data viz

Auklet Family Tree by Michael Johns

Part of the basic seabird monitoring work we do on the Farallones involves tracking the reproductive history and lifespan of Cassin’s auklets that were given uniquely marked metal leg bands as chicks. Just over 400 wooden nest boxes were installed across the island in 1983, which mimic the natural burrows used by the auklets, and birds quickly started breeding in them. Over the past 35 years, each box that contained a known-age pair was checked every 5 days to note when an egg was laid, whether or not that egg hatched, and whether or not the chick reached fledgling age. Some of these chicks from known parents recruited into their own nest boxes and started breeding, resulting in multiple generations of birds all within close proximately to each other. Above is a family tree created with the kinship2 package in R, showing the largest pedigree in the known-age dataset that spans 6 generations from 1987 up until 2018. Click HERE for a higher resolution version.

Bill Load of Fish by Michael Johns

This animation represents the total number of prey delivered by common murre parents to awaiting chicks during a 14-hour diet watch. Each red dot depicts a single breeding site in one of our followed study plots on Southeast Farallon Island. Circles appear when a fish is delivered, and intensify in color as more fish are brought in throughout the day. Common murres deliver a single item after each foraging trip, the size and species of which are identified by Point Blue field scientists as birds fly into their respective sites. On this particular day in 2016, foraging parents were bringing in predominately anchovy, followed by juvenile rockfish and a mix of less common items such as squid, smelt, flatfish, and juvenile salmon.

Kilowatt Plot by Michael Johns

Kilowatt hour (kWh) is the standard unit of energy consumption, equivalent to 1000 watts per hour. For example an electric oven that consumed 1000 watts in an hour, or 100 watt heater that ran for 10 hours, both used 1 kWh of energy. On average, according to the US Energy Information Administration, an American household consumes just over 850 kWh per month. Looking at this plot, where each blue dot represents total kWh used each month, even in the dead of winter here in Alaska Casey and I stay well under the national average. Of course we don’t have an kids, don’t have air conditioning, and live in a small 800 square foot cabin heated by burning oil. Still, temperatures regularly dip below -10F in the winter, and we have to do things like plug in our cars to keep the engine oil warm, so I think we’re doing alright. Just for fun, I fit a simple linear model to our monthly energy consumption, which takes into account average monthly low temperature, day length on the 15th of each month, and number of days per billing cycle. The model (yellow line with shaded confidence region) predicts our monthly usage pretty well, tracking lower consumption during the longer warmer days of summer, and higher consumption during longer colder nights of winter. Of course the model isn’t perfect, but something odd did happen during the months leading up to 2017. A mystery that has yet to be solved.

South of a Sunburnt Country by Michael Johns

Using a gridded sea surface temperature dataset from NOAA, and a handy orthographic projection of Earth centered on the South Pole, you can see Tasmania hovering just above a cold ring of water wrapping around the frozen continent of Antarctica. Although a part of the sunburnt country of Australia, Tasmania’s southern position and proximity to this cooler band of ocean temperatures gives the island a more temperate climate. February in the Southern Hemisphere means shorter days and cooler nights, marking the beginning of a transition to fall. Cooler temps and rain couldn’t come soon enough, as the whole of Australia has been hit with the one of the most extreme heat waves on record, with bush fires sparked by lightning strikes raging across much of Tasmania. These heat waves may become the new norm for this and many other parts of the world, as global average temperatures begin to creep up from a long-term baseline. While not as pronounced as places like the Arctic, records indicate sea and air temperatures are slowly on the rise for this unique southern island of Australia.

Graphics created in R with packages ggplot2 and touched up in Photoshop. SST data are interpolated high resolution average daily values for January 30th, 2019. I tested out a cool new package put out by the BBC graphics team on the temperature anomaly plot, which allows you to apply the graphing styles they use for publications. Check out the link HERE.

Where Are the People? by Michael Johns

Aside from a major city and a handful of townships, Tasmania is mostly an island of rugged landscapes and remote wilderness. There are roughly 522,000 people currently living on this island state of Australia, nearly half of whom reside in the greater Hobart region; Tasmania’s only city center. The heat maps above depict the spatial distribution and densities of people across the island. Each circle represents a 0.05 x 0.05 degree pixel within a larger spatial grid, colored by the total number and density of people within each pixel. Rather than using a raster or contours to display the population data, I went with a simple grid of points using the package ggplot2 in R, which I think gives it a retro “Lite-brite” look. If you never had one as a kid then you missed out. Hobart glows red hot, followed by the town Launceston (called “Launy” by the Aussies) and the northern coastline. We will be flying into Hobart and exploring the city for a few days, before heading out in a camper van rental to check out some of the darker corners of these maps.

Population data used to create the maps above can be found at the following link: http://sedac.ciesin.columbia.edu/data/set/gpw-v4-admin-unit-center-points-population-estimates-rev10/data-download

Rather messy but mostly functional R code used to make maps can be downloaded HERE.

