Dr. Mark Gardener


Pelagic Publishing

Writer's Bloc

On this page you can find out about my latest writings. I am usually working on a writing project of some kind (the current project is shown in the sidebar). I'll post updates on progress, tables of contents and also some of the R scripts (and possibly Excel spreadsheets) I am developing in support of the projects. I'll try to keep the material reasonably up to date.

Table of Contents | Index of R scripts

Latest Topic

Abundance-based dissimilarity metrics

When your community data samples include abundance information (as opposed to simple presence-absence) you have a wider choice of metrics to use in calculating (dis)similarity. When you have presence-absence data you use the number of shared species (J) and the species richness of each sample (A & B). Measures of (dis)similarity obtained are therefore slightly "crude".

When you have abundance data your measures of (dis)similarity are a bit more "refined" and you have the potential to pick up patterns in the data that you would otherwise not see using presence-absence data... more

Previous project available now:

Managing Data Using Excel  Cover

Get £5 discount when you buy "Managing Data" direct from the publisher. Enter voucher code MDUE20 in the shopping basket at Pelagic Publishing


Table of Contents

Here is a brief table of contents for the Writer's Bloc in date order (latest at top). It will be similar to the index of R scripts but not all pages will contain R scripts.

Statistics for Ecologists Using R and Excel (Edition 2): Data Collection, Exploration, Analysis and Presentation

Managing Data Using Excel: Organizing, summarizing and visualizing scientific data

Community Ecology: Analytical Methods Using R and Excel



Index of R scripts

Here's an index to the R scripts mentioned here in the Writer's Bloc. Click the link to jump directly to that entry. Custom commands and scripts will generally be available as part of the support for a particular project so look at the Publications page for links to support pages.

Post Hoc analysis for Kruskal-Wallis; functions to calculate post hoc significance using a modified version of the U-test. There are functions to determine critical values, exact p-values, and harmonic mean (you can see the KW posthoc.R file directly).

Species richness from rows of a community dataset.

Estimated species richness from a community dataset, or specaccum() result. Includes summary, print and plot routines.

Entropy profiles plotted for several samples in one plot window for comparison. Takes the result of a Rényi or Tsallis calculation as the starting point.

Chi-Squared Species Association Computes a chi squared co-occurrence matrix and carries out a species association test. The result includes a dissimilarity matrix, which can be plotted as a hierarchical cluster dendrogram.

Providing training for:

  • Ecology
  • Data analysis
  • Statistics
  • R The statistical programming language
  • Data management
  • Data mining

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