The Problem

You have environmental data (pH, organic matter, nutrients) and biodiversity data (Shannon index). You want to know: which environmental factors significantly affect diversity?

The quickest way to answer this is scatter plots + linear regression .

Here's a complete, runnable R workflow using real soil microbiome data — from a simple lm() call to a multi-panel publication-ready figure. Everything uses base R graphics , no ggplot2 required.

Data

This dataset has 24 soil samples with 6 environmental factors and 2 diversity indices:

Variable Description Unit

pH Soil acidity —

AK Available potassium mg/kg

AP Available phosphorus mg/kg

AN Available nitrogen mg/kg

OM Organic matter g/kg

W Water content %

Shannon Species diversity —

PD Phylogenetic diversity —

# Read and inspect df <- read.csv ( "sandian.csv" , header = TRUE ) str ( df ) head ( df )

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Single Factor: pH → Shannon

x <- df $ pH y <- df $ Shannon fit <- lm ( y ~ x ) summary ( fit…