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How Much Water Will This Soil Hold?

From its sand, silt and clay, organic carbon, density, pH and depth, how much water does this soil hold at field capacity? Measuring it in a lab is slow, so an estimate from cheaper measurements helps every irrigation and flood model.

Use caseClimatePredictionModel evaluation

The table

Soil samples from around the world with texture, organic carbon, bulk density, pH and depth, and the water content measured at 33 kPa. It's in Welt's research catalogue as SoilHydroDB: Global Soil Hydraulic Properties, 155,649 rows by 38 columns, licensed CC BY-SA. The catalogue measures its signal at 0.82. At 155,649 rows and 37 features the table is larger than the model limits allow, so the walkthrough evaluates and fits on a seeded sample of 4,000 rows. TabICLv2 and Kumo Tabular Medium compete.

Walkthrough

  1. Load it from the catalogue

    Find the table, read its recorded target and print the column names.

    import pandas as pd
    from welt import Client
    
    with Client() as client:
        item = client.research_datasets(q="SoilHydroDB", limit=1)["items"][0]
        info = client.research_dataset(item["id"])
        data = client.load_research_dataset(item["id"])
    
    target = info["targets"][0]
    target = target["name"] if isinstance(target, dict) else target
    print([column["name"] for column in info["schema"]], target)
  2. Pick the rows

    Set aside 20 rows to predict at the end. The models learn from a seeded sample of 4,000 of the rest, the most this table's width allows.

    known = data.dropna(subset=[target])
    new_rows = known.sample(20, random_state=1)
    table = known.drop(new_rows.index).sample(4000, random_state=7)
  3. Compare the models and predict

    The models compete on the same folds against a simple guess, then the top-ranked one is fitted on the whole table. RMSE and MAE are average errors in the target's own units, so lower is better. The last table puts each prediction next to the real answer.

    with Client() as client:
        evaluation = client.evaluate(table, target, task="regression", seed=7,
                                     models=["tabicl-v2", "kumo-medium"])
        model = evaluation.fit()
    
    print(evaluation.summary()[["name", "rank", "rmse_mean", "mae_mean"]])
    features = new_rows.drop(columns=target)
    print(pd.DataFrame({"actual": new_rows[target].values, "predicted": model.predict(features)}))

What you get

Water content per sampleAn estimate from routine soil measurements.
Fewer lab testsMeasure the cheap properties and predict the expensive one.
A strong signalThe catalogue measures a high signal for this table.

Try it

Use Open with to run the research datasets notebook in Colab, Kaggle or Jupyter and search for "SoilHydroDB", or run the code above after pip install "welt-client[parquet]".