Description of programs

This page is intended to provide some of the code I developed throughout the years to automatize re-occurring tasks, or to overcome problems with the absence of some advanced but as yet not widely applied statistical methods in standard statistical software packages. For each file a short description of the method and purpose is given, and all files come with a basic in-file description of the use. However, those short descriptions mainly deal as user manuals, rather than an in-depth description of the methods. Whenever applicable, citations for further reading are provided, in most cases covering the original work in which the respective method was described. Any user is strictly encouraged to acquire at least a basic knowledge of the process before using the software. No liability whatsoever will be accepted for any losses that are directly or indirectly resulting from the use of that software.

Part of the software consists of MS Excel sheets, in most cases saved in the .xlsx file format. This format has been around for a while now, and I assume everyone has access to a system running MS Office 2007 or higher. Principally .xlsx files can be converted to .xls files, and some online- and/or freeware converters for that purpose exist. I cannot guarantee, however, that I did not use expressions that are incompatible with older versions of MS Excel. Whether or not the spread sheets can be used in OpenOffice, LibreOffice, or any other freeware alternative of MS Excel, remains to be tested.

The majority of the code, especially for the more advanced techniques, is written for R or MATLAB, however. It is provided as files in ASCII format, that can be opened with any text editor. The R-codes are normally provided as function, that can either be copied into the R console or imported via the source() command, and thereafter invoked as a normal function call. If third-party packages are required they are loaded automatically if installed, but will not be installed automatically if missing on your R installation. Please check whether or not all necessary packages are installed beforehand, and if not, install them before using the code. Each code file further contains one or more examples (either in-code or as separate files), demonstrating the use and also serving as examples for the required input file format.

Just before providing my own small contribution, I would like to give you a list of other useful programs and web pages concerned with statistics (feel free to spread the word):

• Graham, D. and Midgley, N. Tri-plot: Ternary diagram plotting software.

• Hammer, Ø., Harper, D. A. T., and Ryan, P. D. (2001) PAST: Paleontological Statistics software package for education and data analysis. Palaeontologia Electronica 4 (1): 1–9.

• McDonald, J. H. Handbook of Biological Statistics.

• Wood, M. Making Sense of Statistics: A Non-Mathematical Approach.

How To use

Within the three GitHub repositories you will find files suitable for different analytical tasks. The files in the R program codes and Matlab program codes pages are provided as ASCII-coded .txt file. You can principally open them in any text-editor, and copy the code into the R or Matlab console. In R you can also use source("FilePath") to make the functions known to R, and then work directly from the command prompt. However, it is often more convenient to write code in an editor and send command lines directly to R. For that, two possible options are either Notepad++ with the NppToR extension installed on your computer, or the use of Tinn-R as an editor.

MS Excel spreadsheets are provided as .xls or .xlsx format in the Excel spreadsheets page. Whether or not they work in OpenOffice, LibreOffice, or alike is unknown to me. Due to Excels limitations they are not by far as advanced as comparable R code, and some of the used Excel equations are rather complicated and confusing, which makes it difficult to adapt the spreadsheets for individual needs.

Disclaimer

Since all that software was written for my own purposes, and also since I am not a professional programmer, it does not cover up all possibilities. It basically follows my own habits and provides some options, but there might be occasions when it requires file formats which you would normally not use, or when it does not give you a choice which you would have deemed useful. That's how it is, live with it!

In any case you are allowed to alter and correct all the code as pleases you. Just give a correct reference when using the code. And if you find some true bug or error, or significantly improved some of the code (everything above small changes according to your own taste like ‘Hey, I added a line so that all plotted curves change colour every second and the program plays the Star Wars soundtrack while running’), I would be more than happy if you could send me the reworked version.

Program codes