Dr. Mark Gardener 



Writer's BlocOn 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 TopicAbundancebased dissimilarity metrics When your community data samples include abundance information (as opposed to simple presenceabsence) you have a wider choice of metrics to use in calculating (dis)similarity. When you have presenceabsence 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 presenceabsence data... more 

Previous project available now: 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 ContentsHere 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 scriptsHere'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 KruskalWallis; functions to calculate post hoc significance using a modified version of the Utest. There are functions to determine critical values, exact pvalues, 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. ChiSquared Species Association Computes a chi squared cooccurrence 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:


Follow me... 

Top  Contact  DataAnalytics Homepage 