README: Chapter 6 – Characterisation of the Vitamin C Profiles of British Strawberry Genotypes Grown Under Commercial Cultivation Systems 
==================================================================================  
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: 26/06/2025  
Contact:  
- D.Fisher@soton.ac.uk  
- eleftheria.stavridou@niab.com  
- J.Baverstock@soton.ac.uk  

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Description  
-------------  
The purpose of Chapter 6 is to assess the vitamin C content of a range of popular UK strawberry genotypes grown under standard commercial conditions. The intent for these data is to help inform strawberry breeding programmes on high and low vitamin C genotypes, and to assess whether vitamin C coud be integrated as an additional targetted trait in modern breeding programmes.

Date Ranges
------------

The data collected for chapter 6 covers two consecutive starwberry growing seasons from May 2023 to August 2024

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Geographic Information
-----------------------

All data were generated at Niab, East Malling, United Kingdom (51°17’09.6”N 0°27’10.8”E)

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File Structure  
-----------------
chapter-06_strawberry_genotypes/
│
├── code/
│   ├── acids_processing_func_v0.0.6.R
│   ├── chap-06_analysis-figures.R
│   ├── datacompilation_STS_v0.0.4.R
│   └── datacompilation_VT_v0.1.3.R
│
└── data/
   │
   │
   ├── primary/
   │   ├── VT23
   │   │   ├── experimental_design
   │   │   │     └── 20231220_VT23_P8_genotype_setup.csv
   │   │   ├── hplc
   │   │   │     ├── extraction_weights
   │   │   │     │     └── 20240630_VT23_acids_extraction_weights.csv
   │   │   │     └── results
   │   │   │          ├── 20240630_VT23_WK3_acids_results.csv
   │   │   │          └── 20240705_FS23_VT23_WK2_acids_results.csv
   │   │   ├── spectrophotometer
   │   │   │          ├── calibration
   │   │   │          │     ├── gae
   │   │   │          │     │    ├── 20240515_VT23_TP_ex01_calibration.csv
   │   │   │          │     │    ├── 20240529_VT23_TP_ex02_calibration.csv
   │   │   │          │     │    ├── 20240530_VT23_TP_ex03_calibration.csv
   │   │   │          │     │    └── 20240605_VT23_TP_ex04_calibration.csv
   │   │   │          │     └── teac
   │   │   │          │          ├── 20240514_VT23_AX_ex01_calibration_manualentry.csv
   │   │   │          │          ├── 20240528_VT23_AX_ex02_calibration_manualentry.csv
   │   │   │          │          ├── 20240529_VT23_AX_ex03_calibration.csv
   │   │   │          │          └── 20240604_VT23_AX_ex04_calibration.csv
   │   │   │          ├── extraction_weights
   │   │   │          │     ├── 20240722_VT23_TP_extraction_weights.csv
   │   │   │          │     ├── 20240723_VT23_TP_uvspec_sampleorder.csv
   │   │   │          │     ├── 20241007_VT23_AX_extraction_weights.csv
   │   │   │          │     └── 20241007_VT23_AX_uvspec_sampleorder.csv
   │   │   │          └── results
   │   │   │                ├── gae
   │   │   │                │    ├── 20240515_VT23_TP_ex01_results.csv
   │   │   │                │    ├── 20240529_VT23_TP_ex02_results.csv
   │   │   │                │    ├── 20240530_VT23_TP_ex03_results.csv
   │   │   │                │    └── 20240605_VT23_TP_ex04_results.csv
   │   │   │                └── teac
   │   │   │                     ├── 20240514_VT23_AX_ex01_results.csv
   │   │   │                     ├── 20240528_VT23_AX_ex02_results.csv
