvetica"),
      panel.border = element_rect(color = NA, fill = NA)
    ) +
    scale_fill_manual(values = palette) +
    guides(fill = guide_legend(title = "Species"))
  ggsave(here::here("figures/maizuru_network_subset.pdf"),
    maizuru_network_subset,
    width = 8, height = 6
  )

  ## plot eigenvalues ----
  ds_plot <- results$eigenvalues %>%
    plot_eigenvalues() +
    scale_color_manual(values = NA) +
    scale_x_date(
      limits = as.Date(c("2005-03-01", "2011-01-01")),
      date_breaks = "1 year", date_labels = "%Y", expand = c(0.01, 0)
    )

  ggsave(here::here("figures/maizuru_ds_blank.pdf"),
    ds_plot,
    width = 10, height = 5
  )
  ggsave(here::here("figures/maizuru_ds_threshold.pdf"),
    ds_plot + geom_hline(yintercept = 1.0, size = 1, linetype = 2),
    width = 10, height = 5
  )
  ggsave(here::here("figures/maizuru_ds.pdf"),
    ds_plot + scale_color_manual(values = "black") +
      geom_hline(yintercept = 1.0, size = 1, linetype = 2),
    width = 10, height = 5
  )
}