**Christoph´s mixed R functions**

This is a continuously updated file containing useful snippets of R code.

General collection of useful R functions, Version 2015-01-22

**Multinomial models**

When fitting **multinomial models** with the nnet package (multinom() function), it is sometimes desirable to** increase the number of weights** (especially when there is a large number of response categories). This may happen for example in the analysis of **next-generation sequencing data**. The Anova() function from John Fox´s package "car" can not deal with the MaxNWts argument and hence cannot be used for multinomial models with **user-specified maximum number of weights**. Below, I provide a function called **Anova.multinom2**, which allows MaxNWts to be set to any desirded number.

Anova for models with user-specified weights, fitted with the multinom() function

**Nonlinear regression**

In nonlinear regression situations, one often wishes to use power law functions of the form **y=a+b*x^c**. The following code allows starting estimates for this function to be estimated automatically.

Self-starting non-linear power law function in R

**Model selection**

StepAICc function for linear, generalized linear and mixed models

selMod function for model selection in mixed models

**Contrast matrices**

Working with orthogonal contrasts in R

Test for orthogonality of a contrast matrix

**Linear mixed models**

Extract lme ANOVAs from multiple models

Extract lme summaries from multiple models

**Generalized linear mixed models**

**Time series analysis**

A short introduction to time-series analysis in R

**Graphics**

Creating publication-quality R Graphics

**Ecological diversity**

Calculate Shannon´s diversity index

**Seed bank data analysis**