Sigmoid curve fitting for transpiration measurements from porometer at different water potentials (pressure):Read more »
Blog Archives
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...
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...
Bootsrap Confidence Intervals, Stratified Bootstrap
Here's a worked example for comparing group averages with bootstrap confidence intervals and allowing for different subsample sizes by calling the strata argument within the bootstrap function.The data is set up analogous to an before-after impac...
Custom Labels for Ordination Diagram
Here is how you do custom labels, hull, spider in a vegan ordination diagram: Read more »
Test Difference Between Diversity-Indices of Two Samples with Abundance Data
I adapted a scheme for a permutation test from the PAST Software (Hammer & Harper, http://folk.uio.no/ohammer/past/diversity.html) that tests difference between diversity-indices of two samples with abundance data... Read more »
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 ...
Zero Inflated Models and Generalized Linear Mixed Models with R.
Zuur, Saveliev, Ieno (2012).