   │   │   │                     ├── 20240529_VT23_AX_ex03_1_results.csv
   │   │   │                     ├── 20240529_VT23_AX_ex03_2_results.csv
   │   │   │                     └── 20240604_VT23_AX_ex04_results.csv
   │   │   └── yield
   │   │         ├── 20240604_FS23_VT23_P8_yield.csv
   │   │         └── 20240604_FS23_VT23_composite_samples.csv
   │   │
   │   ├── VT24
   │   │   ├── storage_scenarios
   │   │   │     ├── hplc
   │   │   │     │     ├── extraction_weights
   │   │   │     │     │    └── 20240729_STS_extraction_weights.csv
   │   │   │     │     └── results
   │   │   │     │          └── 20240709_STS_acids_results.csv
   │   │   │     └── sampling
   │   │   │          ├── 20240606_STS_exp02_extraction_weights.csv
   │   │   │          └── 20240708_STS_exp02_subextraction_weights.csv
   │   │   └── variety_trial
   │   │         ├── experimental_design
   │   │         │          └── 20240304_VT24_P8_genotype_design_positions.csv
   │   │         ├── hplc
   │   │         │     ├── extraction_weights
   │   │         │     │    └── 20240722_VT24_acids_extraction_weights.csv
   │   │         │     └── results
   │   │         │          ├── 20240705_VT24_acids_R1R2_results.csv
   │   │         │          └── 20240705_VT24_acids_R3R4_results.csv
   │   │         ├── quality
   │   │         │     ├── 20240610_VT24_P8_firmness.csv
   │   │         │     ├── 20240610_VT24_P8_fleshcolour.csv
   │   │         │     ├── 20240627_VT24_P8_brix.csv
   │   │         │     ├── 20240627_VT24_P8_firmness.csv
   │   │         │     └── 20240627_VT24_P8_fleshcolour.csv
   │   │         ├── spectrophotometer
   │   │         │          ├── calibration
   │   │         │          │     ├── gae
   │   │         │          │     │    ├── 20240705_VT24_TP_calibration.csv
   │   │         │          │     │    └── 20240706_VT24_TP_calibration.csv
   │   │         │          │     └── teac
   │   │         │          │          ├── 20240704_VT24_AX_calibration.csv
   │   │         │          │          └── 20240705_VT24_AX_calibration.csv
   │   │         │          ├── extraction_weights
   │   │         │          │     ├── 20240723_VT24_TP_extraction_weights.csv
   │   │         │          │     ├── 20240723_VT24_TP_uvspec_sampleorder.csv
   │   │         │          │     ├── 20241007_VT24_AX_extraction_weights.csv
   │   │         │          │     └── 20241007_VT24_AX_uvspec_sampleorder.csv
   │   │         │          └── results
   │   │         │                ├── gae
   │   │         │                │    ├── 20240705_VT24_TP_results.csv
   │   │         │                │    └── 20240706_VT24_TP_results.csv
   │   │         │                └── teac
   │   │         │                     ├── 20240704_VT24_AX_results.csv
   │   │         │                     └── 20240705_VT24_AX_results.csv
   │   │         └── yield
   │   │              └── 20240809_VT24_P8_yield.csv
   │   │
   │   │
   │   └── weather_data
   │         ├── 20241007_VT_minmaxtemp_Aug22Aug24.csv
   │         ├── 20241007_VT_pyranometer_Aug22Aug24.csv
   │         ├── 20241007_VT_rainfall_Aug22Aug24.csv
   │         └── 20241007_VT_relativehumidity_Aug22Aug24.csv 
   │              
   ├── processed/
   │   ├── 20241008_STS_compiled_dataset.csv
   │   ├── 20241008_STS_compiled_dataset.RData
   │   ├── 20241009_VT_compiled_dataset.csv
   │   └── 20241009_VT_compiled_dataset.RData
   │
   └── dictionaries/
       ├── STS_compiled_dataset_dictionary.txt
       └── VT_compiled_dataset_dictionary.txt


