Twenty — minutes — maybe — more.choose four words

# statistics: fun

Workshop at Brain and Mind Symposium, Långvik Congress Center, Kirkkonummi, Sep 17–18 2015.

# Nature Methods: Points of Significance

Points of Significance column in Nature Methods. (Launch of Points of Significance)

## A Statistics Primer and Best Practices

The Points of Significance column was launched in September 2013 as an educational resource to authors and to provide practical suggestions about best practices in statistical analysis and reporting.

This month we launch a new column "Points of Significance" devoted to statistics, a topic of profound importance for biological research, but one that often doesn’t receive the attention it deserves.

The "aura of exactitude" that often surrounds statistics is one of the main notions that the Points of Significance column will attempt to dispel, while providing useful pointers on using and evaluating statistical measures.
—Dan Evanko, Let's Give Statistics the Attention it Deserves in Biological Research

The column is co-authored with Naomi Altman (Pennsylvania State University). Paul Blainey (Broad) is a contributing co-author.

## Free Access

In February 2015, Nature Methods announced that the entire Points of Significance collection will be free.

When Nature Methods launched the Points of Significance column over a year ago we were hopeful that those biologists with a limited background in statistics, or who just needed a refresher, would find it accessible and useful for helping them improve the statistical rigor of their research. We have since received comments from researchers and educators in fields ranging from biology to meteorology who say they read the column regularly and use it in their courses. Hearing that the column has had a wider impact than we anticipated has been very encouraging and we hope the column continues for quite some time.
—Dan Evanko, Points of Significance now free access

Also, in a recent post on the ofschemesandmemes blog, a new statistics collection for biologists was announced.

The pieces range from comments, to advice on very specific experimental approaches, to the entire collection of the Points of Significance columns that address basic concepts in statistics in an experimental biology context. These columns, originally published in Nature Methods thanks to Martin Krzywinski and guest editor Naomi Altman, have already proven very popular with readers and teachers. Finally, the collection presents a web tool to create box plots among other resources.
—Veronique Kiermer, Statistics for biologists—A free Nature Collection

## continuity and consistency

Each column is written with continuity and consistency in mind. Our goal is to never rely on concepts that we have not previously discussed. We do not assume previous statistical knowledge—only basic math. Concepts are illustrated using practical examples that embody the ideas without extraneous complicated details. All of the figures are designed with the same approach—as simple and self-contained as possible.

# Bayes' Theorem

Wed 22-04-2015

In our first column on Bayesian statistics, we introduce conditional probabilities and Bayes' theorem

P(B|A) = P(A|B) × P(B) / P(A)

This relationship between conditional probabilities P(B|A) and P(A|B) is central in Bayesian statistics. We illustrate how Bayes' theorem can be used to quickly calculate useful probabilities that are more difficult to conceptualize within a frequentist framework.

Nature Methods Points of Significance column: Bayes' Theorem. (read)

Using Bayes' theorem, we can incorporate our beliefs and prior experience about a system and update it when data are collected.

Puga, J.L, Krzywinski, M. & Altman, N. (2015) Points of Significance: Bayes' Theorem Nature Methods 12:277-278.

Oldford, R.W. & Cherry, W.H. Picturing probability: the poverty of Venn diagrams, the richness of eikosograms. (University of Waterloo, 2006)

# Happy 2015 Pi Day—can you see pi through the treemap?

Sat 14-03-2015

Celebrate pi Day (March 14th) with splitting its digit endlessly. This year I use a treemap approach to encode the digits in the style of Piet Mondrian.

Digits of pi, phi and e. (details)

The art has been featured in Ana Swanson's Wonkblog article at the Washington Post—10 Stunning Images Show The Beauty Hidden in pi.

I also have art from 2013 pi Day and 2014 pi Day.

# Split Plot Design

Tue 03-03-2015

The split plot design originated in agriculture, where applying some factors on a small scale is more difficult than others. For example, it's harder to cost-effectively irrigate a small piece of land than a large one. These differences are also present in biological experiments. For example, temperature and housing conditions are easier to vary for groups of animals than for individuals.

