Inputs and Outputs for Radiocarbon Calibration Pipeline

They live here.

Tutorials

Here, we present a couple of usage scenarios.
Before any of the steps below, you should:

1. Export the data to a CSV file
2. Make sure the column that has the C14 dates is called C14Age, and the column that has the error is called C14SD

Scenario 1: New file to calibrate

Let's say the file that we want to calibrate is called example.csv:

1. Open this repository and navigate to the inputs folder
2. Add the new CSV file, example.csv, for calibration:
   1. Top right corner
   2. Add file
   3. Upload files
   4. Choose your files
   5. Choose the file you want to calibrate
   6. Commit changes
3. Watch the status of the pipeline change from In progress to Success or Failure
4. In case of Success, check the outputs folder for a file called example.radiocarbon.csv and for new PDFs, those are your outputs!

Scenario 2: Run a file with another script and confidence value

Let's say the file that we want to calibrate is called sedimentary_charcoal.csv:

1. Open this repository and navigate to the inputs folder
2. Create a new folder file inside inputs, inside the folder we will create a config file:
   1. Top right corner
   2. Add file
   3. Create new file
   4. Write "/sediment_analysis/config"
      (The folder name can be whatever you want!)
   5. Copy the structure of the default config file to the text field
   6. Change confidence to the desired value, and script to the name of a script that exists on the scripts folder, for example sediments.r
   7. On the top right, Commit changes...
   8. Commit changes
3. Navigate to the new folder you just created
4. Add the new CSV file, sedimentary_charcoal.csv, for calibration (Top right corner -> Add file -> Upload files -> Choose your files -> Choose the file you want to calibrate -> Commit changes)
5. Watch the status of the pipeline change from In progress to Success or Failure
6. In case of Success, check the outputs folder, then sediment_analysis for a file called sedimentary_charcoal.sediments.csv and for new PDFs, those are your outputs!

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config files

You can modify the config files to adjust settings such as confidence intervals, time steps, filtering, and the script to be used for a file. For example:

step=20
confidence=0.90
column=Site
value=SMM
script=my_script.r

This configuration uses a 20-year step, a confidence interval of 90%, filter on all rows with the value SMM on the column named Site, and runs the script my_script.r on the file.

Warning

The order of values is important!
All values can be empty, except for script.

Default and folder configs

Folder-specific config files override the default for all CSV files within that folder. If a file lacks a folder config, the default config is applied. Folder config files have the same structure and content as the default config.

By organizing your scripts and configurations this way, you can easily manage and customize the processing of different input files.

Warning

Whenever a folder config file is changed, the outputs for all files in that folder get recomputed!

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Folder Structure

The structure of the directories looks like this:

.
├── config                         # Default configuration for input files. Files without a nearby config use this.
├── inputs/                        # Location of input files.
│   ├── folder_1/                  # Files can be organized in folders.
│   │   ├── example1.csv           # This file uses the config next to it.
│   │   └── config
│   ├── folder_2/
│   │   └── example2.csv           # This file uses the default config.
│   └── example3.csv               # And this one too.
├── outputs/                       # Output files are stored here. Folder structure mirrors the inputs.
│   ├── folder_1/
│   │   ├── example1.my_script.csv # Processed file name includes the script used.
│   │   └── example1.pdf           # PDF files generated by the script are also stored here.
│   ├── folder_2/
│   │   └── example2.default_script.csv
│   └── example3.default_script.csv
└── scripts/                       # Location of the scripts.
    ├── default_script.r
    └── my_script.r

You can nest even more folders inside inputs if you like! It's all about organization. The structure is automatically mirrored on the outputs, so everything stays where you expect it to.

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Scripts

For more information about how to create more scripts, check out their information page.