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Doing Hydrogeology in R

Doing Hydrogeology in R

Post by Sam Zipper (@ZipperSam), current Postdoctoral Fellow at the University of Victoria and soon-to-be research scientist with the Kansas Geological Survey at the University of Kansas.


Using programming languages to interact with, analyze, and visualize data is an increasingly important skill for hydrogeologists to have. Coding-based science makes it easier to process and visualize large amounts of data and increase the reproducibility of your work, both for yourself and others. 

There are many programming languages out there; anecdotally, the most commonly used languages in the hydrogeology community are Python, MATLAB, and R. Kevin previously wrote a post highlighting Python’s role in the hydrogeology toolbox, in particular the excellent FloPy package for creating and interacting with MODFLOW models. 

In this post, we’ll focus on R to explore some of the tools that can be used for hydrogeology. R uses ‘packages’, which are collections of functions related to a similar task. There are thousands of R packages; recently, two colleagues and I compiled a ‘Hydrology Task View’ which compiles and describes a large number of water-related packages. We found that water-related R packages can be broadly categorized into data retrieval, data analysis, and modelling applications. Though packages related to surface water and meteorological data constitute the bulk of the package, there are many groundwater-relevant packages for each step of a typical workflow.

Here, I’ll focus on some of the packages I use most frequently. 

Data Retrieval:

Instead of downloading data as a CSV file and reading it into R, many packages exist to directly interface with online water data portals. For instance, dataRetrieval and waterData connect to the US Geological Survey water information service, tidyhydat to the Canadian streamflow monitoring network, and rnrfa for the UK National River Flow Archive.

Data Analysis:

Many common data analysis tasks are contained in various R packages. hydroTSM and zoo are excellent for working with timeseries data, and lfstat calculates various low-flow statistics. The EcoHydRology package contains an automated digital filter for baseflow separation from streamflow data.

Modelling:

While R does not have an interface to MODFLOW, there are many other models that can be run within R. The boussinesq package, unsurprisingly, contains functions to solve the 1D Boussinesq equation, and the kwb.hantush package models groundwater mounding beneath an infiltration basin. The first and only package I’ve ever made, streamDepletr, contains analytical models for estimating streamflow depletion due to groundwater pumping. To evaluate your model, check out the hydroGOF package which calculated many common goodness-of-fit metrics.

How do I get and learn R?

R is an open-source software program, available here. RStudio is a user-friendly interface for working with R. RStudio has also compiled a number of tutorials to help you get started!

Other Useful Resources

Louise Slater and many co-authors currently have a paper under discussion about ‘Using R in Hydrology’ which has many excellent resources.

While not hydrogeology-specific, there are many packages for generic data analysis and visualization that will be of use to hydrogeologists. In particular, the Tidyverse has a number of packages for reading, tidying, and visualizing data such as dplyr and ggplot2.

Claus Wilke’s Fundamentals of Data Visualization book (free online) was written entirely within R and shows examples of the many ways that R can be used to make beautiful graphs.

Dowsing for interesting water science – what’s exciting at EGU 2019?

Dowsing for interesting water science – what’s exciting at EGU 2019?

Joint post by Sam Zipper (an EGU first-timer) and Anne Van Loon (an EGU veteran).


Every April, the European Geophysical Union (EGU) holds an annual meeting in Vienna. With thousands of presentations spread out over a full week, it can feel like you’re surrounded by a deluge of water-related options – particularly since the conference center is on an island!  To help narrow down the schedule! Here, we present a few water-related sessions and events each day that caught our attention. Feel free to suggest more highlights on Twitter (using #EGU19) or in the comments section!


Monday 8 April

Using R in Hydrology (SC1.44)

  • Short course 16:15-18:00.
  • This short course will cover R packages and tools for hydrology with both newcomers and experienced users in mind.

Innovative sensing techniques for water monitoring, modelling, and management: Satellites, gauges, and citizens (HS3.3).

  • Posters 16:15-18:00.
  • Curious about new approaches to hydrological science? This session features citizen science, crowdsourcing, and other new data collection techniques.

Plastics in the Hydrosphere: An urgent problem requiring global action


Tuesday 9 April

Nature-based solutions for hydrological extremes and water-resources management (HS5.1.2)

  • Posters 08:30-10:15Orals 10:45-12:30
  • Nature-based solutions are meant to be ‘living’ approaches to address water management challenges – this session will explore how they are used in both urban and rural areas.

HS Division meeting: If you want to know more about the organisation of the Hydrological Sciences Division of EGU (and you like free lunch) check this out!

Plinius Medal Lecture by Philip J. Ward: Global water risk dynamics


Wednesday 10 April

Large-sample hydrology: characterising and understanding hydrological diversity (HS2.5.2)

Sustainability and adaptive management of groundwater resources in a changing environment (HS8.2.1)

  • Posters 10:45-12:30, Orals 16:15-18:00.
  • This session features examples of groundwater sustainability (and challenges) all over the world, with a particular focus on Integrated Water Resources Management.

HS Division Outstanding ECS Lecture by Serena Ceola: Human-impacted rivers: new perspectives from global high-resolution monitoring

Geoscience Game Night (SCA1)


Thursday 11 April

How can Earth, Planetary, and Space scientists contribute to the UN SDGs? (ITS3.5)

  • PICOs 16:15-18:00.
  • Check out the fun PICO format – a combination of posters and talks – and help figure out what the role of earth science is in meeting the United Nations Sustainable Development Goals.

Urban groundwater: A strategic resource (HS8.2.7)

  • PICOs 10:45-12:30.
  • Urban groundwater is understudied relative to groundwater in agricultural areas – what do we know about urban groundwater, and what remains to be learned?

