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https://github.com/gavinsimpson/palaeopcurvepaper

Use of principal curves for analysis and summary of palaeoecological stratigraphic data
https://github.com/gavinsimpson/palaeopcurvepaper

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Use of principal curves for analysis and summary of palaeoecological stratigraphic data

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## Summarising stratigraphic data using principal curves



This is a public repository for a paper I am writing on the use of principal curves for summarising stratigraphic palaeoecological data. The paper is being written in markdown with embedded R code. **knitr** is used to covert the embedded R code to outputs used in the paper in a markdown source file. The `pandoc()` **knitr** function is then used to render the markdown source to PDF via LaTeX. This stage uses the default Pandoc LaTeX template currently, but I plan to modify that template to give nicer rendered output.



This is a work in progress *and* an experiment in writing a paper in the open using Github and the ideals of reproducible research; if you have any comments or suggestions uses the [issues tab](https://github.com/gavinsimpson/palaeopcurvepaper/issues) to make them.



### Dependencies

To run the R code in the `Rmd` file you will need the development version of my **analogue** package. You can get this from R-forge; anything version `>= 0.11-1` should be OK. To install this version from within R use



    install.packages("analogue", repos="http://R-Forge.R-project.org")



You'll see some warnings about `scaling` not being a graphical parameter if you don't have a fairly recent development version of the **vegan** package. This annoyance was fixed in revision `r2533`, but because of the silly build process on R-Forge even though **vegan** builds fine for us it fails there so you'll need to compile **vegan** yourself. The warning is totally harmless and nothing will change if you have the right version of **vegan** installed; the warning in the paper just looks odd and annoying.



You'll also need



 * [knitr](http://yihui.name/knitr/), Yihui Xie's excellent R package for processing embedded R code in documents (on CRAN)

 * [vegan](http://cran.r-project.org/web/packages/vegan/index.html), our R package for multivariate & community ecology methods --- **analogue** depends on this so that shouldn't be an issue

 * [coenocliner](https://github.com/gavinsimpson/coenocliner), my coenocline simulator package for R. **coenocliner** is not on CRAN yet, but can be installed using Hadley Wickham's **devtools** package. See the [coenocliner](https://github.com/gavinsimpson/coenocliner) on [github](http://github.com) for installation instructions.

 * [Pandoc](http://johnmacfarlane.net/pandoc/) the wonderful universal document converter from John MacFarlane



### Licence

#### The manuscript

The paper (the markdown source file [prcurve_palaeo.md](https://github.com/gavinsimpson/palaeopcurvepaper/blob/master/prcurve_palaeo.md) and the resulting PDF [prcurve_palaeo.pdf](https://github.com/gavinsimpson/palaeopcurvepaper/blob/master/prcurve_palaeo.pdf)) are copyright © Gavin L. Simpson 2013, some rights reserved. You are free to use the text under the terms of the Creative Commons By-Attribution 3.0 Unported licence.



Creative Commons Licence
Summarising stratigraphic data using principal curves by Gavin L. Simpson is licensed under a Creative Commons Attribution 3.0 Unported License.



#### R Code

In so far as I can (it is simply interpretted code calling existing R functions in existing R packages), I waive all copyright and related or neighboring rights to the R Code embedded in the file [prcurve_palaeo.Rmd](https://github.com/gavinsimpson/palaeopcurvepaper/blob/master/prcurve_palaeo.Rmd).



  

    CC0

  

  


  To the extent possible under law,

  

    Gavin L. Simpson

  has waived all copyright and related or neighboring rights to

  R code for the paper "Summarising stratigraphic data using principal curves".

This work is published from:



  Canada.




## Compiling the Rmd source

I am using **knitr** to write the manuscript with embedded R code. To process the files into the final PDF, the following R code can be used



    require("knitr") ## load the knitr package

    

    render_markdown() ## set the output render hooks, allows Pandoc-flavour markdown

    

    opts_chunk$set(dev = "pdf") ## prefer PDF figures

    

    ## process the R code into a final markdown source file

    ## assumes you are in the directory where the file is located

    knit("prcurve_palaeo.Rmd")

    

    ## process the final markdown source to PDF using Pandoc

    pandoc("prcurve_palaeo.md", format = "latex")