Waiting for Australia by Michael Johns

Casey and I still have 5 weeks to go before our belated honeymoon to Tasmania, and already I’m dreaming up cool ways to display data from our trip. So far I have plans for comparing our heart rates in response to different situations using data collected from our Fitbits, tracking the routes we take during our 3-week road trip around the island, and summarizing the different species of plants and animals encountered along the way. To kick things off, I’ve put together a map showing the 8 different flights required to complete a roundtrip ticket from Fairbanks Alaska to Hobart Tasmania. Aside from some text, airplane vector art, and a custom legend (designed to look like a passport stamp) which I added in Photoshop, all of the features of the plot were assembled in R using the ggplot2 package. The coord_map( ) function in ggplot created a spherical projection of the earth, and the white stipples you see on the continents depicts light pollution data, highlighting the city centers. Not counting layover times, it will take us nearly 46 hours to complete the journey.

Seabird Sizes by Michael Johns

This figure depicts the relative sizes of seabirds that breed on the Farallon Islands. Larger circles mean more massive birds, smaller circles less massive. Species in the order Pelecaniformes, colored in shades of blue, are among the largest birds that breed on the island. The Ashy Storm-petrel in yellow, although a part of the order Procellariiformes which includes some of the largest seabirds like albatrosses, is small enough to fit inside the palm of your hand. The diverse order Charadriiformes in shades of red includes all of the gulls and auks, the latter of which contains all of the wing-propelled pursuit divers like puffins, murres, guillemots, and auklets. Mass information was gathered from the Sibley guide to birds. This plot was made almost entirely in R, with a few minor tweaks made in Photoshop. A full size image can be downloaded HERE.

Make It An Animation by Michael Johns

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Sometimes, an animated figure tells the story better than a static one. We have been tracking the non-breeding movement patterns of Cassin’s auklets from Southeast Farallon Island since 2015, in an effort to understand the environmental drivers of their winter dispersal. Part of the work I’m doing for my PhD is linking the movements of auklets to remotely sensed conditions relevant to their foraging ecology, in the case of this animation chlorophyll-a concentration (left) and sea surface temperature (right) from November 2017 through January 2018. Chlorophyll, the photosynthetically active molecule that gives plants, algae, and certain types of bacteria their green pigment, is used as a measure of the concentration of phytoplankton. Krill, which comprises much of the Cassin's auklet diet, graze on phytoplankton, so it’s reasonable to assume productive areas with high concentrations of chlorophyll-a likely contain greater densities of krill than areas of low chlorophyll-a. Similarly, lower sea surface temperatures are generally associated with nutrient rich cold water from depth, which help spark blooms of phytoplankton. One hypothesis, visualized with this animation, is that Cassin’s auklets are searching for colder regions of higher productivity during the winter months. The next step is to test this hypothesis with a series of competing models, to see which best explains the patterns observed in the data.

Visualizing Long-term Data by Michael Johns

Point Blue Conservation Science has amassed an impressive long-term dataset on the breeding histories of known-age Cassin's auklets on Southeast Farallon Island. These data are visualized in the figure above. The dedication to maintaining and checking 400+ artificial nest boxes every 5-days for the past 34 years has allowed researchers to reveal some unique patterns in the life history of this small seabird. For example, Cassin's auklets are the only member of the taxonomic Alcid family to attempt two complete broods in a single breeding season, known as double brooding. In a recent study published in the journal Proceedings of the Royal Society B, my colleagues and I used these data to examine how double brooding impacts future reproductive potential and survival for birds that attempt such a behavior multiple times over the course of their lives. It turns out that so called "repeat double brooders" represent a subset of high quality individuals that can offset the short-term costs of increased reproductive effort, living well into old age and producing more offspring than birds that never double brood. Visit the publisher’s website by clicking HERE

Winter Movements by Michael Johns

After several years of geolocator tagging work (see image below), we finally have enough information to begin to paint a better picture of the non-breeding winter distribution of Cassin's auklets from Southeast Farallon Island. At the start of any research project, the most important first step in the analysis process is to visualize the data. The idea behind this visualization was to depict three key environmental characteristics of the auklet's winter habitat in a single plot; sea surface temperature (SST), depth, and distance from island. SST will be used as a proxy for productivity, as colder water in this region is generally associated with nutrient rich upwelling processes, depth to characterize the preferred ocean zone (shallow shelf, steep slope, or deep abyssal plain), and distance from island to explore the possible limits of their dispersal. 

