Reduction in nitrification during the early transition from conventional to organic farming practices

Introduction

This repository contains all of the scripts needed to replicate the results and output presented in:

Jacob R. Price, Diana Oviedo-Vargas, Marc Peipoch, Melinda D. Daniels, & Jinjun Kan. 2025. Reduction in nitrification during the early transition from conventional to organic farming practices. Ecosphere. (DOI forthcoming)

Note(s):

• These scripts were composed and executed on Mac machines; some modification may be required for use with PC or Linux environments.

Process Flow Chart

If you can’t see the chart make your browser wider and reload the page.

flowchart LR
    A[(Raw Min/Nit)] --> D{{Prepare_Data.R}}
    B[(Raw EEA)] --> D
    C[(Raw qPCR)] --> D
    D --> E[(dat.RDS)]
    D --> Y[Table S1: Sample Counts]
    
    E --> F{{Seasonality.R}} 
    F --> G["Fig. 3: Seasonality"]
    F --> H["Fig. S2: Sup. Seasonality"]
    
    E --> I{{boxplots.R}} --> J["Fig. 4: Boxplots"]

    E --> K{{anova.R}}
    K --> L["Table 3: ANOVA - MS & T "]
    K --> M["Table 4: ANOVA - CC"]
    K --> N["Table 5: Est Marg Means"]

    E --> O{{weather_SMS.R}}
    P[(Weather Station)] --> O 
    Q[(Soil Moist. Sens.)] --> O
    O --> R[(SMS_dat.RDS)]
    O --> S[(raindat.csv)]
    O --> T[(tempdat.csv)]
    O --> Z[Fig. 2: Weather & SMS]

    E --> U{{correlation.R}} 
    R --> U
    U --> V["Table S2: Cor Res"]

    E --> W{{eea.R}} --> X["Fig. S3: EEA Ratios"]

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Repository Contents

• ./ - the project home directory; where you’re currently located :-)
• ./README.Rmd & ./README.md - what you’re reading at the moment
• ./data/ - contains all of the raw data needed to replicate our analysis and processed data in case you just want to look at the results themselves
• ./src/ - contains all of the (R) source files