README: Chapter 1 – General Introduction: Vitamin C Security in the UK Food System
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Thesis Title:
An Investigation of Overlooked Complexities Affecting UK Vitamin C Security and the Potential for Local Crops to Address Insecurities: A Case of UK Strawberries

Author: David Fisher  
Supervisors: Eleftheria Stavridou | Jenny Baverstock | Guy Poppy  
Date: 23/06/2025  
Contact:  
- D.Fisher@soton.ac.uk  
- eleftheria.stavridou@niab.com  
- J.Baverstock@soton.ac.uk

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Description
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Chapter 1 provides an overview of vitamin C security within the UK food system. It synthesises secondary data to explore trends in dietary supply, crop diversity, and the role of local crops such as strawberries. Data visualisations and descriptive analysis highlight key vulnerabilities and opportunities for improving micronutrient security.

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File Structure
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chapter-01/
│
├── code/
│   └── chap-01_analysis-figures.R
│
└── data/
    ├── primary/                ← No primary data used
    ├── processed/
    │   ├── 20220529_Top10VitC_Poppyetal.csv
    │   └── mezzetti2016_asa_genotypes.csv
    └── dictionaries/
        ├── Top10VitC_Poppyetal_dictionary.txt
        └── mezzetti2016_asa_genotypes_dictionary.txt

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Code: ./code/
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**Filename:** chap-01_analysis-figures.R  
**Description:** Annotated R script to process secondary datasets and generate figures. Includes references to data sources and reproduction steps.

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Data: ./data/processed/
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| Filename                          | Description                                                            | Key Variables                            | Data Dictionary                                             |
|-----------------------------------|------------------------------------------------------------------------|------------------------------------------|-------------------------------------------------------------|
| 20220529_Top10VitC_Poppyetal.csv | Nutrient data for 10 fruits/vegetables (via CoFID and Poppy et al.)   | product, vit_c, folate                   | data/dictionaries/Top10VitC_Poppyetal_dictionary.txt        |
| mezzetti2016_asa_genotypes.csv   | Nutrient traits of 15 strawberry genotypes (Mezzetti et al., 2016)    | Cultivar, SS, TA, TPH, ACY, TAC, vit_c   | data/dictionaries/mezzetti2016_asa_genotypes_dictionary.txt |

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Secondary Data Sources
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- **CoFID:** Composition of Foods Integrated Dataset  
  https://www.gov.uk/government/publications/composition-of-foods-integrated-dataset-cofid  
  Accessed: 23/06/2025

- **DEFRA (2023):** Horticulture Statistics  
  https://www.gov.uk/government/statistics/latest-horticulture-statistics  
  Accessed: 24/02/2025

- **Mezzetti et al. (2016):** Breeding strawberry for higher phytochemical content  
  *Int. J. Fruit Sci., 16*, 194–206  
  https://doi.org/10.1080/15538362.2016.1250695

- **Poppy et al. (2022):** Trade and dietary preferences in UK micronutrient security  
  *Nat. Food, 3*, 512–522  
  https://doi.org/10.1038/s43016-022-00538-3

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Usage Notes
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- All datasets are from secondary sources; no primary data was collected for Chapter 1.
- `chap-01_analysis-figures.R` includes all processing steps and citation details for reproducibility.
- For variable descriptions, refer to the corresponding data dictionary files.
- Recommended tools: R version >4.0, see 'chap-01_analysis-figures.R' for required packages 

