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plum's Introduction

Plum

This is a beta version of Plum (see: https://doi.org/10.1007/s13253-018-0328-7).

- this version is the beta version of Plum, for the official R version see rplum.

Plum is a R-package, with dependencies on Python 2.7, which uses a Bayesian approach to construct age-depth models for 210Pb data. At the moment Plum only works in Unix base OS (Linux-Mac) it depends on rPython package which is only available in these systems.

rplum, R's official version

rplum has being accepted into CRAN (the R reposatories). For downloading this version use

install.packages('rplum')

library(rplum)

Plum()

Installing Plum's beta version

Preparing the system for Plum

In order to install plum the following have to be install in your system,

  • R (>=3.0)
  • rPython (R package)
  • Python 2.7
  • numpy (python package)
  • scipy (python package)
  • matplotlib (python package)

In the case of Mac OS, we recommend the installation of Anaconda (https://www.anaconda.com/download/). This will install python 2.7 and the necessary packages.

For linux, Arch pacman -S python2 python2-numpy python2-scipy python2-matplotlib

Fedora yum install python python-numpy python-scipy python-matplotlib

Ubuntu apt install python python-numpy python-scipy python-matplotli

To install rPython use install.packages("rPython", configure.vars= "RPYTHON_PYTHON_VERSION=2") this will let R know to use python 2.7.

To install Plum from R using devtools.

library(devtools)

install_github("maquinolopez/Plum")

For questions contact me at: [email protected]

plum's People

Contributors

maquinolopez avatar

Stargazers

 avatar Laura C Reynolds avatar Henning Teickner avatar Dewey Dunnington avatar Christopher Dutton avatar

Watchers

Nick McKay avatar James Holmquist avatar  avatar

Forkers

maarten14c

plum's Issues

Full set of posterior draws

Hi,
Thanks for putting this set of functions together. With just a little bit of tweaking I was able to get the package running on Windows Subsystem for Linux (using X11 forwarding via Xming Server).

I'm looking through the results of runPlum() and notice that the ages.csv contains posterior information for specified depths, but that these data are only a synthesis of the full data set. I'm curious if there is a way to:

  1. Get the complete set of posterior draws (after burn-in and thinning) at the specified depths.
  2. Get the complete set of posterior draws for the parameters in the model.

Thanks!

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