Henry Darcy Medal Lecture by Petra Döll: Understanding and communicating the global freshwater system


Friday 12 April

Innovative methods to facilitate open science and data analysis in hydrology (HS1.2.7)

  • PICOs 08:30-12:30
  • Learn about how you can make your science more open, whether you are an open science beginner or a long-time data sharer!

History of Hydrology (HS1.2.3)

Social Science methods for natural scientists (SC1.48)

  • Short course 14:00–15:45
  • This short course is for everyone who has some dealings with people in their research, such as stakeholders, citizen science, The aim of the session is to demystify Social Science and give practical tips & tricks.

Other Resources

Several other groups and blogs have also compiled water-relevant sessions. Make sure to check out their recommendations, as well!


Cover image source: https://cdn.pixabay.com/photo/2015/09/09/21/33/vienna-933500_960_720.jpg

 

Crowdfunding Science: What worked and what didn’t, who pledged and how did we reach them?

Crowdfunding Science: What worked and what didn’t, who pledged and how did we reach them?

Post by Jared van Rooyen, MSc candidate in Earth Science at Stellenbosch University, in South Africa.

Part two of three in a Crowdfunding Science series by Jared.

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During March of 2017, myself and a group of students supervised by Dr. Jodie Miller of Stellenbosch University’s Earth Science department (South Africa) completed a 5-week long crowdfunding campaign. The Campaign raised R149 899.00 (€9800) from 120 backers that were both local and international. The campaign used several different mediums to attract potential backers. In this blog I will summarize what engagement methods we used and which ones worked the best.

Before I do this, I have also partitioned backers into three categories that describe to what degree they are separated from myself and the campaign team. Category 1 includes members of family, colleagues and close friends, that would likely contribute to your fundraising campaign regardless of how you marketed it or if they were confident you would succeed. Category 2 included people that myself or the campaign team either are acquainted with, have met before or have been suggested to us by a member of category 1. Category 3 backers are those that myself or my research team have no prior connection to and have been made aware of the campaign through 3rd party methods.

Half of backers fell into category 2 with the other half almost evenly distributed between categories 1 and 3. The distribution of funding received showed a similar distribution with a slightly skewed distribution toward category 3 backers contributing on average more than category 1 backers.

Engagement methods showed some interesting outcomes with direct contact contributing half of the backers as well as half of the funds raised, social media methods, which included Facebook, Instagram and Twitter, contributed the next largest portion of backers (a quarter) but was trumped by word of mouth backer’s average contribution amount. The remaining contributors were those who found out about the campaign through radio/newspaper interviews/articles, internet news and anonymous contributors for whom I have no data (Unknown).

Upon the completion of the campaign, backers were contacted to give feedback on what they believed was effective in the marketing strategy of the campaign. Although radio interviews did not produce a large amount of backers and funds, they produced the largest proportion of category 3 backers.

The data presented above only mentions the successful methods of engagement. In addition, there were several other attempts at fund raising that were somewhat less effective. These included: handing out flyers and putting up posters on campus and surround areas, approaching funding institutions as well as water related government and private entities for support and using mailing robots to send generic emails to large mailing lists.

Before the campaign had ended myself and two honours students had already left on our field sampling trip. In the final part of this blog series, I will break down, what we raised the funds for, what the groundwater sustainability project is trying to accomplish, and what has culminated as a direct result of postgraduate science crowdfunding.

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Jared van Rooyen is an MSc student at the University of Stellenbosch in South Africa. His primary field of interest is in isotope hydrology with major applications in groundwater vulnerability and sustainability. Other research interests include postgraduate research funding solutions and outreach as well as scientific engagement with the use of modern media techniques.

Check out Jared’s (and research group’s) thundafund  page here.

An alternate career path for Groundwater Science-Engineering PhDs

An alternate career path for Groundwater Science-Engineering PhDs

Post by Jim Roy, Research Scientist at Environment and Climate Change Canada.

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A recent editorial in Nature highlighted the relative scarcity of academic positions available to graduating PhD students (Many junior scientists need to take a hard look at their job prospects; 25 October, 2017). It notes that “it has been evident for years that international science is training many more PhD students than the academic system can support”. Firm figures aren’t available, but the article suggests maybe < 5 % will land a full-time academic job. That number may be somewhat higher for Groundwater-related disciplines, but the point remains that many should “make plans for a life outside academic science.”

However, it’s not all doom and gloom; indeed the article goes on to state that “it is good for PhD students and postdocs to pursue careers outside academia. Many will find similar challenges and rewards in industry.” There are a lot of options for Groundwater PhDs in industry and the plethora of supporting consulting firms: in mining, oil and gas, tunnel and dam engineering, municipal water supply, and contaminated site remediation, to list a few. However, there is an additional career path to consider, especially if you want to continue doing research – the government scientist, like me.

According to Wikipedea: A government scientist is a “scientist employed by a country’s government, either in a research-driven job (for example J. Robert Oppenheimer on the Manhattan Project), or for another role that requires scientific training and methods.” I’ll be focusing on those that do research (encompassing science and engineering), at least for much of their work.  And in this blog, I’ll be comparing their job duties and conditions to that of the professor, the research job with which the majority of students and post-docs are most familiar and traditionally aiming for.  It’s what I thought I would be too, coming out of grad school. Now it’s been 10 years since I took up my position as a Research Scientist focusing on groundwater contamination/quality with Environment Canada (now Environment and Climate Change Canada) – enough time to have experienced the ups and downs of the Canadian economy and the changing of the governing party, with repercussions of both for federal science priorities and budgets. The discussion below is based largely on my own experience, with insight gleaned from talking with colleagues in other government agenciesa over the years. It’s also highly generalized; the exact situations will vary by country, agency, and even by individual scientist, and may change over time. But hopefully it’s good enough for a light-hearted introduction to this alternate career area.