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Code Overview: ./code/  
----------------------
- **acids_processing_func_v0.0.6.R**  
  Custom R function to automate the processing of HPLC data. See thesis Section 4.2.2.1 for details.

- **chap-06_analysis-figures.R**  
  Annotated R script used to analyse processed data and generate figures for Chapter 6.

- **datacompilation_STS_v0.0.4.R**  
  Integrates all primary data from the 2024 Storage Scenarios (STS) experiment into a complete dataset.

- **datacompilation_VT_v0.1.3.R**  
  Integrates all primary data from the 2023–2024 Variety Trial (VT) experiments into a complete dataset. Utilises the function in `acids_processing_func_v0.0.6.R`.

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Data Overview

./data/primary/VT23/experimental_design/
--------------------
| Filename                              | Description                                                      		|	
|---------------------------------------|-------------------------------------------------------------------------------|
| 20231220_VT23_P8_genotype_setup.csv	| Randomised positions of genotypes within experimental polytunnel in 2023	|	
-------------------------------------------------------------------------------------------------------------------------

./data/primary/VT23/hplc/
--------------------
| Filename                                              	| Description                                                                           	|
|---------------------------------------------------------------|-----------------------------------------------------------------------------------------------|
| extraction_weights/20240630_VT23_acids_extraction_weights.csv | Mass of dried strawberry material used for organic acid extractions                 		|
| results/20240630_VT23_WK3_acids_results.csv 			| Original organic acid data acquired directly from the hplc system - experimental week 3	|
| results/20240705_FS23_VT23_WK2_acids_results.csv          	| Original organic acid data acquired directly from the hplc system - experimental week 2	|
-----------------------------------------------------------------------------------------------------------------------------------------------------------------


./data/primary/VT23/spectrophotometer/
--------------------
| Filename                                              		| Description                                                           |
|-----------------------------------------------------------------------|-----------------------------------------------------------------------|
| calibration/gae/20240515_VT23_TP_ex01_calibration.csv			| Original absorbance data for gallic acid standards - extraction rep 1	|
| calibration/gae/20240529_VT23_TP_ex02_calibration.csv			| Original absorbance data for gallic acid standards - extraction rep 2 |
| calibration/gae/20240530_VT23_TP_ex03_calibration.csv			| Original absorbance data for gallic acid standards - extraction rep 3 |
| calibration/gae/20240605_VT23_TP_ex04_calibration.csv			| Original absorbance data for gallic acid standards - extraction rep 4 |
| calibration/teac/20240514_VT23_AX_ex01_calibration_manualentry.csv	| Original absorbance data for TROLOX standards - extraction rep 1	|
| calibration/teac/20240528_VT23_AX_ex02_calibration_manualentry.csv	| Original absorbance data for TROLOX standards - extraction rep 2	|
| calibration/teac/20240529_VT23_AX_ex03_calibration.csv     		| Original absorbance data for TROLOX standards - extraction rep 3	|
| calibration/teac/20240604_VT23_AX_ex04_calibration.csv		| Original absorbance data for TROLOX standards - extraction rep 4	|
| extraction_weights/20240722_VT23_TP_extraction_weights.csv		| Mass of dried strawberry material used for TP and AX extractions	|
| extraction_weights/20240723_VT23_TP_uvspec_sampleorder.csv 		| Order in which samples were analysed for TP on the spectrophotometer  |
| extraction_weights/20241007_VT23_AX_extraction_weights.csv		| Mass of dried strawberry material used for TP and AX extractions 	|
| extraction_weights/20241007_VT23_AX_uvspec_sampleorder.csv 		| Order in which samples were analysed for AX on the spectrophotometer  |
| results/gae/20240515_VT23_TP_ex01_results.csv          		| Original absorbance data for sample TP - extraction rep 1          	|
| results/gae/20240529_VT23_TP_ex02_results.csv          		| Original absorbance data for sample TP - extraction rep 2          	|
| results/gae/20240530_VT23_TP_ex03_results.csv          		| Original absorbance data for sample TP - extraction rep 3          	|
| results/gae/20240605_VT23_TP_ex04_results.csv         		| Original absorbance data for sample TP - extraction rep 4          	|
| results/teac/20240514_VT23_AX_ex01_results.csv          		| Original absorbance data for sample AX - extraction rep 1          	|
| results/teac/220240528_VT23_AX_ex02_results.csv         		| Original absorbance data for sample AX - extraction rep 2          	|
| results/teac/20240529_VT23_AX_ex03_1_results.csv          		| Original absorbance data for sample AX - extraction rep 3.1          	|
| results/teac/20240529_VT23_AX_ex03_2_results.csv         		| Original absorbance data for sample AX - extraction rep 3.2          	|
| results/teac/20240604_VT23_AX_ex04_results.csv          		| Original absorbance data for sample AX - extraction rep 4          	| 
-------------------------------------------------------------------------------------------------------------------------------------------------

./data/primary/VT23/yield/
-------------------------
| Filename 					| Description										|
|-----------------------------------------------|---------------------------------------------------------------------------------------|
| 20240604_FS23_VT23_P8_yield.csv		| Mass, number, and classiication of harvested berries					|
| 20240604_FS23_VT23_composite_samples.csv	| Exact mass of each sample used to create composite samples across both sampling weeks	|
-----------------------------------------------------------------------------------------------------------------------------------------

./data/primary/VT24/variety_trial/experimental_design/
-----------------------------------
| Filename                                              | Description									|
|-------------------------------------------------------|-------------------------------------------------------------------------------|
| 20240304_VT24_P8_genotype_design_positions.csv	| Randomised positions of genotypes within experimental polytunnel in 2024	|
-----------------------------------------------------------------------------------------------------------------------------------------

