Ecosyste.ms: Awesome

An open API service indexing awesome lists of open source software.

Awesome Lists | Featured Topics | Projects

https://github.com/nevrome/currycarbon

A radiocarbon calibration module written in and for Haskell
https://github.com/nevrome/currycarbon

archaeology haskell radiocarbon radiocarbon-dates

Last synced: about 2 months ago
JSON representation

A radiocarbon calibration module written in and for Haskell

Host: GitHub
URL: https://github.com/nevrome/currycarbon
Owner: nevrome
License: mit
Created: 2021-06-19T18:50:57.000Z (over 3 years ago)
Default Branch: master
Last Pushed: 2024-11-03T15:18:04.000Z (2 months ago)
Last Synced: 2024-11-03T16:21:40.222Z (2 months ago)
Topics: archaeology, haskell, radiocarbon, radiocarbon-dates
Language: Haskell
Homepage: https://hackage.haskell.org/package/currycarbon
Size: 616 KB
Stars: 10
Watchers: 3
Forks: 1
Open Issues: 4
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- License: LICENSE

Awesome Lists containing this project

README

[![GitHub Workflow Status](https://github.com/nevrome/currycarbon/actions/workflows/normalCheck.yml/badge.svg)](https://github.com/nevrome/currycarbon/actions/workflows/normalCheck.yml)
[![Coverage Status](https://img.shields.io/codecov/c/github/nevrome/currycarbon/master.svg)](https://codecov.io/github/nevrome/currycarbon?branch=master)
[![GitHub release (latest by date including pre-releases)](https://img.shields.io/github/v/release/nevrome/currycarbon?include_prereleases)
![GitHub all releases](https://img.shields.io/github/downloads/nevrome/currycarbon/total)](https://github.com/nevrome/currycarbon/releases)

# currycarbon

Radiocarbon calibration module written in and for [Haskell](https://www.haskell.org). Comes with a small CLI app to run calibration on the command line.

### Library

The Haskell library is available on Hackage [here](https://hackage.haskell.org/package/currycarbon) and on Stackage [here](https://www.stackage.org/package/currycarbon).

### CLI app

For stable release versions we automatically prepare statically built binaries that can be downloaded and run directly.

You can download them here: [ [Linux 📥](https://github.com/nevrome/currycarbon/releases/latest/download/currycarbon-Linux) | [macOS 📥](https://github.com/nevrome/currycarbon/releases/latest/download/currycarbon-macOS) ]. Older release versions (some with Windows builds) are available [here](https://github.com/nevrome/currycarbon/releases).