So here goes – my Top 10 list of how a government scientist job is different than academia:

  1. Freedom

                All scientists want to do work that is meaningful, but not all scientists get to choose on what topic that work will focus. In general, government scientists undertake research on issues of government priority that will advise on federal policy, regulations, and management activities, or that will provide service to important national industries or the public. So their work should have a meaningful impact on their country, if not more broadly; they just don’t get to decide on the priority topics (with exceptions for certain agencies or programs). However, often these priority topics are general enough that there is some range of projects that can fit within them, giving the scientist some flexibility on their research focus. Also, by advising their management and government representatives of important topics, government scientists may influence the direction of government priorities. Also, a government scientist may be afforded some leeway to work on additional topics outside these priority areas with a small fraction of their time. Government research usually targets short- to intermediate-term achievements, as fits the common government election cycle. However, some priority topics may last for decades – see North American Great Lakes eutrophication and algal blooms – waxing and waning in importance with the severity of the problem (costs!) in relation to the other pressures on the government (the economy!). For those who choose this career path – beware, though, when government priorities change, your research area may have to change too.

                For academics, their options are typically much broader, encompassing everything between applied research with immediate implications to research so basic that nobody can predict what may eventually come of it. The caveat to this is that an academic’s research topic often has to be deemed important enough and applied enough for “someone” to fund it. Industry funding is usually quite applied. But even government funding agencies, which are usually the primary support for more basic academic research, are increasingly imposing greater direction over the acceptable topics of proposed research. So perhaps this extra freedom isn’t so vast in practice.

  1. Trading places?

                Many government scientists are appointed to one or more adjunct professor positions at universities where their academic collaborators reside. These could be at nearby universities or those across the globe, and these locations may change over a career. It isn’t a paid position, but allows for closer research ties, including the (co-)supervision of undergraduate and graduate students, which benefits both the university and the government agency. Such positions may also afford access to laboratory space on campus or to additional research funding (held at the university, but directed by the adjunct professor).

                I haven’t heard of a case of the opposite arrangement – adjunct government scientist – but it might exist. Academics may pop in and be given some office space and support during a sabbatical while collaborating with a government scientist, but they’re really just temporary squatters.  If anyone out there knows of such a situation, feel free to post below.

  1. No teaching ( 🙂 or  🙁 )

                An obvious difference, this can be viewed as good or bad news depending on how much you like it.  I enjoyed teaching while I was a grad student. Many scientists give guest lectures or even short-courses at local universities. I taught an entire hydrogeology course for a university colleague during his sabbatical – so this can be an option for some in government who have an interest. Not having required teaching does provide greater flexibility in scheduling your work (especially field trips) and leaves more time for research and/or other important activities, like playing hockey or “family life”.

  1. Professors have grad students; government scientists have technicians

                The model for academic research is based on students and post-docs (a team of them often) carrying out the primary duties of research under the supervision of their professor. Certainly there are exceptions where the professor carries out their own study, but generally they lack the time for this. However, professors may have technicians too. It’s common for some to hire current or past students as technicians for a few years after they graduate, while (senior) professors may have dedicated technicians.

                In contrast, the model for government scientists is to have one or more dedicated and highly-experienced technicians available to assist in their research. Separate analytical laboratory or field teams may also be available. Although, with tightening budgets this technical support seems to be dwindling. It’s also fairly common for post-doctoral fellows to be hired by government agencies to work with their scientists – I’ve worked closely with 2 post-docs over my 10 years at Environment and Climate Change Canada. And what’s more, through adjunct professor positions or just collaborations, government scientists may also work with and (co-)supervise students from a partner university, just not to the same extent as for the academics.

                Thus, there can be a fair bit of overlap between these two models, especially when collaborations extend between academics and government researchers; and this integration, I think, makes for better science all around.

  1. Both are sought out by regulators and policy-makers

                Government scientists might have the inside track to the ear of policy-makers, but advice from academics is often gathered via workshops and contracts for reviews and reports as well.  Sadly, in large departments especially, some bureaucrats may not realize they have internal expertise in an area like hydrogeology. Which leads us to the next point…

  1. Governments typically do a poorer job of selling/showcasing their scientists

                Academics have much more freedom to showcase themselves and their work to the public, the science community, and business/industry. This can be through personalized research web pages, starting a blog (like this one!), and greater freedom to speak to the media (depending on the presiding-government’s rules for their scientists).  They also tend to attend more scientific conferences, where they and their students can advertise their scientific wares to a range of audiences.

  1. No consulting on the side

                Not all professors consult, but many do, which can provide a boost in income and lead to funding or in-kind support opportunities for their research or to job opportunities for their students. I haven’t heard of any government agencies that allow their scientists to consult as a side profession. In part, they want all your time devoted to your job working for them; but it also runs into “conflict-of-interest” concerns.  Now that doesn’t mean you can’t have a side-job (e.g., selling pottery, repairing dishwashers, stand-up comedy, teaching Yoga), but it can’t relate to your science profession.

  1. Border-crossing restrictions

                Working on national (or state/provincial) priority research commonly means government scientists work predominantly on sites in their own country (region), unless inter-jurisdictional agreements are made to combine or share research expertise. In contrast, academics are able and encouraged to work at international sites, which can expand the range of research topics and potentially funding sources available to them.

