reconstruct_env_qual: Reconstruct past qualitative environmental categories using...

In commecometrics: Ecometric Models of Trait–Environment Relationships at the Community Level

Reconstruct past qualitative environmental categories using ecometric models

Description

Uses fossil community trait summaries to reconstruct the most likely environmental category by projecting them onto a qualitative ecometric space built from modern data. Optionally, it assigns each fossil point to the nearest modern sampling point.

Usage

reconstruct_env_qual(
  fossildata,
  model_out,
  match_nearest = TRUE,
  fossil_lon = NULL,
  fossil_lat = NULL,
  modern_id = NULL,
  modern_lon = NULL,
  modern_lat = NULL,
  crs_proj = 4326
)

Arguments

fossildata	A data frame containing fossil trait summaries per fossil site. Must include columns corresponding to the same two summary metrics used for modern communities, using the column names specified by fossil_summ_trait_1 and fossil_summ_trait_2.
model_out	Output list from ecometric_model_qual(), containing modern data, diagnostics, and model settings.
match_nearest	Logical; if TRUE, matches each fossil to the nearest modern point (default = TRUE).
fossil_lon	Name of the longitude column in fossildata. Required if match_nearest = TRUE.
fossil_lat	Name of the latitude column in fossildata. Required if match_nearest = TRUE.
modern_id	Name of the unique ID column in modern points (optional for metadata merging).
modern_lon	Name of the longitude column in modern points. Required if match_nearest = TRUE.
modern_lat	Name of the latitude column in modern points. Required if match_nearest = TRUE.
crs_proj	Coordinate reference system for sf operations (default = EPSG:4326).

Value

A data frame (fossildata) updated with:

fossil_bin_1

Assigned bin number for the first trait axis (based on first summary metric of trait distribution of fossil communities).

fossil_bin_2

Assigned bin number for the second trait axis (based on second summary metric of trait distribution of fossil communities).

fossil_env_est

Predicted environmental category based on trait bin.

fossil_prob_*

Probability of each environmental category for the assigned bin.

nearest_modern_point

(Optional) ID of the nearest modern sampling point (if match_nearest = TRUE).

...

Additional columns from the matched modern site if match_nearest = TRUE.

Examples

# Load internal data
data("geoPoints", package = "commecometrics")
data("traits", package = "commecometrics")
data("spRanges", package = "commecometrics")
data("fossils", package = "commecometrics")

# Step 1: 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
)

# Step 2: Run a qualitative ecometric model (e.g., land cover class)
ecoModelQual <- ecometric_model_qual(
  points_df = traitsByPoint$points,
  category_col = "vegetation",
  min_species = 3
)

# Step 3: Reconstruct qualitative environments for fossil data
reconQual <- reconstruct_env_qual(
  fossildata = fossils,
  model_out = ecoModelQual,
  match_nearest = TRUE,
  fossil_lon = "Long",
  fossil_lat = "Lat",
  modern_id = "ID",
  modern_lon = "Longitude",
  modern_lat = "Latitude"
)

commecometrics documentation built on Aug. 8, 2025, 6:10 p.m.