Plot the mean arrival age of species in an assemblage based in an ancestral area reconstruction across geographic space

Usage

plot_age_arrival(
  age_arrival_comm,
  coords,
  shapefile,
  color_palette = "SunsetDark"
)

Arguments

age_arrival_comm: A list of length two generated by calc_age_arrival containing community-level the mean arrival age of species in an assemblage based in an ancestral area reconstruction.
coords: A rectangular object (it can be a matrix, data.frame or tibble) containing two columns, one with longitude and another with latitude coordinates in this order.
shapefile: An sf object containing the geographic boundaries to be overlaid on the raster map (e.g., continents, biogeographic regions, or study area limits).
color_palette: character string specifying the color palette to be used for quantitative variables in rcartocolor::scale_fill_carto_c.

Value

A ggplot2 object is returned.

Author

Maria Gabriela Junqueira and Gabriel Nakamura

Examples

if (FALSE) { # \dontrun{

# Compute diversification metrics

data("akodon_sites") # site in rows and species and coordinates in columns
data("akodon_newick") # phylogeny

# pre computed evoregion
load(file = system.file("extdata", "regions_results.RData", 
                        package = "Herodotools")) 
site_region <- regions$Cluster_Evoregions # evoregions

# subseting longitude and latitude in a separate dataframe
site_xy <- akodon_sites %>% 
  dplyr::select(LONG, LAT) 

# subsetting species presence in a separate dataframe
akodon_pa <- akodon_sites %>% 
  dplyr::select(-LONG, -LAT)

# joining classification with site coordinates
evoregion_df <- data.frame(
  site_xy, 
  site_region
)

# bioregion/ecoregion/evoregion of each site
biogeo_area <- data.frame(biogeo = chartr("12345", 
                                          "ABCDE", 
                                          evoregion_df$site_region)) 

# pre computed biogeobears model 
load(file = system.file("extdata", 
                        "resDEC_akodon.RData",
                        package = "Herodotools")) 

# subseting occurrence matrix keeping only species in the phylogenetic tree
spp_in_tree <- names(akodon_pa) %in% akodon_newick$tip.label
akodon_pa_tree <- akodon_pa[, spp_in_tree]


# getting the ancestral range area for each node 
node_area <- 
  Herodotools::get_node_range_BioGeoBEARS(
    resDEC,
    phyllip.file = here::here("inst", "extdata", "geo_area_akodon.data"),
    akodon_newick,
    max.range.size = 4 
  )

# calculating age arrival
akodon_age_comm <- 
  Herodotools::calc_age_arrival(W = akodon_pa_tree,
                                tree = akodon_newick,
                                ancestral.area = node_area,
                                biogeo = biogeo_area)


# downloading coastline 
coastline <- rnaturalearth::ne_coastline(returnclass = "sf")

# defining map limits
map_limits <- list(
  x = c(-95, -30),
  y = c(-55, 12)
)

# cropping map keeping only Soutbh America
coastline_crop <- sf::st_crop(coastline,
                              xmin = map_limits$x[1],
                              xmax = map_limits$x[2],
                              ymin = map_limits$y[1],
                              ymax = map_limits$y[2])


# plotting mean age of arrival for each cell
plot_age_arrival(age_arrival_comm = akodon_age_comm,
                 coords = site_xy,
                 shapefile = coastline_crop)

} # }