WaterUnderground

blended learning

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.

Groundwater and Education – Part two

Groundwater and Education – Part two

Post by Viviana Re, postdoctoral researcher at the University of Pavia (Università di Pavia), in Italy. You can follow Viviana on Twitter at @biralnas.

Part two of a two-part series on groundwater and education by Viviana.

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In my last post (“Drawing out groundwater (from the well)”) I wrote about the reasons why, as groundwater scientists, we should engage not only literally, when we collect groundwater samples to perform our research, but also metaphorically, such as raising awareness on the hidden component of the water cycle to stakeholders and civil society.

Education and capacity development can become more integrated in our work, in academia, if we emphasize and increase our attention given to finding the most effective way to train and motivate the new generations of hydrogeologists (e.g. Gleeson et al., 2012). Indeed, in a rapidly changing world where students have mostly unlimited access to information and tools, we cannot simply expect to adopt the “classical” teaching methods and be successful. Additionally, we certainly have to consider life long training of professionals to keep them up to date with respect to new information and contemporary issues (Re and Misstear, 2017).

Even more, I believe that our efforts should not be limited to education and training of groundwater scientists and professionals, but should also aim to bridge the famous gap between science and society.

This can involve a wide range of audiences and goals, but I think the following tips can apply to them all:

  • Consider shifting from a classical hydrogeological approach to a socio—hydrogeological one, particularly if your work entails assessing the impact of human activities on groundwater quality. Strengthening the connection with water end-users and well owners is fundamental to ensure an adequate knowledge transfer of our research results.

Picture 1: When sampling, do not forget to explain to well owners what you are doing and, most importantly, why you are there (photo by Chiara Tringali; Twitter @tringalichiara).

Picture 2: Interviews can be a precious moment for capacity building. If you can sit down with well owners and administer a semi structured interview, not only can you retrieve precious information and embed local know-how in your research, but also you can have time to disseminate results and discuss about the possible implementation of good practices to protect groundwater in the long run (photo by Chiara Tringali; Twitter @tringalichiara).

  • Engage with new media and social networks. It may seem like a waste of time, especially when productivity and “publish or perish” remain dogma in academia, but these are definitely the means everyone uses for communication nowadays. Not fully exploiting their potential can be make us miss a precious occasion for a direct interaction with stakeholders and the public.
  • Keep in mind that people are busy and we all get easily distracted. Try to use visual information as much as possible. Sometimes a short video, a nice picture or an informative graphic are more effective than a thousand words.
  • Improve your science communication skills. In a wold full of inputs, it is not sufficient to have something important to say. It, perhaps, matters more how you say it. For this reason, the time dedicated to learn how to speak in public, how to give an effective presentation (either if you are planning to give a talk in front of a technical audience or at a conference on vegetarianism) and how to write a press release is always well spent.
  • Share your passion. If you choose to work in hydrogeology or groundwater science, you are probably passionate about the environment and protecting our planet. Use these emotions to share your knowledge to civil society and learn how to adapt the content of your research to different audiences without trivializing it.

You can find more on this topic in the chapter Education and capacity development for groundwater resources management” (Re and Misstear, 2017) of the book Advances in Groundwater Governance (Edited by Villholth et al., 2017).

-Cover picture by Cindy Kauss (2018)

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Viviana Re is a post doctoral research fellow at the Department of Earth and Environmental Sciences of the University of Pavia (Italy). Her research interests are: isotope hydrogeology, groundwater quality monitoring and assessment, groundwater for international development.

She is currently working on the development and promotion of a new approach, called socio-hydrogeology, targeted to the effective incorporation of the social dimension into hydrogeochemical investigations.

Twitter: @biralnasPersonal website

Two great science communication tools for conferences and teaching: smart screens and cell phones

Two great science communication tools for conferences and teaching: smart screens and cell phones

A few weeks ago at the European Geosciences Union in Vienna I learned about two dead-easy and great science communication tools for conferences.  These are great for any conference hall or meeting, but could be just as easily be used in the classroom to make a more exciting in class research presentations. For better or worse, most of us are carrying them (or looking at them!) right now: a smart screen or cell phone.