  1. Less competition for funding (except when the coffers are bare)

                Much of my funding is internal, requiring much shorter (i.e., less onerous) proposals than is typical for my academic colleagues seeking funding through centralized national funding agencies (e.g., NSERC in Canada) or from industry partners. My proposals may still go through a competitive process, though, sometimes with external reviews.  How substantive this internal funding is compared to academic funding will depend on the agency, how science is viewed by the current government, the state of the economy, and the importance of the topic. When internal research budgets are tight, there may not be sufficient funding to go around, especially for those not working directly on key priorities. Of note, some government agencies allow their scientists who have adjunct status at a university to apply for the same set of grants as academics. Whether such proposals are frowned upon or judged differently by funding agencies is up for debate.

  1. Joy in their work

                Frustrations with too-much time devoted to administrative tasks and seeking funding are prevalent in both government and academic research areas. But still, the opportunity to do research on interesting, challenging, and important topics at the edge of our current scientific understanding brings enjoyment / fulfillment to both government scientists and academics. We all feel that slight quickening of the pulse when “the data is in” and we learn if the expected outcomes were realized or (better yet) something different (new!) might be going on.  It’s why we do what we do. In hydrogeology, there remains much to explore, especially at the inter-disciplinary mixing zones around the edges of our specialty. And we’ll need new concepts, new methods, and new connections to move our understanding forward. Scientists from academia and government and industry and other groups can all contribute to this quest. For graduating PhDs, hopefully this leaves you with multiple career path options for joining in the fun.

a In Canada, besides Environment and Climate Change Canada there are also PhD-holders doing groundwater-related research in Natural Resources Canada, Agriculture and Agri-Food Canada, and the National Research Council. In the U.S., much great groundwater research is carried out by the U.S. Geological Survey, with research also carried out by other federal and state agencies. Many other countries have similar geological or environmental departments or agencies with PhDs doing some or much research.  You can look these up on the web, though often government scientist pages aren’t nearly as good as those for academia.

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Jim Roy is a Research Scientist at Environment and Climate Change Canada. His current research focuses on: groundwater contaminant impacts on surface waters and aquatic ecosystems, groundwater contributions of phosphorus to surface waters, potential leakage of Alberta oil sands tailings ponds to the Athabasca River, and groundwater and gas systems. Find out more about Jim by clicking on the links below.

Twitter Page | Research Profile

Crowdfunding Science: A personal journey toward a public campaign

Crowdfunding Science: A personal journey toward a public campaign

Post by Jared van Rooyen, MSc candidate in Earth Science at Stellenbosch University, in South Africa.

Part one of three in a Crowdfunding Science series by Jared.

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When my supervisor, Dr Jodie Miller, suggested to me last year that we should look at crowdfunding as a way to potentially to fund my master’s project, I had no idea of what I was about to get myself into. All through my honours year I was not really interested in doing further postgraduate study. She kept warning me that I might change my mind and that I should apply for funding “just in case”. But I was sure of my position.  And then, as I started the final five weeks of my honours year, I finally got to focus 100% on my research project. Suddenly, as I focused in on my data, all the possibilities started to leap out at me. I went from a BSc (Hons) student, who was not considering continuing my postgraduate studies at all, to someone who is passionate about water resource research and continuing my postgraduate career. This is apparently common amongst postgraduate students in science, who become exponentially more immersed in their field of study as they realise that their work isn’t just numbers and experiments, but has significant real world applications.

Once I had committed – there was no turning back. The learning curve for mounting a successful crowdfunding campaign is steep and slippery. As much as it is hard, stressful work it is also fulfilling, fun, and full of surprises. The biggest obstacle is one that most modern day scientists are confronted with already: How do I make my research attractive to people who don’t have years of passion invested in my work?

Well, the answer is not simple.

I have completed a wide variety of modules in my tertiary studies but none in any forms of multi-media marketing skills. So naturally, when I had this crowdfunding campaign in front of me, I was so far out of my comfort zone that I felt like a geologist at a slam poetry evening. After numerous conversations with my peers who had experiences in marketing and graphic design, I had gathered a basic understanding of the inner workings of the unfathomably enormous media machine.

From the very first day I arrived back at the University in Stellenbosch I was drowning in ideas and administration. Setting up the social media accounts alone was a mission. Little did I know that running a social media campaign takes days and even weeks of preparation and planning each public post, including the post’s time, target market, outcome goals, and context. Each post on each platform had to be vetted and boosted appropriately. I was genuinely missing the late nights combing through complicated scientific articles and pounding through textbooks.

Making the campaign video was by far the hardest but definitely the most fun part of the process. The hours and hours of footage I have of retakes and drone videos culminated in, what I believe, is the pinnacle of my creative career (which is minuscule).

About a week before the initial launch date, we ran into some red tape within the University. Naturally, as someone who has never done anything more than post a couple photos of rocks on Instagram, I had no idea that a project like this needed to go through a number of stages before being approved by the university (which included: legal, ethics, corporate, marketing, and the faculty itself). A couple of panic-ridden meetings and documents later, we were ready for lift off, although a week later than originally planned.

As a geologist, I am not afraid of hard work, so engulfing myself in learning as much as I could in the little time I had came more naturally. What was most intimidating though, was the thought of putting myself and what I am passionate about out there. Publicly declaring the fact that what I wanted to achieve was not funded was daunting at first, but in time became a revelation in self-awareness and that asking for help is more constructive than admitting defeat.

