Supplement 1. R scripts for fitting the base- and full-model structures to sample data.

<h2>File List</h2><div> <p><a href="run_base_full_models.R">run_base_full_models.R</a> (MD5: adc930d6094b52c44838c1530c662920)</p> <p><a href="base_model.txt">base_model.txt</a> (MD5: 36b6b952b0c31b1921cee7a53e48b83a)</p> <p><a href="full_model.txt">full_model.txt</a> (MD5: 211e7b9afd6bc402f307653661e168ab)</p> <p><a href="jags_data.Rd">jags_data.Rd</a> (MD5: b10e52de46c11eeb2477960681a631e6)</p> <p><a href="viterbi_funs.R">viterbi_funs.R</a> (MD5: 7d6e8db0684738d8ea1722c95b8c7eba)</p> </div><h2>Description</h2><div> <p>The code included in run_base_full_models.R fits the 'base' and 'full' models described in the main text (Table 2). The base model (Model structure 2) is fitted with 5 states and fixed step length (FS). The full model (Model structure 9) is fitted with 6 states and time-varying step length (TS). The script then calls Viterbi_funs.R to estimate the Viterbi sequence of states based upon the posterior state-dependent parameter estimates. Running the script requires jags software (freely available at <a href="http://mcmc-jags.sourceforge.net/">http://mcmc-jags.sourceforge.net/</a>) and the r package 'R2jags'. Sample data, priors, and example R2jags fitting objects are supplied in jags_data.Rd which can be directly loaded into r. The text files contain the model structures in jags script. To run the script, place all the files into your r working directory.</p> </div

Time series of behavior states during baseline and controlled exposure experiments from 12 DTAG records

Data set used to model effects of sonar and killer whale sound playbacks on sperm whale state-switching, probability of buzzing and locomotion effort in 1-min time steps. Each row represents 1-min time steps. Columns give the identifier for each tagged whale (tagid), seconds since tag-on (sfromtot), depth at the start of the 1-min bin (depth), estimated behavior state (state; 1-surface, 2-descent, 3-layer restricted search, 4-ascent, 5-drifting, 6-active non-foraging), probability of the state (state_prob), presence/absence of terminal echolocation buzz (buzz), locomotion effort measured by overall dynamic body acceleration (ODBA), and experimental phase (experiment). The remaining columns show candidate exposure covariates, as described in Table 2 of the manuscript

Tissue density estimates from the best model with the lowest DIC.

<p>The top panel shows posterior distribution of individual body tissue density for each tag deployment. Blue and magenta lines indicate whales from Antarctica and the Gulf of St Lawrence, respectively. Box plots in the bottom panel show median and interquartile range of tissue density estimates from each location.</p

Relationship between gliding patterns and relative tissue density.

<p>The y-axis indicates differences in the percentage of time spent gliding during ascent and descent phases of non-feeding dives by each whale. Vertical and horizontal error bars show standard deviation and 95% credible interval range, respectively. A relative tissue density of >1 indicates that tissue density was denser than surrounding seawater.</p

Example data records for dive profile and pitch.

<p>Dive profile with gliding and stroking periods are indicated in green and blue, respectively. Red circles indicate feeding events. Examples are taken from an adult male during (a) early feeding season (Mn11_H607_1; tissue density = 1037.0 kg m^-1) and (b) late feeding season (Mn11_H607_2; 1031.2 kg m^-1), (c) a pregnant female (Mn11_H002; 1026.5 kg m^-1) and (d) a calf (Mn10_139a; 1040.8 kg m^-1).</p

The number of 5-s sub-glides in relation to tag duration and 95% CI range.

<p>Number of 5-s sub-glides that could be used for the hydrodynamic glide model in relation to tag duration (a) and the range of 95% credible interval for tissue density estimates (b). Magenta circles and blue crosses indicate data from Gulf of St Lawrence and Antarctica, respectively. A solid line shows a regression line: log(y) = -0.0062x + 0.90.</p

Summary of dive statistics.

<p>Summary of dive statistics.</p

Model parameter values.

<p>Model parameter values.</p

Prior and posterior distributions from the model with lowest DIC (Table 3).

<p>Prior and posterior distributions of tissue density (a, b, c), drag term (d, e, f) and diving gas volume (g, h, i) are shown in each panel. Solid green and black lines indicate the prior and posterior distributions, respectively. Dashed green lines show the estimated global distribution that can be interpreted as the population distribution for that parameter. The left and middle panels show global parameters (a, b, d, e, g, h) and the right parameters show individual and dive-specific parameters.</p

Humpback whale dataset used for analysis.

<p>Humpback whale dataset used for analysis.</p