The EGU conference uses smart screens in their innovative PICO (Presenting Interactive COntent) sessions. Every PICO author first presents orally in a 2-minute science blitz and then has a smart screen pre-loaded with a dynamic presentation to discuss further with colleagues. Simple and effective.

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Jan Siebert (University of Zurich) showing off just how dynamic PICO sessions are.

While I was a traditional poster session, Hannes Müller Schmied of Frankfurt University pulled out his cell phone to show me some additional visualizations (in this case global hydrologic model results posted on their website – this was connected to his poster with a QR code!). It was great to for him to be able to walk me through the results right there rather than be limited by the static images on his poster. We immediately realized this should be called micro-PICO!

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Hannes Müller Schmied showing off model results in this micro-PICO session with his poster in the background.

Thanks EGU for teaching me about two super simple and effective science communication tools, which I hope will cross the pond to AGU and other meetings.

What busy profs would like to read in a blog post about active learning

What busy profs would like to read in a blog post about active learning

During a great workshop today on active learning in engineering at McGill I asked two questions (using Socrative) , of the audience. Here is a summary of 24 answers I received:

1) I would like to read blog posts about:

  • activities for large classes (18% of people)
  • activities for small classes (30% of people)
  • technology in active learning (22% of people)
  • wacky or creative ideas for active learning(30% of people)

2) I might read a blog post about teaching and supervision if…

  • It takes into account the sheer lack of time and resources for preparation; ie quick and easy ideas to engage a bored class!
  • it was linked through twitter
  • It was regularly updated and interesting!
  • It does not take too long
  • it helps me achieve better my teaching objectives compared to my current teaching practice
  • It related to economics / social science a bit
  • Its short and introduce tips and examples
  • It gives concrete practical examples of activities for teaching and making students more active
  • I was interested
  • I knew where to find it
  • It dealt with distance education
  • they talked about encouraging creativity and critical thinking
  • it was about new and creative strategies that I can use in my class
  • it included the occasional evidence-based pieces that demonstrate real impact
  • Give ideas about how to get the students more active
  • It’s concrete, thoughtful and provides ideas
  • it was relevant and to the topic. I also would like to see it promoted within the departments to encourage conversation about teaching and learning
  • It is useful

My summary is that people want to hear about all types of different aspects of active learning and they would be motivated to read posts if it interesting and provided something useful.

Thanks Michael Prince of Bucknell for the great workshop and Milwaukee Mag for the image.

Surprises and lessons learned from co-teaching an inter-university graduate course

Surprises and lessons learned from co-teaching an inter-university graduate course

GrantFergusonContributed by Grant Ferguson, University of Saskatchewan
grant.ferguson@usask.ca

 

In an earlier blog post, Tom discussed some of the advantages and disadvantages of co-teaching a blended graduate course to students at McGill University, the University of Wisconsin – Madison and the University of Saskatchewan. This course wrapped up last month… we definitely learned a few things during its delivery, some of which were surprises that we hope you can learn from.

Surprise #1: The course outline and structure came together rather quickly and there was minimal debate on the content that we would cover. We did not attempt to be comprehensive in our coverage and chose to teach to our research interests. At the same time, we did not feel that there were obvious gaping holes in the curriculum. We included a review of what we expected the students to understand coming into the course. Although we were teaching students from a variety of backgrounds including civil engineering, environmental science, geosciences and forestry our expectation was that everyone should have been exposed to similar content in their undergraduate hydrogeology course. A recent review on the content of undergraduate hydrogeology courses by Gleeson et al. (2012) indicated that the core content of these courses does not vary that much from university to university.

However, surprise #2: students had very different interests and strengths. Some universities had students that excelled at MatLab while others were far more proficient with GIS. The interests of students also tended to mirror those of their home institutions. Students from McGill tended to be interested in water resource sustainability and large-scale problems, students from Saskatchewan were focused on problems associated with resource-extraction and students from Wisconsin tended to be more interested on hydrological processes and ecosystems. Exposing these biases, strengths and weaknesses was valuable for both instructors and students.