I believe that postgraduate crowdfunding may prove to be invaluable in the future of students that have all the potential but their projects remain unfunded. Not only does it allow for the financial security of your project, but it attracts people that are interested in your field to you and to your work. The most significant consequence of this crowdfunding approach is that when you graduate, you already have a network of people in the industry that know who you are and know of your potential.

The crowdfunding campaign was completed in early April of 2017. In the next blog I will talk about what worked and what didn’t work, who pledged funding and how did we reach them.

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Jared van Rooyen is an MSc student at the University of Stellenbosch in South Africa. His primary field of interest is in isotope hydrology with major applications in groundwater vulnerability and sustainability. Other research interests include postgraduate research funding solutions and outreach as well as scientific engagement with the use of modern media techniques.

 

Check out Jared’s (and research group’s) thundafund  page here.

Just in case you weren’t sure…groundwater flow around a fault zone is complex!

Just in case you weren’t sure…groundwater flow around a fault zone is complex!

By Erin Mundy – a plain language summary of part of her Masters thesis

Groundwater is the water that collects underground in pores and cracks in the rock. Understanding, protecting and sustaining groundwater flow is critical because over two billion people drink groundwater every day. The flow of groundwater can be impacted by geologic structures, such as fractures and faults. A fracture is a break in the rock; a fault is a break in the rock where the rocks move relative to each other (ie. one rock will move up, one rock will move down, as seen in Figure 1).

CTF1

Figure 1. Diagram of a thrust fault

Faults can act as barriers slowing down groundwater flow, they can be a conduit speeding up groundwater flow, or amazingly they can act both slow it down and speed it up!

How groundwater moves through these rock structures is difficult to directly observe because it all happens underground and rarely exposed on the surface. The Champlain thrust fault at Lone Rock Point in Burlington, Vermont, provides a unique opportunity to study groundwater flow around a fault because approximately 1 km of the fault is exposed along the edge of Lake Champlain (Figure 2). Here, an older rock

CTF2

Figure 2: Photograph of the Champlain Thrust fault at Lone Rock Point, Burlington, Vermont. Note the person at the bottom right for scale

(yellow) is thrust over a younger rock (black). No one has studied groundwater flow around this fault in detail, so we hoped to find out a basic understanding of the relationship between the fault and groundwater flow at this location.

To understand groundwater flow around this fault, we did three things: 1) we walked along the fault and made note of changes in the fault (ie. the width of the fault, the angle of the fault, the shape of the fault, etc.); (2) we looked for areas where groundwater was leaking from the rock surface (this is known as groundwater seepage – we wanted to see if there was a relationship between where groundwater was leaking out and the changes in the angle/width of the fault); and (3) we drilled three wells and then pumped water out of these wells. We pumped water out of one well and measured the water level in the other wells – this gives you an idea of how the groundwater moves. For example, if you pump water out of one well and the water level in a nearby well declines drastically, this suggests that the water is easily moving through the rock. So if you’re pumping water from the fault and that happens, then the fault is most likely channeling water along the fault. If the opposite happens, then the fault may be acting as a barrier to groundwater flow.

We found four main geologic structures at the Champlain thrust fault: (1) the main fault, (2) an area where the fault splayed into many smaller faults, (3) areas where the fault thickness increased to 3 m, and (4) areas where there are traces of older, cemented fault rock (Fig. 3).

CTF3

Figure 3. Most important structures we observed at the Champlain thrust fault. the thin dashed white line follows the main fault, thicker black dashed line follows the main structural features. Hanging wall is the older rock; footwall is the younger rock. a) main fault; b) fault splay; c) increased fault thickness; and d) older abandoned fault rock

We found 19 areas along the rock where groundwater was leaking out of the cliff (Note: This was done in the winter so the groundwater was frozen into ice). We found that most of the groundwater seepage occurred in the younger (black) rock, with a few at the fault and where the fault splays out into smaller faults (Figure 4).

CTF4

Figure 4. Seeps located a) at the intersection of a multi-stranded fault structure and b) at the fault core. Note measuring tape for scale (1 foot)

While drilling the two wells at the site, we had two unexpected problems. One, there was a large difference between the depth of the fault in the two wells. The fault depth in one well was 27.4m, while in the other well (which was 10 m away), the fault depth was 70 m. This suggests that there must be another fault in between these two wells that offsets the fault depth. The other unexpected complication was that we drilled into 1.8 m and 2.1 m caves beneath the ground. Caves are common features in limestone, but the rock at our site is a dolostone, which is usually more resistant, so caves are an interesting find! The pumping test revealed a complex system. Further testing is needed to better refine these results.

Combining the data from the surface and subsurface observations, we created a preliminary three-dimensional model of the Champlain thrust fault (Figure 5). Where the rock is exposed at the edge of Lake Champlain, the fault thickness varies, splaying out into smaller faults and showing traces of older fault rock. Groundwater is leaking out of the younger rock (footwall) and along the fault. At the well-site, the fault is offset by another fault and caves are present. The three approaches we used (geology, seepage, pumping tests) all revealed different aspects of the Champlain Thrust fault, and exposed the complexity of groundwater flow around faults.

 

CTF5

Figure 5. Three-dimensional conceptual model of the Champlain thrust fault.

 

Can we use an infrared camera to tell us how much groundwater is coming out of the side of a cliff?

Can we use an infrared camera to tell us how much groundwater is coming out of the side of a cliff?

