## Analyzing Ecological Data

Text Books

- Analyzing Ecological Data, Dr. Alain Zuur, R codes
- Statistical rethinking, a bayesian course with examples in R and Stan [Dr. Richard McElreath]
- A biologist's guide to statistical thinking and analysis [WormBook]

Tutorials

- Performing linear mixed effects analyses [Bodo Winter]

## Stats Basics

Vocabularies

- Difference between predictor and independent variables [Study.com]

Standard Error and Standard Deviation

- Reporting SEM, SD, CI [Prism]
- Standard deviations and standard errors [NCBI]

(Page 28) "Which error bar should you choose? It is easy to be confused about the difference between the standard deviation (SD) and standard error of the mean (SEM). The SD quantifies scatter, how much the values vary from one another. The SEM quantifies how accurately you know the true mean of the population. The SEM gets smaller as your samples get larger. This makes sense, because the mean of a large sample is likely to be closer to the true population mean than is the mean of a small sample. The SD does not change predictably as you acquire more data. The SD quantifies the scatter of the data, and increasing the size of the sample does not increase the scatter. The SD might go up or it might go down. You can't predict. On average, the SD will stay the same as sample size gets larger. If the scatter is caused by biological variability, your probably will want to show the variation. In this case, graph the SD rather than the SEM. You could also instruct Prism to graph the range, with error bars extending from the smallest to largest value. Also consider graphing every value, rather than using error bars. If you are using an in vitro system with no biological variability, the scatter can only result from experimental imprecision. In this case, you may not want to show the scatter, but instead show how well you have assessed the mean. Graph the mean and SEM or the mean with 95% confidence intervals. Ideally, the choice of which error bar to show depends on the source of the variability and the point of the experiment. In fact, many scientists always show the mean and SEM, to make the error bars as small as possible."

If we want to say how widely scattered some measurements are, we use the standard deviation. If we want to indicate the uncertainty around the estimate of the mean measurement, we quote the standard error of the mean.

Comparing Means and Medians

- Homogeneity of variance [Cookbook for R]
- Making Sense of Mann-Whitney Test for Median Comparison [iSixSigma]
- Probability distributions in R [Univ. Minnessota]
- Student t.test, non paired data [Click HERE]
- Student t.test, paired data [Click HERE]
- ANOVA, basic [EXPLORABLE]
- ANOVA, walk-through for quick oneway ANOVA [Barbara Webb]
- ANOVA, general guide (Good tutorial) [Bodo Winter]
- ANOVA in R using summary data [StackOverflow]

Growth Analysis

- Growth analysis, model comparison [Language & Cognitive Dynamics Laboratory]

Survival analysis

- Kaplan-Meier survival analysis [YouTube]
- Ayumi's Biostatistics Tutorial, survival analysis [YouTube]
- Plot method for survfit objects [R Documentation]

Web Based Stat Analysis

- Web-based ANOVA program [StatPages]

## Creating Figures

Basics in R

- Producing simple graphs in R [Harding Univ.]

ggplot in R

- Beautiful plotting in R [ZevRoss]
- Scatter plots using ggplot2 [ggplot2 0.9.3.1]
- Reordering the factor levels in R boxplots [DPhilicious Genome Med&Stat]
- Copying Data from Excel to R and Back [R-bloggers]

Heatmaps

- A guide to elegant tiled heatmaps in R [rmf]

Annotating Figures

- Textual annotations in R [ggplot2 2.1.0]
- How do I add an asterix to a boxplot to represent significance? [Stackoverflow]

Creating Figs for Geographical Data in R

- R sp graphics [R-Forge]
- SpatialPoints and SpatialPointsDataframe [StackOverflow]
- Making Maps with R (pie charts) [The Molecular Ecologist]
- Admixture maps in R for Dummies [The Molecular Ecologist]
- Display pie charts with varying alpha transparencies upon a Google static map [Jean-Pierre Rossi-Blog]
- R plot coordinates on map [StackOverflow]
- Plotting pie graphs on map in ggplot [StackOverflow]