Surprise #3: this may not be a more ‘efficient’ way to teach since we spent far more time preparing lectures for this course than we normally do for other courses. Teaching to students and other universities with other instructors present brought teaching to a different level.   This effectively negated the initial thought that this would be a more efficient way of teaching because we were only on the hook for a third of the lectures. Part of this preparation was related to knowing that we would be forced to rely on slides more heavily than in a conventional classroom. However, the greater motivation was knowing that this presentation was going outside the walls of the home institution and that colleagues from other universities would be following along.

Surprise #4: Communication during the course went more smoothly than expected. Aside from a few momentary hiccups, there were few problems hearing the lecturer. Talking between institutions during the lecture went well, although questions were generally repeated by the lecturer or someone nearer to the microphone at other schools. The biggest obstacle might have been for the lecturers. Despite some efforts to situate cameras and explore different views within Microsoft Lync, it was difficult for the lecture to see the remote classrooms. Without being able to see facial expressions or body lan20140325aguage, it was difficult to assess how the material was being received at the other locations. This problem can likely be resolved to some extent with additional monitors and better cameras.

The feedback from the students was largely positive. Most of them seemed happy to participate in this experiment and get some exposure to other institutions. Tom, Steve and I all agreed that we would do this again given the chance. However, it appears that the stars might not align for us in 2015 due to some other commitments. We will see if we still feel this way in 2016.

Re-posted on Inside Higher Ed blog.

Co-teaching a blended class across universities: why? and why not?

Co-teaching a blended class across universities: why? and why not?

This term I am co-teaching a graduate class in advanced groundwater hydrology with Grant Ferguson (University of Saskatchewan) and Steve Loheide (University of Wisconsin – Madison). In co-developing and co-delivering this course we have learned a lot – I’ll start here with our initial motivations and write later about our pedagogic decisions, software tools and reflections after the course. It is mostly win-win for students and professors, but I’ll describe some of the disadvantages below.

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Teaching in an active learning classroom. Photo by Owen Chapman, courtesy of Faculty of Engineering, McGill University

Instead of being a MOOC, the course is a SPOC – a small, private, online classroom. Students and professors simultaneously meet in real classrooms at each university and connect as a video conference. Students collaborate on projects across universities and each professor leads instruction for part of the term and participates in all classes. We use a variety of software tools for blended learning including polling (socrative), content management (wikispaces), and video conferencing (microsoft lync).

Students are exposed to topics, tools and skills they would never learn in a regular classroom. Probably most importantly, students learn about varied topics that would not normally be covered at their university. One idea that has worked well is focusing on cutting-edge research ideas and techniques including research ugly babies that are not often discussed in the literature. They learn to collaborate internationally using virtual tools. And they develop an international professional network spanning multiple universities.

A  number of students have said ‘wow, it’s like three courses in one!’ and as instructors we have noticed there is not lull in the middle or end of term where students and/or instructors are tired of the course, tired of each other, or just tired. Instead it is just on to the next topic and instructor.

Many of the same advantages are true for the instructors: we learn new ideas from the other instructors, we collaborate internationally in co-developing and co-teaching this course and we expand and enrich our professional network. And we share the teaching load.
You can probably guess the two main disadvantages: the software tools are not perfect and interaction between real classrooms can be stilted. Both are true and we were very honest and clear about this with students from the start:

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Almost every class there has been a minor glitch with the audio or video but it’s always been minor problem with a reasonable solution – with the myriad of ways to connect today there are many plan B options.

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Connecting with other classrooms using video conferencing. Photo by Owen Chapman, courtesy of Faculty of Engineering, McGill University

During our weekly class time, interaction between individual students in different real classrooms is difficult. During class time, most of the interactions are between students and the lead instructor or between students in the same real classroom during an active learning activity. But outside of class time, students interact via discussion on the content management system and collaborate on projects using skype, google chat etc.

So far, co-teaching a blended graduate class across universities has been a win-win for students and professors – I’d be happy to hear about other SPOC classes.

Re-posted on Inside Higher Ed blog.