Nature Methods Points of Significance column: Split plot design. (read)

The split plot design is an expansion on the concept of blocking—all split plot designs include at least one randomized complete block design. The split plot design is also useful for cases where one wants to increase the sensitivity in one factor (sub-plot) more than another (whole plot).

Altman, N. & Krzywinski, M. (2015) Points of Significance: Split Plot Design Nature Methods 12:165-166.

1. Krzywinski, M. & Altman, N. (2014) Points of Significance: Designing Comparative Experiments Nature Methods 11:597-598.

2. Krzywinski, M. & Altman, N. (2014) Points of Significance: Analysis of variance (ANOVA) and blocking Nature Methods 11:699-700.

3. Blainey, P., Krzywinski, M. & Altman, N. (2014) Points of Significance: Replication Nature Methods 11:879-880.

# Color palettes for color blindness

Tue 03-03-2015

In an audience of 8 men and 8 women, chances are 50% that at least one has some degree of color blindness1. When encoding information or designing content, use colors that is color-blind safe.

A 12-color palette safe for color blindness

# Points of Significance Column Now Open Access

Tue 10-02-2015

Nature Methods has announced the launch of a new statistics collection for biologists.

Nature Methods Points of Significance column is now open access. (column archive)

As part of that collection, announced that the entire Points of Significance collection is now open access.

This is great news for educators—the column can now be freely distributed in classrooms.

# Before and After—Designing Tiny Figures for Nature Methods

Tue 13-01-2015

I've posted a writeup about the design and redesign process behind the figures in our Nature Methods Points of Significance column.

I have selected several figures from our past columns and show how they evolved from their draft to published versions.

Fig 2 from Points of Significance: Nested designs. (Krzywinski, M. & Altman, N. (2014) Nature Methods 11:977-978.) (...more)

Clarity, concision and space constraints—we have only 3.4" of horizontal space— all have to be balanced for a figure to be effective.

Fig 2c (excerpt) from Points of Significance: Designing comparative experiments. (Krzywinski, M. & Altman, N. (2014) Nature Methods 11:597-598.) (...more)

It's nearly impossible to find case studies of scientific articles (or figures) through the editing and review process. Nobody wants to show their drafts. With this writeup I hope to add to this space and encourage others to reveal their process. Students love this. See whether you agree with my decisions!

# Sources of Variation

Thu 08-01-2015

Past columns have described experimental designs that mitigate the effect of variation: random assignment, blocking and replication.

The goal of these designs is to observe a reproducible effect that can be due only to the treatment, avoiding confounding and bias. Simultaneously, to sample enough variability to estimate how much we expect the effect to differ if the measurements are repeated with similar but not identical samples (replicates).

Nature Methods Points of Significance column: Sources of Variation. (read)

We need to distinguish between sources of variation that are nuisance factors in our goal to measure mean biological effects from those that are required to assess how much effects vary in the population.

Altman, N. & Krzywinski, M. (2014) Points of Significance: Two Factor Designs Nature Methods 11:5-6.

1. Krzywinski, M. & Altman, N. (2014) Points of Significance: Designing Comparative Experiments Nature Methods 11:597-598.

2. Krzywinski, M. & Altman, N. (2014) Points of Significance: Analysis of variance (ANOVA) and blocking Nature Methods 11:699-700.

3. Blainey, P., Krzywinski, M. & Altman, N. (2014) Points of Significance: Replication Nature Methods 11:879-880.

# Two Factor Designs

Tue 09-12-2014

We've previously written about how to analyze the impact of one variable in our ANOVA column. Complex biological systems are rarely so obliging—multiple experimental factors interact and producing effects.

ANOVA is a natural way to analyze multiple factors. It can incorporate the possibility that the factors interact—the effect of one factor depends on the level of another factor. For example, the potency of a drug may depend on the subject's diet.

Nature Methods Points of Significance column: Two Factor Designs. (read)

We can increase the power of the analysis by allowing for interaction, as well as by blocking.

Krzywinski, M., Altman, (2014) Points of Significance: Two Factor Designs Nature Methods 11:1187-1188.