./data/primary/VT24/variety_trial/hplc/
-----------------------------------
| Filename							| Description										|
|---------------------------------------------------------------|---------------------------------------------------------------------------------------|
| extraction_weights/20240722_VT24_acids_extraction_weights.csv	| Mass of dried strawberry material used for organic acid extractions			|
| results/20240705_VT24_acids_R1R2_results.csv			| Original organic acid data acquired directly from the hplc system - sample batch 1 	|
| results/20240705_VT24_acids_R3R4_results.csv			| Original organic acid data acquired directly from the hplc system - sample batch 2	|
---------------------------------------------------------------------------------------------------------------------------------------------------------


./data/primary/VT24/variety_trial/quality/
-----------------------------------
| Filename				| Description								| 
|---------------------------------------|-----------------------------------------------------------------------|
| 20240610_VT24_P8_firmness.csv 	| Original penetrometer data for all genotypes EXCLUDING Malwina	|
| 20240610_VT24_P8_fleshcolour.csv	| Original colorimeter data for all genotypes EXCLUDING Malwina		|
| 20240627_VT24_P8_brix.csv		| Original refractometer data for all genotypes				| 
| 20240627_VT24_P8_firmness.csv		| Original penetrometer data for Malwina ONLY				|
| 20240627_VT24_P8_fleshcolour.csv	| Original colorimeter data for Malwina	ONLY				|
-----------------------------------------------------------------------------------------------------------------

./data/primary/VT24/variety_trial/spectrophotometer/
-----------------------------------
| Filename							| Description                                                           |
|---------------------------------------------------------------|-----------------------------------------------------------------------|
| calibration/gae/20240705_VT24_TP_calibration.csv		| Original absorbance data for gallic acid standards - sample batch 1	|
| calibration/gae/20240706_VT24_TP_calibration.csv		| Original absorbance data for gallic acid standards - sample batch 2	|
| calibration/teac/20240704_VT24_AX_calibration.csv		| Original absorbance data for TROLOX standards - sample batch 1	|
| calibration/teac/20240705_VT24_AX_calibration.csv		| Original absorbance data for TROLOX standards - sample batch 2	|
| extraction_weights/20240723_VT24_TP_extraction_weights.csv	| Mass of dried strawberry material used for TP and AX extractions	|
| extraction_weights/20240723_VT24_TP_uvspec_sampleorder.csv	| Order in which samples were analysed for TP on the spectrophotometer  |
| extraction_weights/20241007_VT24_AX_extraction_weights.csv	| Mass of dried strawberry material used for TP and AX extractions 	|
| extraction_weights/20241007_VT24_AX_uvspec_sampleorder.csv	| Order in which samples were analysed for AX on the spectrophotometer  |
| results/gae/20240705_VT24_TP_results.csv			| Original absorbance data for sample TP - sample batch 1          	|
| results/gae/20240706_VT24_TP_results.csv			| Original absorbance data for sample TP - sample batch 2          	|
| results/teac/20240704_VT24_AX_results.csv			| Original absorbance data for sample AX - sample batch 1          	|
| results/teac/20240705_VT24_AX_results.csv			| Original absorbance data for sample AX - sample batch 2          	|
-----------------------------------------------------------------------------------------------------------------------------------------

./data/primary/VT24/variety_trial/yield/
-----------------------------------
| Filename			| Description						|
|-------------------------------|-------------------------------------------------------|
| 20240809_VT24_P8_yield.csv	| Mass, number, and classiication of harvested berries	|
-----------------------------------------------------------------------------------------

./data/primary/VT24/storage_scenarios/hplc/
--------------------------------------
| Filename							| Description								|
|---------------------------------------------------------------|-----------------------------------------------------------------------|
| extraction_weights/20240606_STS_exp02_extraction_weights.csv	| Mass of dried strawberry material used for organic acid extractions	|
| results/20240709_STS_acids_results.csv			| Original organic acid data acquired directly from the hplc system	|
-----------------------------------------------------------------------------------------------------------------------------------------

./data/primary/VT24/storage_scenarios/sampling/
-----------------------------------------------
| Filename					| Description											|
|-----------------------------------------------|-----------------------------------------------------------------------------------------------|
| 20240606_STS_exp02_extraction_weights.csv	| Total mass of strawberries at T=0 in stroage experiments					|
| 20240708_STS_exp02_subextraction_weights.csv 	| Fresh and dried mass of berries sub-sampled at different time throught the storage experiment	|
-------------------------------------------------------------------------------------------------------------------------------------------------

