Blog Archives

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

August 8, 2011
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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...

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Lattice-xyplot without Border/Box, with Axes at Bottom & Left Side Only, with Custom Ablines/Grid & Axis-Labelling

August 4, 2011
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Lattice-xyplot without Border/Box, with Axes at Bottom & Left Side Only, with Custom Ablines/Grid & Axis-Labelling

Here's how you do a lattice-xyplot without border/box, with axes at bottom & left side only, with custom ablines/grid & axis-labelling Read more »

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Multiple Comparisons for GLMMs using glmer() & glht()

June 14, 2011
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Multiple Comparisons for GLMMs using glmer() & glht()

...that's an example of how to apply multiple comparisons to a generalised linear mixed model using the function glmer from package lme4 & glht() from package multcomp. By the way you see a nice example for visualizing data from a nested sampli...

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Drawing Grids in R

June 1, 2011
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Drawing Grids in R

Here's an example of how to draw a grid in R and how to fill it.I did use the grid-package and its functions for displaying species cover values at squares of a recording frame...Read more »

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Legendre & Borcard: Nested ANOVA by Permutation

May 30, 2011
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Legendre & Borcard: Nested ANOVA by Permutation

..here's a very illustrative R-Script example by Legendre & Borcard showing how a Nested ANOVA can be done by permutation.Read more »

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Summarize Data by Several Variables

May 23, 2011
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Summarize Data by Several Variables

Here's an example how to conveniently summarize data with the cast function (package reshape). By the way you see how this could be done "in-conveniently" by hand. You also see how a for-loop works and how a matrix is constructed and fill...

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Bootstrap Confidence Intervals for Diversity Indices

April 30, 2011
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Bootstrap Confidence Intervals for Diversity Indices

Here's the bootstrap refinement of the normal asymptotic interval (Mills and Zandvakili, 1997; Dixon et al., 1987; Efron and Tibshirani, 1997) - where Diversity (div, g) is the Simpson Index calculated from the observed sample, k is the number boot...

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Fit Sigmoid Curve with Confidence Intervals

April 28, 2011
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Fit Sigmoid Curve with Confidence Intervals

Sigmoid curve fitting for transpiration measurements from porometer at different water potentials (pressure):Read more »

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Adonis (PERMANOVA) – Assumptions

April 26, 2011
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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...

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Permutation Test with Stratified Data and Repeated Measurements

April 21, 2011
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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...

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