# Lynch Lab Represents at Stony Brook Undergraduate Research & Creativity Symposium

This week, six undergraduates from the Lynch Lab presented their research at Stony Brook’s Undergraduate Research & Creative Activities (URECA) Symposium:

**Adaptive Significance of King Penguin ( Aptenodytes patagonicus) Crèches**

Lisa Caligiuri, Catherine Foley, and Heather Lynch

**Variation in Population Dynamics of King Penguins, Aptenodytes patagonicus, Across Phylogenetic and Regional Scales**

Vanessa Kennelly, Maureen Lynch, Catherine Foley, and Heather Lynch

**Variation in the ecstatic display call of the gentoo penguin ( Pygoscelis papua) associated with behavioral responses**

Medha Pandey, Maureen Lynch, and Heather Lynch

**Climate indices explain variation in fur seal pup mortality**

Katla Thorsen, Casey Youngflesh, and Heather Lynch

**The Effect of Oceanographic Conditions on Pygoscelis Penguin Population Dynamics**

Arianna West, Catherine Foley, Heather Lynch

**Phylogenetic Relationships between Conservation Risk and Life History Traits in Seabirds**

Helen Wong, Maureen Lynch, Heather Lynch

Congratulations to each of these outstanding students!

# Lynch Lab Undergraduate Student Wins Summer Research Award

The Lynch Lab is proud to announce that Sara Vincent, an undergraduate student working in the lab, has been awarded Stony Brook’s 2017 Undergraduate Research and Creative Activities (URECA) Biology Alumni Research Award. With the receipt of this award, Sara will spend the summer in the lab working on her independent project examining the spatial patterns of elephant seal harems.

Congratulations, Sara!

# Youngflesh et al. study featured in April issue of Ecology

A recent study on Adélie penguin phenology, led by Lynch Lab Ph.D. candidate Casey Youngflesh, is featured as the cover story in this month’s issue of *Ecology*. This study highlights some, heretofore, unappreciated nuances of phenological mismatch and advances our understanding of phenology and mismatch in highly variable systems. Freely available copy here!

# Visualizing and wrangling MCMC output in R with `MCMCvis`

Model results can be thought of as a reward for the many hours of model design, troubleshooting, re-design, etc. that analyses often require. Following the potentially exhausting mental exercise to acquire these results, I think we’d all like the interpretation to be as straightforward as possible. Analyzing MCMC output from Bayesian analyses, which may include hundreds of parameters and/or derived quantities, however can often require a fair amount of code and (more importantly) time.

The `MCMCvis`

package was designed to alleviate this problem, and streamline the analysis of Bayesian model results. The latest version (0.7.1) is now available on CRAN with bug fixes, speed improvements, and added functionality.

## Why `MCMCvis`

?

Using `MCMCvis`

provides three principal benefits:

1) MCMC output fit with Stan, JAGS, or other MCMC samplers can be fed into all package functions as an argument with no further manipulation needed. No need to specify the type of object or how it was fit; the package does all of that behind the scenes.

2) Specific parameters or derived quantities of interest can be specified within each function, to avoid additional steps of data processing. This works using a `grep`

like call for optimal efficiency.

3) The package creates ‘publication-ready’ posterior estimate visualizations (below). Parameters can now be plotted vertically or horizontally.

## The package has four functions for basic MCMC output tasks:

`MCMCsummary`

– summarize MCMC output for particular parameters of interest

`MCMCtrace`

– create trace and density plots of MCMC chains for particular parameters of interest

`MCMCchains`

– easily extract posterior chains from MCMC output for particular parameters of interest

`MCMCplot`

– create caterpillar plots from MCMC output for particular parameters of interest

The vignette can be found here.