By Erin Mundy – a plain language summary of part of her Masters thesis

Groundwater is an important resource, with approximately 2 billion people around the world using groundwater everyday. Although most groundwater is beneath our feet, sometimes groundwater leaks out of stream-banks, hill sides and cliff faces – this is called groundwater seepage. Current scientific methods are not able to measure the amount of groundwater that leaks out of these landscapes. Scientists have used infrared cameras (cameras that show the heat of an objects) to identify groundwater seepage on hill-slopes and stream banks (Figure 1).

seep1

Figure 1. Digital image (a) and temperature image (b) of a seep in the summer and a digital image (c) and temperature image (d) of the same seep in the winter

This is because groundwater has an distinct heat signal, having a relatively constant temperature throughout the year (~10 degrees Celsius). Building on these studies, we hoped to find out the possibilities and limitations of using infrared cameras to measure the amount of groundwater that leaks out of the side of a cliff. We wanted to test if groundwater was flowing out of a cliff face slowly in the summer would warm up as it traveled down the rock, so the heat signature of the groundwater would go from cool water (that comes out of the rock, ~10 °C) to warmer water (warmed due to the sun and air temperature). On the other hand, we wondered if groundwater was flowing fast out of the cliff-face, it would not have time to warm, because the cool groundwater would be consistently running over it. In the winter, we believed the opposite would happen, that the groundwater would be warmer, relative to the surroundings, and show a cooling trend as the water traveled down the rock.

 

We found an unused mining pit in Saint Dominique, Quebec, that had lots of groundwater seeps coming out of the exposed rock, and used this as our test location. The mining pit had 3 different levels, as shown in Figure 2.

seep2a

Figure 2: an aerial shot of the quarry with the seeps labeled.

We took infrared and optical photographs of the seeps during seven visits that spanned from January 2013 – October 2014. Three visits took place during the winter (January – February 2013), coinciding with periods of below freezing so that the effect of extreme cold on seeps could be analyzed. Four visits took place during the summer/fall (June – October 2014), coinciding with sunny and hot conditions, and cloudy and warm conditions in order to determine the effect warmer temperatures have on seepage. In addition to these visits, we also completed a 24-hour experiment, where we took infrared pictures of two seeps every half hour for 24-hours, to determine the effect of sunlight and changing air temperature on the seep temperature signature. We also created an “artificial seep” experiment, where we released water from two large tubs over the cliff at the pit for 8 hours; one tub had water released at a slow rate, while the other at a faster rate, to see if we could replicate the heat signals from the real seeps. We took pictures with the infrared camera every half hour for eight hours for that experiment. We analyzed the infrared photos from each visit using a computer software that allowed us to determine the temperature along the seep.

In the winter, groundwater flows out the rock at warmer temperatures than it’s surroundings, making it easily distinguishable. We found that there was a clear relationship between seeps with active groundwater flow and areas of ice growth on the following visit. So, in the winter, if you use an infrared camera to locate where groundwater is flowing on the side of a cliff, you can assume there is a good chance that ice will eventually form at these spots. However, the groundwater did not cool along the rock face, as we had expected it would. This suggests frozen seeps are complex and it is unlikely that temperature pictures can determine the rate of flow of groundwater seeps in the winter.

In the summer, we found that lower flowing seeps did warm up as the water traveled down the rock face, as compared to faster flowing seeps, which did not show as much warming. However, in the 24-hour experiment (where we took infrared pictures every half hour for 24 hours of two seeps), we found that the temperature signature of the seeps changed throughout the day. During the day, there was much more warming of the groundwater as it traveled down the cliff, whereas at night it did not warm as much. This is most likely due to the presence of sunlight and warmer air temperature during the day, which warms the water more as it is traveling down the rock.

In the “artificial seep” experiment, we found that the “seeps” showed more warming than the real seeps. This is probably because we only ran the experiment for 8 hours, so it did not have time to mimic the conditions of real seeps. Also, we noticed that instead of flowing down the rock face, some of the water was actually seeping into the rock, along the breaks in the rock. This may be another reason why the seeps showed more warming, as not enough water was flowing down the rock (instead it was flowing into it).

After completing these experiments, we have concluded several possibilities and limitations for infrared pictures of groundwater seeps.

Possibilities:

  • Locate groundwater seeps in all seasons
  • Locate groundwater seeps in winter and from this, areas of ice growth can be predicted
  • Distinguish between lower flowing seeps and higher flowing seeps in summer (lower flowing seeps have more warming as the water travels down the rock face, higher flowing seeps do not have as much warming)

 Limitations:

  • Need to have a large difference in temperature between the air and groundwater to notice seeps. During the third winter visit, only one seep was identified to be flowing by the infrared camera. However, visual observations showed that eight seeps had groundwater flowing. This is because the temperature of the groundwater was too similar to the temperature of the air, making it not possible to detect the groundwater flow.
  • Groundwater seeps in the winter are complex and do not show a cooling trend, therefore it is unlikely that temperature pictures can determine the rate of flow of groundwater seeps in the winter
  • Breaks in the rock affect the flow of seeps, redirecting the flow, making it hard for temperature pictures to accurately determine flow
  • Sunlight and air temperature affect the “warming” and “cooling” of the groundwater flow, with more warming present during the day and less at night. Focus needs to be on determining the optimal time to use infrared pictures to show the “warming” (or “cooling”) trend.
  • The infrared camera itself has limitations. To use some functions of the camera, you have to correct your data for certain factors (like angle of the camera, humidity, etc.). If you don’t, you won’t be showing accurate data. This limits the amount of things you can do with the infrared camera and must be taken into account in order to ensure the pictures you captured are correct.