So in Linux you can run the following commands to get started:

```bash
# download the current stable release binary
wget https://github.com/nevrome/currycarbon/releases/latest/download/currycarbon-Linux
# make it executable
chmod +x currycarbon-Linux
# test it
./currycarbon-Linux "Sample1,4990,30"
```

```
currycarbon v0.3.0.1 (UTF-8)
Method: Bchron {distribution = StudentTDist {ndf = 100.0}}
Curve: IntCal20
Calibrating...
CalEXPR: [1] Sample1:4990±30BP
Calibrated: 3936BC >> 3794BC > 3757BC < 3662BC << 3654BC
1-sigma: 3794-3707BC, 3666-3662BC
2-sigma: 3936-3874BC, 3804-3697BC, 3684-3654BC
▁▁▁ ▁▁▁▁
▁▁▒▒▒▁▁▁▁▒▒▒▒▁
▒▒▒▒▒▒▒▒▒▒▒▒▒▒ ▁
▁▁ ▁▒▒▒▒▒▒▒▒▒▒▒▒▒▒▁ ▁▒
▁▁▒▒▁ ▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒ ▁▒▒▁
▁▁▁▁▁▒▒▒▒▒▁ ▁▁▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▁▁▁▁▒▒▒▒▁
▁▁▁▒▒▒▒▒▒▒▒▒▒▒▁▁▁▁▁▁▁▁▁▁▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▁
-3950 ┄─────────┬───────────────┬────────────────┬─────────┄ -3640
> > ^ < <
──────────────── ─
─────────── ────────────────── ──────
Done.
```

```
Usage: currycarbon [--version] [CalEXPRs] [-i|--inputFile FILE]
[--calCurveFile FILE] [--method DSL] [--allowOutside]
[--noInterpolation] [-q|--quiet] [--densityFile FILE]
[--hdrFile FILE]
[[--seed INT] (-n|--nrSamples INT) --samplesFile FILE]
[--calCurveSegFile FILE] [--calCurveMatFile FILE]

Intercept calibration of radiocarbon dates

Available options:
-h,--help Show this help text
--version Show version
CalEXPRs ---
A string to specify "calibration expressions", so
small chronological models for individual events.
These can include uncalibrated radiocarbon ages,
uniform age ranges and operations to combine the
resulting age probability distribution as sums or
products.
The expression language includes the following
functions:

- calExpr(id = STRING, expr = EXPR)
- uncalC14(id = STRING, yearBP = INT, sigma = INT)
- rangeBP(id = STRING, start = INT, stop = INT)
- rangeBCAD(id = STRING, start = INT, stop = INT)
- sum(a = EXPR, b = EXPR)
- product(a = EXPR, b = EXPR)

The order of arguments is fixed, but the argument
names ' =' can be left out. The 'id' arguments
are optional. Some functions can be shortened with
syntactic sugar:

- calExpr(STRING, EXPR) -> id: EXPR
- uncalC14(STRING, INT, INT) -> STRING,INT,INT
- sum(EXPR, EXPR) -> EXPR + EXPR
- product(EXPR, EXPR) -> EXPR * EXPR

Parentheses '()' can be used to specify the
evaluation order within an expression. Multiple
expressions can be chained, separated by ';'.

Examples:
1. Calibrate a single radiocarbon date with a mean
age BP and a one sigma standard deviation:
"3000,30" or "uncalC14(yearBP = 3000, sigma = 30)"
2. Calibrate two radiocarbon dates and sum them:
"(3000,30) + (3100,40)" or
"sum(uncalC14(3000,30), uncalC14(3100,40))"
3. Compile a complex, named expression:
"Ex3: ((3000,30) + (3100,40)) * rangeBP(3200,3000)"
---
-i,--inputFile FILE A file with a list of calibration expressions.
Formatted just as CalEXPRs, but with a new line for
each input expression. CalEXPRs and --inputFile can
be combined and you can provide multiple instances of
--inputFile. Note that syntactic sugar allows to read
simple radiocarbon dates from a headless .csv file
with one sample per row: ,,.
--calCurveFile FILE Path to an calibration curve file in '.14c' format.
The calibration curve will be read and used for
calibration. If no file is provided, currycarbon will
use the 'intcal20' curve.
--method DSL The calibration algorithm that should be used:
',,'.
The default setting is equivalent to
"Bchron,StudentT,100" which copies the algorithm
implemented in the Bchron R package. For the Bchron
algorithm with a normal distribution
("Bchron,Normal") the degrees of freedom argument is
not relevant
Alternatively we implemented "MatrixMult", which
comes without further arguments.
--allowOutside Allow calibrations to run outside the range of the
calibration curve.
--noInterpolation Do not interpolate the calibration curve.
-q,--quiet Suppress the printing of calibration results to the
command line.
--densityFile FILE Path to an output file to store output densities per
CalEXPR and calender year.
--hdrFile FILE Path to an output file to store the high probability
density regions for each CalEXPR.
--seed INT Seed for the random number generator for age
sampling. The default causes currycarbon to fall back
to a random seed. (default: Nothing)
-n,--nrSamples INT Number of age samples to draw per CalEXPR.
--samplesFile FILE Path to an output file to store age samples for each
CalEXPR.
--calCurveSegFile FILE Path to an output file to store the relevant,
interpolated calibration curve segment for the first
(!) input date. This option as well as
--calCurveMatFile are meant for debugging.
--calCurveMatFile FILE Path to an output file which stores the relevant,
interpolated calibration curve segment for the first
(!) input date in a wide matrix format.
```

### For developers who want to edit the code

To install the latest development version you can follow these steps:

1. Install the Haskell build tool [Stack](https://docs.haskellstack.org/en/stable/README/)
2. Clone the repository
3. Execute `stack install` inside the repository to build the tool and automatically copy the executables to `~/.local/bin` (which you may want to add to your path). This will install the compiler and all dependencies into folders that won't interfere with any installation you might already have.

#### Running the golden tests

Because the golden tests can not run on stackage as they are set up now (see the discussion [here](https://github.com/nevrome/currycarbon/issues/17)) I hid them behind an environment variable. You can run them with

```bash
CURRY_RUN_GOLDEN=true stack test --pedantic
```

Just calling `stack test --pedantic` without this variable will skip any test with the pattern `"Golden"` in their descriptors.

#### Preparing a new stable release

The Github Actions script in `.github/workflows/release.yml` registers a new draft release and automatically builds and uploads currycarbon binaries when a new Git tag with the prefix `v*` is pushed.

```bash
# locally register a new tag (e.g. 0.3.1)
git tag -a v0.3.1 -m "see CHANGELOG.md"
# push tag
git push origin v0.3.1
```

In case of a failing build delete the tag and the release draft on Github and then delete the tag locally with

```bash
git tag -d v0.3.1
```

before rerunning the procedure above.

#### Profiling

```
stack build --profile
stack exec --profile -- currycarbon "1000,200;2000,200;3000,200;4000,200;5000,200;6000,200;7000,200;8000,200" -q --densityFile /dev/null +RTS -p
stack exec -- currycarbon "1000,200;2000,200;3000,200;4000,200;5000,200;6000,200;7000,200;8000,200" -q --densityFile /dev/null +RTS -s
```