Sediment core age modeling in Python

Warning

The project is under heavy development. Code and documentation are not complete.

snakebacon is an open source Python package that blah blah

Our goal is to blah blah blah Bacon.

Documentation

What’s New

v0.0.6

Patch for a minor but annoying bug.

Bug fixes
  • Fix minor bug where certain min and max depths could cause an IndexError (Issue #20).

v0.0.5

Minor patch mostly fixing compile issues and documentation.

Bug fixes
  • Documentation spelling errors.
  • Fixed bad compiling C++ module (Issue #19).

v0.0.4

A patch with minor refactoring and bug fixes.

Bug fixes
  • All *_kwargs arguments are now *_kws (Issue #12).
  • Fixed some Constant Calibration curve prior dates looking bloated (Issue #14).
  • Fixed bug from default t_a and t_b values in calibrate_dates() (Issue #13)
  • Fixed bad label in prior accumulation memory plots. The ‘thick’ had been ‘K’. This has been corrected.
  • Fix AttributeError in AgeDepthModel.plot_prior_dates() (Issue #9).

v0.0.3

A quick patch to fix a show-stopping bug.

Bug fixes
  • Fixes missing curves for bacon MCMC fitting (Issue #7).

v0.0.2

Enhancements
  • DateRecord class has been renamed ChronRecord to avoid confusion with DatedProxyRecord (Issue #3). The read_chron() is also now read_chron().
  • AgeDepthModels now can plot prior distributions.
  • Can now query AgeDepthModels to get prior distribution for chronology dates, sediment rates, and sediment rate memory (Issue #5).
  • Now can use snakebacon.mcmcbackends.bacon.fetch_calibcurve() and the @registercurve() decorator to define and fetch calibration curves by name (Issue #6).
  • McmcSetup and McmcResults now throw bacon its tasks through mcmcbackends.Bacon. This should make snakebacon more bacon-agnostic. Have a look at McmcSetup’s mcmcbackend arg.
  • suggest_accumulation_rate() is no longer a method, but a humble function.
Bug fixes
  • Fixed common AssertionError in AgeDepthModel.agedepth caused by float precision bug (Issue #4).
  • Fixed problem with ProxyRecords and DatedProxyRecords not making copies of Pandas DataFrame attributes. (Issue #2).

v0.0.1

This is the initial, alpha release of snakebacon.

Frequently Asked Questions

Warning

The project is under heavy development. Code and documentation are not complete.

Where did the name “snakebacon” come from?

The heart of the code is based on the C/C++ from the original Bacon, which is based on an interface in R. I was looking to write something similar in Python, thus “snakebacon” was born. I’ve kept the name because it makes me smile.

Examples

Warning

The project is under heavy development. Code and documentation are not complete.

Installation

Warning

The project is under heavy development. Code and documentation are not complete.

Required dependencies

Reading and writing files

Warning

The project is under heavy development. Code and documentation are not complete.

Plotting

Warning

The project is under heavy development. Code and documentation is not complete.

Introduction

API reference

This page is an auto-generated summary of snakebacon’s API.

AgeDepthModel

Creating an AgeDepthModel
AgeDepthModel
Attributes

CalibCurve

Creating a CalibCurve
CalibCurve
read_14c
Attributes

DatedProxyRecord

Creating a DatedProxyRecord
DatedProxyRecord
AgeDepthModel.date
Attributes

ChronRecord

Creating a ChronRecord
ChronRecord
read_chron
Attributes

ProxyRecord

Creating a ProxyRecord
ProxyRecord
read_proxy
Attributes

snakebacon Internals

Warning

The project is under heavy development. Code and documentation are not complete.

snakebacon builds on and wraps around the C/C++ in the Bacon from …

See also

  • Look at this list of all the cool things we publish.

Get in touch

  • Report bugs or view the source code on GitHub.

License

snakebacon is available under the open source GPLv3.