 

Despite the large number of limitations, infrared pictures is effective at locating groundwater seeps in all seasons, and able to distinguish between lower flowing seeps and higher flowing seeps (in the summer), which makes this technique a valuable, non-invasive way to study groundwater seepage. Future work should look at determining the optimal time to capture infrared pictures of seeps to determine a relationship between groundwater flow and temperature signatures.

 


 

Baseflow, groundwater pumping, and river regulation in the Wisconsin Central Sands

Baseflow, groundwater pumping, and river regulation in the Wisconsin Central Sands

By Sam Zipper, postdoctoral fellow at Madison and author of tacosmog.com

We often think of groundwater as a nonrenewable reservoir, deep underground, and with good reason – less than ~6% of groundwater globally entered the ground within the past 50 years. However, where a river or stream intersects the water table, water is able to move from the aquifer to the stream (or vice versa). This supply of shallow groundwater to streams is called ‘baseflow’, and is an important supply of water for many streams worldwide, especially during dry seasons or periods of drought. Below, we can see that baseflow makes up more than 50% of total streamflow over most of the world:

global_baseflow

Global estimates of baseflow index – the proportion of streamflow that comes from groundwater or other slowly varying sources, like upstream lakes and wetlands.

The ability of groundwater to contribute to streamflow depends on the water level of the aquifer in the area surrounding the stream. Therefore, human actions that lower groundwater levels (such as pumping for urban or agricultural use) can impair the ability of an aquifer to supply water to streams during dry periods, with potentially devastating consequences for streamflow.

One example close to my home is the Central Sands region of Wisconsin, which is a large region found (not surprisingly) in the center of the state with particularly sandy soils. The sandy soils are perfect for growing potatoes, and the Central Sands is primarily an agricultural region; however, because water drains quickly from sandy soils, irrigation has become an increasingly important part of the landscape:

centralsands

In addition to agriculture, however, the Central Sands region is home to many rivers, lakes, and streams. Recently, one river in particular has become a microcosm of the debate surrounding the impacts and trade-offs of agricultural water use: the Little Plover River. While only 6 miles long, the Little Plover is a prized brook trout fishery and important ecosystem within the region. According to American Rivers, which listed the Little Plover as one of America’s 10 most endangered rivers in 2013, streamflow in the Little Plover has been decreasing since the 1970s and flows today are roughly half of the historical normal. The situation in the Little Plover came to a head in 2005, when several stretches of the Little Plover dried up, with predictably negative consequences for the fish.

Over the past decade, the Little Plover has been mired in legal controversy. In 2009, the Wisconsin Department of Natural Resources established what they call a “Public Rights Flow”, or a required amount of streamflow that the public is entitled to flow through the river. The advocacy leading to the establishment of this Public Rights Flow was primarily by conservation groups like the River Alliance and Trout Unlimited, with the goal of protecting fish and the rest of the stream ecosystems. In order to set the threshold, the Wisconsin Department of Natural Resources first established a baseline level as the 7-day average low flow with a 10% probability of occurring in a given year, and then adjusted this value upwards based on estimates of the flow necessary for to provide fish habitat and recruit trout. Despite the positive step of establishing a Public Rights Flow, measurements during the 2012 drought were consistently below the thresholds set by the Department of Natural Resources, and the Little Plover even dropped below the thresholds in 2013 and 2014, both of which were relatively wet years for Wisconsin.

plover

The Little Plover in 1997 and the first time in ran dry in 2005 (Friends of the Little Plover)

The current debate surrounding the Little Plover hinges on whether the Department of Natural Resources is legally allowed to consider cumulative impacts when permitting new high capacity wells in the region. Previously, the Department of Natural Resources was not considering cumulative impacts, which means that for every well application, they are only allowed to think about that well in isolation – and the effects of a single well are typically small enough that the Department of Natural Resources does not have sufficient grounds to deny a permit. However, the relatively small impacts of many individual wells can add up to cause a big overall effects on local groundwater resources. This changed in 2014, when a judge ruled that the Department of Natural Resources should be considering cumulative impacts. The effects of this ruling remain to be seen, but it improves the DNR’s ability to manage groundwater and surface water resources while considering the interactions between the two.

Thus, the Little Plover River provides a powerful example of a case where a little bit of groundwater drawdown can lead to big environmental, political, and economic issues. Currently, hydrogeologists at the Wisconsin Geological Natural History Survey and USGS Wisconsin Water Science Center are working on developing a groundwater flow model of the region to help understand the impacts of groundwater withdrawals on the aquifer, and what that means for local surface water features like streams and lakes. Because the waters of the Central Sands are valued for many different uses, including farming, urban supply, and outdoor recreation, the team building this model has been working closely with different groups of users to determine the priorities and needs of the various water users the region, and make sure that their scientific tool they develop is both useful to and trusted by the decision-makers in the region. As the future of the Little Plover and other rivers unfold under increasing human pressures and climate change, it is critical that water scientists work together with the public to conduct fair and unbiased science that provides timely and useful information for the decision-making process.

A social media dashboard for researchers – taming the digital anarchy for nerds

A social media dashboard for researchers – taming the digital anarchy for nerds

Is anyone else overwhelmed by updating their many webpages, blogs, streams etc?

Jason Priem described the shift from a paper-native academia to a web-native academia, in an excellent article last year in Nature, a shift well beyond the traditional peer-reviewed journal to more diverse outlets of information, interaction and discussion. I am part of the first generation of researchers who are excited to use social media but we need more and better tools to make social media work even better for ourselves and others. Something like HootSuite for Prof 2.0!

