reconstruct_env_qual {commecometrics}R Documentation

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"
)


[Package commecometrics version 1.0.0 Index]