Posts Tagged ‘ Vegan Package ’

Two-Way PERMANOVA (with Vegan-Function adonis) Using Customized Contrasts

August 8, 2011
By
Two-Way PERMANOVA  (with Vegan-Function adonis) Using Customized Contrasts

...say you have a multivariate dataset and a two-way factorial design - you do a PERMANOVA and the aov-table (adonis is using ANOVA or "sum"-contrasts) tells you there is an interaction - how to proceed when you want to go deeper into the ana...

Read more »

Adonis (PERMANOVA) – Assumptions

April 26, 2011
By
Adonis (PERMANOVA) – Assumptions

Before you use PERMANOVA (R-vegan function adonis) you should read the user notes for the original program by the author (Marti J. Anderson) who first came up with this method. An important assumtption for PERMANOVA is same "multivariate spread&qu...

Read more »

Permutation Test with Stratified Data and Repeated Measurements

April 21, 2011
By
Permutation Test with Stratified Data and Repeated Measurements

This is an example for a permutation test on stratified samples with repeated measurements. Samples are interdependent firstly because they come from several sites and secondly because the sampling was repeated a second time. That is samples of the sam...

Read more »

Custom Labels for Ordination Diagram

April 20, 2011
By
Custom Labels for Ordination Diagram

Here is how you do custom labels, hull, spider in a vegan ordination diagram:Read more »

Read more »

Multivariate Repeated Measurements With adonis():

April 18, 2011
By
Multivariate Repeated Measurements With adonis():

Lately I had to figure out how to do a repeated measures (or mixed effects) analysis on multivariate (species) data. Here I share code for a computation in R with the adonis function of the vegan package. Credit goes to Gavin Simpson providing most of ...

Read more »