./data/primary/weather_data/  
------------------
| Filename					| Description												|
|-----------------------------------------------|-------------------------------------------------------------------------------------------------------|
| 20241007_VT_minmaxtemp_Aug22Aug24.csv		| Daily min and max air temperatures recorded by local weather station between August 2022 and 2024	|
| 20241007_VT_pyranometer_Aug22Aug24.csv	| Daily daily solar irradience recorded by local weather station between August 2022 and 2024		|
| 20241007_VT_rainfall_Aug22Aug24.csv		| Daily rainfall recorded by local weather station between August 2022 and 2024				|
| 20241007_VT_relativehumidity_Aug22Aug24.csv	| Daily realtive humidity recorded by local weather station between August 2022 and 2024		|
---------------------------------------------------------------------------------------------------------------------------------------------------------

./data/processed/  
------------------
| Filename                              | Description                                                                                                       	    | Data Dictionary                                       |
|---------------------------------------|---------------------------------------------------------------------------------------------------------------------------|-------------------------------------------------------|
| 20241008_STS_compiled_dataset.csv     | Integrated dataset derived from all datafiles in 'data/primary/VT24/storage_scenarios': see 'datacompilation_STS_v0.0.4.R'| data/dictionaries/STS_compiled_dataset_dictionary.txt |
| 20241008_STS_compiled_dataset.RData 	| Image of R environment containing 1 dataframe, equivalent to '220241008_STS_compiled_dataset.csv'          	    	    | data/dictionaries/STS_compiled_dataset_dictionary.txt |
| 20241009_VT_compiled_dataset.csv 	| Integrated dataset derived from all datafiles in 'data/primary/VT24/variety_trial': see 'datacompilation_VT_v0.1.3.R'	    | data/dictionaries/VT_compiled_dataset_dictionary.txt  |
| 20241009_VT_compiled_dataset.RData	| Image of R environment containing 1 dataframe, equivalent to '20241009_VT_compiled_dataset.csv' plus weather data 	    | data/dictionaries/VT_compiled_dataset_dictionary.txt  |
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Identifier abbreviations
------------------

| Identifier    | Description                                                                       							    				    |
|---------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| VT       	| experiment ID - Varitey Trial - relates collectively to the genotype experiments in 2023 and 2024 									    | 
| VT23 		| experiment ID - Varitey Trial 2023 - relates specifically to the genotype experiments in 2023         	    							    | 
| VT24 		| experiment ID - Varitey Trial 2023 - relates specifically to the genotype experiments in 2023           	    							    | 
| STS 		| experiment ID - Storage Scenarios - relates specifically to the stroage experiments in 2024 										    |
| WK[0-9]	| additional data descriptor - distinguishes the week of sample collection within the 2023 genotype experiment          	    					    |          	    
| P8 		| additional data descriptor - name of the polytunnel used for the 2023 and 2024 experiments         	    								    | 
| TP 		| additional data descriptor - Total Phenolics - relates to phenolics analysis for the genotype experiments          	    						    |
| AX 		| additional data descriptor - Antioxidants - relates to antioxidants analysis for the genotype experiments 								    |
| R[0-9] 	| additional data descriptor - Row number - 2024 hplc samples were analysed in batches grouped by the polytunnel row they came from         	    		    	    |
| exp[0-9][0-9] | additional data descriptor - Experiment number - relates to the experiment number for the 2024 stroage experiment - only data for exp02 is stored here, exp01 was a pilot | 
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Usage Notes 
---------
- All primary data filenames follow the format: `YYYYMMDD_StudyID_AnalyteID_Descriptor.csv`
	- e.g. '20231220_VT23_P8_genotype_setup.csv' - see above for list of identifer abbreviations.
- '20241009_VT_compiled_dataset.RData' and '20241008_STS_compiled_dataset.RData' can be used to load all necessary data directly into an R environment. 
	- The .RData files comprise dataframes equivalent to '20241009_VT_compiled_dataset.csv' and '220241008_STS_compiled_dataset.csv', with additional weather data.
- For descriptions of variable names used in each datfile, please see the relevant data dictionaries for each datafile.
	- data dictionaries only included for the processed datafiles that were used for analysis
	- please contact the author if you need more information on the primary datafiles
- All figures used in Chapter 6 are included in the main thesis.
- Please cross-reference 'chap-06_analysis-figures.R' for more context on how the statistical analyses were conducted and how the figures were generated and utilised for the thesis.
- Recommended tools: R ≥ 4.0, see 'chap-06_analysis-figures.R ' for required packages