Glancing at this plot, you can see by October birds are fairly spread out between 45°N (dark purple colors - Northern California area) and roughly 33°N (orange colors - Southern California). They are also exposed to quite a range of SST, from 14°C up to nearly 22°C. By late January, all of the birds are relatively close to the island (small bubble size) and experiencing roughly the same SST, before spreading out again in late February, with most birds staying at around 35°N. The 2015-16 season was a particularly warm year for SST, which my explain why only birds in the northern reaches were finding water colder than 14°C. The next step in this exploratory process is to look at auklet movements during the 2016-17 and 2017-18 seasons, which were moderate to average years for SST in the eastern north Pacific. Ultimately, these and possibly additional environmental covariates will be used to model the winter habitat use of Cassin's auklets off the California Coast. 

Note the geolocator tag on the left leg of this Cassin's auklet. Geolocators are devices which record ambient light levels that are later used to estimate latitude and longitude. 

Tagging data courtesy of a partnership between Point Blue Conservation Science and the USFWS. Remotely sensed environmental data were downloaded from the NOAA repository https://coastwatch.pfeg.noaa.gov/erddap. This plot was created in R with the ggplot2 package. 

Listers by Michael Johns

The Farallon Islands are uniquely situated for people interested in the hobby of finding and identifying birds, otherwise known as "birding". The cluster of jagged rocks are located just far enough offshore to provide a stable platform for spotting rare pelagic species like the Cook's petrel, and close enough to the mainland to catch vagrant song birds and other terrestrial species lost in the fog at sea. Over the course of 50 years of research out on the Farallones, some biologists and staff have been keeping a detailed list of all of the different bird species they've encountered while out on the island, a record known as "The Faralist". This figure is a graphical interpretation of that list, modified from R code for a similar graphic depicting the number of days spent on island by various people over the years. Collectively, a total of 429 different species have been seen from the Farallones; not bad for a small collection of guano-covered rocks with only 3 trees.

Download a high resolution file of this figure HERE.  

Landscape of a Year by Michael Johns

Animals tend to be fairly predictable in their reproductive timing and migration patterns. The figure above depicts a series of density curves, with peaks and troughs corresponding to the average timing of key biological events for a select number of marine species that are monitored on or from Southeast Farallon Island.

Pinnipeds, a taxonomic group that includes seals and sea lions, are found hauled out on the island year round, with peak pupping events occurring in the summer. Northern fur seals, which have made an astounding recovery on the Farallones following the days of the Russian Fur Trade, remain at sea for several months of the year and are only seen in force from summer to late fall. Whales are also visible from the island year round. Gray whale numbers peak in January as they migrate south to their breeding grounds off Baja California Mexico, and again in March during a northward migration back to their feeding grounds in Alaska. Humpback and blue whales are most abundant in the productive summer months, where they are seen gorging themselves on krill and schooling fish. For seabirds, breeding occurs only in the summer months, with the exception of the ashy storm-petrel which extends chick rearing well into October. Three distinct peaks represent the timing of egg laying, hatching, and chick fledging. 

The study of seasonal life-history patterns is called phenology, and it can tell us a lot about the stability of a system. As I mentioned, animals tend to be fairly predictable in their phenology. Individuals cue in on environment and biological signals, so shifts in the timing of reproduction or migration can indicate changes in environmental condition, food availability, or the health of a population. For species found on the Farallones, the major cause for concern in the face of a warming ocean is the availability of key prey items, namely krill, which sustain the rich biodiversity in this region. A mismatch between the timing of krill and the timing of reproduction for seabirds can lead to major declines in breeding success, and subsequent declines in population numbers. 

Data courtesy of a partnership between Point Blue Conservation Science and the USFWS. The plot was created in R with the ggplot2 and ggridges packages. 

Relative Size by Michael Johns

Probably the most important question in the conservation work that we do, and the most popular question people have about the Farallones, is the population size of the various seabird species on the island. The answer, such as roughly 250,000 murres, 20,000 auklets, and 500 puffins, may not be fully appreciated when taken at face value. The figure above is an attempt to put these numbers into context by representing each population as a collection of boxes, where the area of each box is scaled in proportion to the other boxes. With this visualization, you can see just how abundant Common Murres are in relation to Pigeon Guillemots or Tufted Puffins. With continued monitoring and management, hopefully all of these boxes will continue to grow in size.

Data courtesy of a partnership between Point Blue Conservation Science and the USFWS. The plot is called a "Treemap", created in R with the ggplot2 and treemapify packages. 

50 Years of Bands by Michael Johns

It's been 50 years since scientists from Point Blue Conservation Science (then Point Reyes Birds Observatory) began a continuous monitoring effort on SE Farallon Island. Some of this work includes banding certain species of seabirds to learn more about their movement patterns, survival and mortality rates, population status, and individual breeding behavior and success; all important information guiding management decisions and tracking the potential effects of climate change. Point Blue has amassed an impressive sample of banded birds since work first started in 1967, totaling nearly 125,000 individuals as of 2016. The graphic below illustrates the total bands put out by year and cumulatively since 1967 for 8 target species.