## An example workflow may go as follows:

**– summarize posterior estimates for just beta parameters**

#install package install.packages('MCMCvis') #load package require(MCMCvis) #load example data data(MCMC_data) #run summary function MCMCsummary(MCMC_data, params = 'beta')

## mean 2.5% 50% 97.5% Rhat ## beta[1] 0.16 0.06 0.15 0.25 1 ## beta[2] -7.77 -25.82 -7.68 9.78 1 ## beta[3] -5.64 -28.53 -5.76 17.23 1 ## beta[4] -10.39 -25.98 -10.63 5.27 1 ## beta[5] 7.52 6.03 7.52 9.05 1 ## beta[6] 10.89 10.10 10.89 11.68 1 ## beta[7] -1.91 -4.83 -1.92 1.08 1 ## beta[8] 5.38 -6.86 5.45 17.67 1 ## beta[9] 13.39 3.28 13.38 23.60 1 ## beta[10] 17.63 14.41 17.63 20.86 1

**– check posteriors for convergence**

MCMCtrace(MCMC_data, params = c('beta[1]', 'beta[2]', 'beta[3]'), ind = TRUE)

**– extract chains for beta parameters so that they can be manipulated directly**

ex <- MCMCchains(MCMC_data, params = 'beta') #find 22nd quantile for all beta parameters apply(ex, 2, function(x){round(quantile(x, probs = 0.22), digits = 2)})

## beta[1] beta[2] beta[3] beta[4] beta[5] beta[6] beta[7] beta[8] beta[9] beta[10] ## 0.12 -14.86 -14.80 -16.48 6.91 10.58 -3.09 0.68 9.29 16.36

**– create caterpillar plots for posterior estimates. Shading represents whether 50% CI (gray with open circle), 95% CI (gray with closed circle), or neither (black) overlap 0. This option can be turned off (as below). A variety of options exist, including the ability to plot posteriors vertically rather than horizontally**

MCMCplot(MCMC_data, params = 'beta', horiz = FALSE, rank = TRUE, ref_ovl = FALSE, xlab = 'My x-axis label', main = 'MCMCvis plot', labels = c('First param', 'Second param', 'Third param', 'Fourth param', 'Fifth param', 'Sixth param', 'Seventh param', 'Eighth param', 'Nineth param', 'Tenth param'), labels_sz = 1.5, med_sz = 2, thick_sz = 7, thin_sz = 3, ax_sz = 4, main_text_sz = 2)

## Follow Casey Youngflesh on Twitter @caseyyoungflesh. The

`MCMCvis`

source code can be found on GitHub.

# NASA press release for Lynch Lab-developed penguin monitoring tool

Latest press release from NASA about the Mapping Application for Penguin Populations and Projected Dynamics (MAPPPD) tool, developed as a part of a NASA-funded project. The development of MAPPPD was led by lab PI Heather Lynch and NASA Goddard Space Flight Center Scientist Mathew Schwaller, with the goal of making scientific data more accessible to Antarctic scientists and decision makers. The tool will provide necessary information for key conservation-decisions in the region.

MAPPPD allows users to explore population trends in different regions of Antarctic by selecting an area of interest. It is also designed to incorporate information from citizen scientists in order to ‘fill in the gaps’ in knowledge in the Antarctic.

Learn more about MAPPPD here!

# R package `MCMCvis` now on CRAN

`MCMCvis`

, an R package for visualizing, manipulating, and summarizing MCMC output is now available on CRAN!

It can be installed with: `install.packages('MCMCvis')`

The vignette (tutorial) can be run with: `vignette('MCMCvis')`

`MCMCvis`

was designed to perform key functions for MCMC analysis using minimal code, in order to free up time/brainpower for interpretation of analysis results. Functions support simple and straightforward subsetting of model parameters within the calls, and produce presentable and ‘publication-ready’ output. Model output can be from JAGS, Stan, or other MCMC samplers. The package deals with different data types behind the scenes so you don’t have to think about it. You can specify which parameters you want to visualize or extract within the functions.

For example, this plot can be made using just one line of code (after loading package/data, of course)!

`library('MCMCvis') #load package`

`data(MCMC_data) #load example data`

`MCMCplot(MCMC_data, params = 'beta') #create plot`

More information can be found within the package vignette. The package was created and authored by Lynch Lab PhD candidate, Casey Youngflesh. He can be found here on Github and here on Twitter.