Publications by Kay Cichini
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 the important pieces of the below code in R-Help. Read more » Related To leave a comment for ...
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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 » Related To leave a comment for the author, please follow the link and comment on their blog: theBioBucket*. R-blog...
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Custom Labels for Ordination Diagram
Here is how you do custom labels, hull, spider in a vegan ordination diagram: Read more » Related To leave a comment for the author, please follow the link and comment on their blog: theBioBucket*. R-bloggers.com offers daily e-mail updates about R news and tutorials about learning R and many other topics. Click here if you're looking to p...
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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 impact experiment conducted on plots across four different successional stages. Similarity was calculated...
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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 same sites are dependent and sample t1 and sample t2, taken from the very same places are dependent...
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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” among groups, which is similar to variance homogeneity in univariate ANOVA.I'll show why you may d...
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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 » Related To leave a comment for the author, please follow the link and comment on their blog: theBioBucket*. R-bloggers.com offers daily e-mail updates about R news and tutorials about learning R and many other topics. Clic...
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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 bootstrap resamples, bs (g star) is the statistic of interest calculated from a bootstrap sample, SEb ...
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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 filled. In addition this serves as an illustrative example how flexible “indexing” in R works,...
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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 » Related To leave a comment for the author, please follow the link and comment on their blog: theBioBucket*. R-bloggers.com offers daily e-mail updates about R news and tutorials about learning R an...
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