ecometric_space {commecometrics} | R Documentation |
Plot ecometric space for quantitative environmental variables
Description
Visualizes the ecometric space for quantitative environmental variables
based on the output from ecometric_model()
.
Usage
ecometric_space(
model_out,
env_name = "env_var",
fossil_data = NULL,
fossil_color = "#000000",
modern_color = "#bc4749",
palette = c("#bc6c25", "#fefae0", "#606c38"),
x_label = "Summary metric 1",
y_label = "Summary metric 2"
)
Arguments
model_out |
Output from |
env_name |
Name to display for the environmental variable (used in the legend title). |
fossil_data |
Optional. Output from |
fossil_color |
Outline color for fossil data bins (default: |
modern_color |
Outline color for modern data bins (default: |
palette |
Vector of colors to use for the gradient scale representing environmental values. |
x_label |
Label for the x-axis in the output plots (default: "Summary metric 1"). |
y_label |
Label for the y-axis in the output plots (default: "Summary metric 2"). |
Value
A ggplot2 object visualizing the ecometric trait-environment surface.
Examples
# Load internal data
data("geoPoints", package = "commecometrics")
data("traits", package = "commecometrics")
data("spRanges", package = "commecometrics")
data("fossils", package = "commecometrics")
# Summarize trait values at sampling points
traitsByPoint <- summarize_traits_by_point(
points_df = geoPoints,
trait_df = traits,
species_polygons = spRanges,
trait_column = "RBL",
species_name_col = "sci_name",
continent = FALSE,
parallel = FALSE
)
# Run ecometric model
ecoModel <- ecometric_model(
points_df = traitsByPoint$points,
env_var = "precip",
transform_fun = function(x) log(x + 1),
inv_transform_fun = function(x) exp(x) - 1,
min_species = 3
)
# Reconstruct environments for fossil sites
recon <- reconstruct_env(
fossildata = fossils,
model_out = ecoModel,
match_nearest = TRUE,
fossil_lon = "Long",
fossil_lat = "Lat",
modern_id = "ID",
modern_lon = "Longitude",
modern_lat = "Latitude"
)
# Plot the ecometric trait–environment space
ecometricPlot <- ecometric_space(
model_out = ecoModel,
env_name = "Precipitation (log mm)",
fossil_data = recon
)
# Display plot
print(ecometricPlot)
[Package commecometrics version 1.0.0 Index]