I love Hootsuite, a dashboard for managing various social media profiles  (twitter, facebook etc.) in one handy place, across multiple platforms (phone, computer, tablets etc.). It looks something like this…

hootesuiteWe need something similar to manage the various facets of academic life. Just to give you some idea, these are all the pages and sites I try to maintain: personal research webpage, this Water Underground blog, twitter, LinkedIn profile, Google scholar, ResearchGate, ResearcherID, Vimeo, Groundwater footprint. I am happy to do this but it can be overwhelming in the midst of the other pulls of academic life – and I don’t even use facebook!

Ideally, this new platform would be a simple, user-friendly, open-source dashboard that would integrate various social media outlets academics use, plus be a simple place to update citations. A great and relatively simple first step would be a single place to update reference lists, which are a crucial part of how academics are evaluated so it is useful to keep them updated. Currently, my references are listed on Google Scholar, ResearchGate, ResearcherID, as well as a couple university webpages. It would be great to be able to export citations (already in standard formats like EndNote or BibTeX) and have these citations populate and update all my reference lists. I know Google Scholar already does this automatically (and usually correctly) but it would be great for consistency across outlets.

It would be great to link all kinds of altmetrics with this simple, social professor dashboard. Altmetrics are alternative metrics to the widely-used journal impact factor and personal citation indices like the h-index. An aggregate metric is calculated from how much as article, person, event (or blog post – subtle hint!) is viewed, discussed, saved, cited or recommended. As Priem writes, altmetrics will “draw new maps of scholarly contribution, unprecedented in subtlety, texture and detail.” And I find this to be already true – I often follow meandering altmetrics paths from a scientific article to news articles or discussions about the scientific article, and then I use this to enrich blog posts or tweets.

I flit across the web throughout my day and week – this dashboard would help me stay grounded and organized on the web. When I publish a new article, I would automatically update it in the various the places listing my citations, then write a quick tweet about it, check for news articles about it etc. Or I may see a comment on LinkedIn about a scientific article that could be useful for a paper I am writing. The comment in one column of the dashboard would be linked to the article, and the PDF posted on ResearchGate may be in another column of the dashboard. I take the PDF, export the citation to my library and pop it into the paper I am working on, in a series of smooth, integrated steps.

This HootSuite for Prof 2.0 could be a simple tool to enable the shift from a paper-native academia to a web-native academia by leveraging and extending information, interaction and discussion.

Originally published in University Affairs Careers Cafe.

How I start good supervisory relationships with graduate students

How I start good supervisory relationships with graduate students

Many professors are confused about why a certain graduate student is happy or unhappy, under performing or performing well. I am far from a perfect supervisor, but I try to avoid this confusion by getting to know my graduate students on a relatively deep but professional level as quickly as possible, by doing the following in our first meeting:

  • sharing results of a personality test;
  • discussing our biggest goals, hopes and fears about their graduate work; and
  • planing a very short two-week research project.

Before the meeting, the student and I take a free online personality test and prepare to discuss goals, hopes, fears and a research project. Below I outline the how and why of each part of the first meeting… hopefully I will never be this professor:

phd012609s

1. Share results of a personality test

Sharing the results of a personality test is often the perfect ice breaker since it is talking about emotions, but not about a student’s personal life. I use the Myers-Briggs Type Indicator because it is what i am most familiar and comfortable with but other personality tests such as colour code or FourSight could also work.  Myers-Briggs is a physiological test that highlights how people perceive the world and make decisions; a free online version can be completed very quickly.

I usually start by describing my personality type (INTJ) and that there are 16 different personality types, emphasizing that no type is better or worse than any other for science or any other part of life.  Then I ask them if they are comfortable sharing their personality type and we discuss how the two types fit together. I find this very effectively focuses on how we can work best together and acknowledges that everyone is different.  And for students who are uncomfortable, each Myers-Brigg’s type is linked to a Harry Potter character which can be fun:

Harry Potter Myers Briggs

http://inthefrontseat.blogspot.ca/2013/09/harry-potter-myers-briggs-chart.html

2. Discuss our biggest goals, hopes and fears about their graduate work

The Myers-Briggs sharing often naturally leads to this important discussion where both the student and I share our biggest goals, hopes and fears for their graduate work. I usually start by sharing, and I am usually brutally honest. I usually have a goal of how their project fits into my broader research program, and sometimes specific hopes of how the student and I may grow, learn or interact. In some cases I have been really honest about my fears that I don’t know enough about the topic, I don’t have as much time to devote to supervising them as I would like, or the project may fail, etc. Most students find the honesty refreshing.

Then I ask the student to share and we end up writing down shared goals, hopes and fears so that they can be reviewed at later meetings. This becomes the template of what we hope we will both get out of their graduate work, so we return to these goals, hopes and fears a couple of times per year to check in and re-evaluate.

goals

www.runnersgoal.com

3. Plan a very short two-week research project

Finally, we decide on a mini research project which should actually be doable in two weeks, and is not just be a literature review. The topic can be related to their overall graduate project or not, and can come from the student, professor or both. It could involve analysis, modeling, field work etc. In two weeks time  a 1000-2000 word research paper is due.

This mini-project often accomplishes a lot:

  • focuses on the student on research rather than their new classes, new apartment, new city etc.
  • helps both of us figure out how to best work together (i.e. lots of meetings and guidance or not)
  • Builds the student’s confidence in starting something new in this new environment
  • helps me evaluate their research and writing skills so that we can better tailor their graduate project.

It is a pretty intense first meeting that takes preparation, emotional intelligence and usually two hours but I find the dividends are always well worth the effort.


Thanks to DISCCRS for teaching me the value of the Myers-Briggs test and Mark Jellinek for the short research project idea.