tag-to-whale-frame.RmdWelcome to the tag orientation vignette!
Thanks for taking some time to work with our package. We hope you’re having a great day!
This vignette deals with estimating and correcting the orientation of a tag on an animal. It will use tag data that are not aligned to the animal’s body axes, e.g., because the tag was applied to a free-moving whale. Your task will be to align the data to the animal’s body axes.
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Estimated time for this vignette: 25 minutes.
These practicals all assume that you have R/Rstudio installed on your machine, some basic experience working with them, and can execute provided code, making some user-specific changes along the way (e.g. to help R find a file you downloaded). We will provide you with quite a few lines. To boost your own learning, you would do well to try and write them before opening what we give, using this just to check your work.
For tags placed on free-swimming animals, the tag axes will not generally coincide with the animal’s axes. The tag A and M data will therefore tell you how the tag, not the animal, is oriented. This can be corrected if you know the orientation of the tag on the animal, i.e., the pitch, roll and heading of the tag when the animal is horizontal and pointing north. Three steps are needed to do this: First the tag orientation on the whale is inferred by looking at accelerometer values when the animal is near the surface. The orientation may change if the tag moves or slides during a deployment and so we make an ‘orientation table’ that describes the sequence of orientations of the tag. This table is then used to convert tag frame measurements into animal frame.
Use load_nc() to read testset5.nc, which is from a pilot whale in the Canary Islands. Write it to the object sw to follow along with the code in this vignette. This dataset is built into the tagtools package, so you can access it using system.file.
library(tagtools)
sw_file_path <- system.file("extdata", "testset5.nc", package = "tagtools", mustWork = TRUE)
sw <- load_nc(sw_file_path)We will use prh_predictor1() to infer the tag-to-animal orientation. This function is for animals like pilot whales that log (more or less) at the surface before diving steeply. It assumes two things:
If these are not good assumptions for your animal, prh_predictor2() may work. It is suitable for whales such as beaked whales that make short dives between breaths at the surface. Both tools try to predict the tag orientation on the whale parameterized by its pitch, roll and yaw (which we shall call p0, r0, and h0). To use prh_predictor1(), we need to define a minimum dive depth to analyse—let’s say 400 m. Then call the tool like this:
PRH = prh_predictor1(sw$P, sw$A, TH = 400)A graphical interface will open showing the dive profile (top), the estimated tag-to-animal orientations throughout the deployment (middle panel), and the quality of these estimates (bottom panel). In the middle panel, the colored stars show the p0, r0 and h0 estimates at the start of each dive.
A quality measure of <0.05 in the bottom panel indicates that the data fit well with the assumptions of the method.
If the tag does not move on the animal from dive to dive, then p0, r0 and h0 should be fairly constant across dives. If they are not constant it can be due to a sudden change (e.g., the tag gets hit) or a slow movement of the tag on the animal. In this case it seems that there is a change in orientation between dives 6 and 7.
The function automatically picks segments of data to analyse, and you should check that it did this well, especially if the ‘quality’ number is > 0.05. The third dive has a slightly bad quality: type e on the main figure to “edit” and then click on one of the third dive orientation points. Note that prompts will appear at the very top of the figure window(s), which will update based on the most recent user actions.
A new plot will be drawn in the second figure window (pull it up if it does not automatically come to the front) in which the top panel shows the acceleration data in the tag frame for the current dive edge. Blue, orange or red (depending on your Matlab/Octave version) and yellow represent the x, y and z axes, respectively.
The bottom panel shows the acceleration data after correction using the p0, r0 and h0 estimates printed above the panel.
Two black rectangles show the data segments that have been chosen for analysis and these may need to be moved:
The segment edges are numbered 1 to 4 from the left. To change a segment, hover the mouse over the plot and type the relevant number, then click the mouse where you want the newly-drawn box edge to be. The segment will move and the p0, r0, h0 and quality will be re-calculated. When you are satisfied with the estimate quality, type q and then return to the first figure.
We need to create an orientation table (OTAB) that summarizes the tag orientation on the animal as a function of time. Each row of the OTAB matrix describes the orientation of the tag on the animal over a time interval. If there are two moves, the OTAB will have three lines: the initial orientation and the orientation after each move.
Each row defines how the tag is oriented on the animal and has columns: t1, t2, p0, r0, h0. t1 and t2 are the start and end times of the move (in seconds-since-tag-on), and p0, r0, h0 are the new orientation Euler angles after the move (in radians).
The initial orientation (i.e., the first row in the OTAB) always has t1 = t2 = 0. For subsequent moves, if the move is instantaneous, use t2 = t1. If the move is gradual, set t1 to the time at which the movement appears to start and set t2 to the time when the move appears to be complete.
Making the OTAB is a bit of a black art. prh_predictor1() is not infinitely precise, and an apparent change of less than 10 degrees is probably not worth worrying about.
We are going to assume there is just one move (i.e., during the 6th dive) in our pilot whale data. Position the mouse over the blue (p0), red or orange (r0), and yellow (h0) lines before the move and click the left button on each to get the angle (in degrees). Make the first OTAB line:
where p0, r0 and h0 are your readings. The pi/180 converts these into radians.
For the second OTAB line, read off the p0, r0 and h0 values after the move and decide when the move actually happens (let’s say it is a sudden move at the end of the dive, e.g., at 10100 seconds). Then:
Finally, type ‘q’ to quit prh_predictor1. Now you can make the OTAB matrix:
OTAB <- rbind(otab1,
otab2)Use your OTAB to convert tag frame measurements (A or M) to animal frame:
Aa <- tag2animal(sw$A, OTAB = OTAB) For this particular dataset, only A is provided, but in case you want to also convert tag frame magnetometer measurements to animal frame, you could do so in a similar way, using code of the form:
Ma <- tag2animal(sw$M, OTAB = OTAB)Aa should now contain acceleration data like what would have been recorded by a tag aligned with the animal’s axes, i.e., in the animal frame. Compute pitch and roll from Aa and plot them to check they make sense:
pr <- a2pr(Aa)
pitch <- pr$p
roll <- pr$r
rm(pr)
plott(X = list(depth = P, pitch = pitch*180/pi, roll = roll*180/pi),
fsx = Aa.sampling_rate, interactive = TRUE)The pitch and roll vectors are in radians (hence the *180/pi to covert to degrees) and have the same sampling rate as Aa. Zoom in to check if the animal is in a realistic orientation when it is at the surface, or during an ascent or descent.
When you are comfortable that the tag is well aligned to the animal frame, you can add the corrected data to the archive file:
add_nc('testset5_animal_frame', Aa)There is no need to also save pitch and roll because these can be easily re-computed from Aa. The archive file should only contain source data or data that has been corrected. The orientation correction steps and the OTAB are stored in Aa, and so this information is saved automatically in your archive file. Nice work!
If you have time and want something extra, do the following check.
The code below will compute the smoothed pitch angle; 12 is the smoothing parameter. Signal components above 1/12 of the Nyquist frequency are filtered out.
Now find the whale’s vertical speed in m/sec:
v <- depth_rate(sw$P) And plot it. Feel free to convert to your favorite graphics system - I love ggformula…
plot(v, pitch_s*180/pi, type = 'p', pch = 16,
ylab = 'smooth pitch (degrees)',
xlab = 'speed (m/sec)') If Aa is done right, there should be a fairly good negative correlation between depth rate and pitch. There will be some outliers because we didn’t put the tag orientation change in quite the right place. If you feel like making some fine adjustments, improve your OTAB and perform this check again. With your own data, you will likely spend a lot of time making these small adjustments.
You’ve learned how to estimate tag orientation over time, as well as how to correct for it when these estimates are problematic.
Congrats! You made it through this vignette.
If you’d like to continue working through these vignettes, consider acceleration-filtering. In it, you’ll look at acceleration data, and consider quick changes in acceleration (high-frequency acceleration) versus slower changes (low-frequency acceleration) to interpret an animal’s behavior.
vignette('acceleration-filtering')Animaltags home pages: http://animaltags.org/ (old), https://animaltags.netlify.app/ (new), https://github.com/stacyderuiter/TagTools (for latest beta source code), https://stacyderuiter.github.io/TagTools/articles/TagTools (vignettes overview)