Again on Modelling. On modelling and data.

I was invited to talk to Ph.D students at the 2019 Warredoc School on data rich Hydrology. This follows other more or less opinionated talks I give at the GEOframe Winter School, and complete them. In hindsight I actually scratched the surface of the topic. I would have made a more substantial contribution if I had added examples with GEOframe for clarifying "where do datasets integrate best in models".  Never mind: there is then still matter for the next reflections and investigations.

Notwithstanding, I hope you will find my contribution interesting and useful. Click on the Figure to access the presentation.

How to misinterpret photosynthesis measurements and develop incorrect ecosystem models

At recent EGU General Assembly in Wien, I saw an interesting presentation by Professor Ian Colin Prentice (GS) entitled: How to misinterpret photosynthesis measurements and develop incorrect ecosystem models. I believe I already cited some of his papers (in our Precise proposal and “Can we trust Climate models?”), however, I did not faced his thinking directly. I would lie if I said that I understood his point. I am far too ignorant of the Carbon cycle and the way to measure it to understand. However, I accept the challenge to to start somewhere, because understanding the carbon cycle helps certainly to understand evapotranspiration. 

Please find below some relevant picture of his slides and, just after the paper(s) he cited. Probably reading those papers can be a starting point to understand.

I. C. Prentice, X. Liang, B. E. Medlyn , and Y.-P. Wang, Reliable, robust and realistic: the three R’s of next-generation land-surface modelling, ACP, 2015 

Hoffman, F. M., J. T. Randerson, V. K. Arora, Q. Bao, P. Cadule, D. Ji, C. D. Jones, M. Kawamiya, S. Khatiwala, K. Lindsay, A. Obata, E. Shevliakova, K. D. Six, J. F. Tjiputra, E. M. Volodin, and T. Wu (2014), Causes and implications of persistent atmospheric carbon dioxide biases in Earth System Models, J. Geophys. Res. Biogeosci., 119, 141–162, doi:10.1002/2013JG002381.

H. D. Graven, R. F. Keeling, S. C. Pipe, P. K. Patra, B. B. Stephens, S. C. Wofsy, L. R. Welp, C. Sweeney, P. P. Tans, J. J. Kelley, B. C. Daube, E. A. Kort, G. W. Santoni, J. D. Bent Enhanced Seasonal Exchange of CO2 by Northern Ecosystems Since 1960, Science 2013

Thomas, R. T., et al. (2016), Increased light-use efficiency in northern terrestrial ecosystems indicated by CO2 and greening observations, Geophys. Res. Lett., 43, 11,339–11,349, doi:10.1002/2016GL070710.

Wenzel, S., P. M. Cox, V. Eyring, andP. Friedlingstein (2014), Emergent constraints on climate-carbon cycle feedbacks in the CMIP5 Earth system models, J. Geophys. Res. Biogeosci., 119,794–807, doi:10.1002/2013JG002591 

Ainsworth EA1, Long SP, What have we learned from 15 years of free-air CO2 enrichment (FACE)? A meta-analytic review of the responses of photosynthesis, canopy properties and plant production to rising CO2., New Phytol. 2005 Feb;165(2):351-71.

Ning Dong, Iain Colin Prentice, Bradley J. Evans , Stefan Caddy-Retalic, Andrew J. Lowe, and Ian J. Wright, Leaf nitrogen from first principles: field evidence for adaptive variation with climate, Biogeosciences, 14, 481–495, 2017 doi:10.5194/bg-14-481-2017 

Zaehle, S., Medlyn, B. E., De Kauwe, M. G., Walker, A. P., Dietze, M. C., Hickler, T., Luo, Y., Wang, Y.-P., El-Masri, B., Thornton, P., Jain, A., Wang, S., Warlind, D., Weng, E., Parton, W., Iversen, C. M., Gallet-Budynek, A., McCarthy, H., Finzi, A., Hanson, P. J., Prentice, I. C., Oren, R. and Norby, R. J. (2014), Evaluation of 11 terrestrial carbon–nitrogen cycle models against observations from two temperate Free-Air CO2 Enrichment studies. New Phytol, 202: 803–822. doi:10.1111/nph.12697 

César Terrer, Sara Vicca,Bruce A. Hungate,Richard P. Phillips,I. Colin Prentice, Mycorrhizal association as a primary control of the CO2 fertilization effect, Science 2016 

A good (hydrological) model according to Thorsten Wagener

This is what Thorsten Wagener (GS) thinks is a good model. Almost no comment is necessary.

About graphs, DSL and replicable research in Francesco Serafin's work

This is the summary of what Francesco Serafin (his blog) did in its first year of doctoral studies, defending for his admission to his second year Ph.D. Undoubtedly he did a lot of work and he programs to do even more. Three are the lines of his research:

• implementing a new flexible structure based on graphs for commanding simulations of interacting systems; 
• implementing a domain specific language for doing environmental models (and particularly to solve ordinary and partial differential equations); 
• deploying a system that makes easier to do replicable science. 

Clicking on the Figure above you will find his presentation. Obviously the committee admitted him to the second year of his Ph.D. studies.

Java for Hydrologists 101

There are a few postings on Java in this blog. Since I want to teach it to my students, I am quietly starting to populate this page with presentations which, eventually, will constitute the core of an informal class (;-)) the Java for Hydrologsts 101.

The focus of the JfH-101 is not simply to gain Java knowledge from the scratch (or so), but to address those topics and issues that have to do with my experience of hydrologist. So, I will try to cover Java as well as OMS3, and at the right time Geotools, and jgrasstools, not forgetting the tools of the tool (Ant, Maven, Git)^*, but in the meanwhile I will try to address the topics related to object oriented programming.  Programming is actually very much not talking about  that but doing it, so many of the slides will actually recall to actions.

Topics

0 - Getting Started (mostly things to read -or start to read- before the start) (YouTube 2018 video)
1 - Your first program (You Tube Video 2018)
2 - Solving a linear equation

• Introduction (YouTube 2018)
• The linear equation (YouTube 2018)

3 -  A few diversions

• Short Intro to UML*  class diagram (YouTube 2018)
• UML - stands fro Universal Modelling Language. It is a set of graphic tools that can be used to sketch OO programs. The classical reference is Martin Fowler's, UML 2.0 distilled, 2003. It is a short and nice and time-affordable reading.
• Naming Conventions (YouTube2018)
• The Structure of a Java Class and something about Javadoc (YouTube2018)

4 - Reading  data from the system's console

• Reading data from the console 
• LiveStream YouTube Video I
• Livestream YouTube Video II

5 - Reading data from a File

• Storyboard of the classes
• Reading data from  a File (no frills, no much design) (YouTube Live Video)
• Writing data to a File (no frills, no much design) (YouTube Live Video)
• Reading and writing data to a File. Designing the classes (YouTube Live Video)
• Reading and writing data to a File with Java 8. (YouTube Live Video) 
• For getting more on Streams see the chapter 3 of Modern Java in Action (a book worth to buy).
• For Getting more on Lambdas, Chapter 6 to 9 of Modern Java in Action .
• Learning a little better what is a regular expression
•  Reading and writing data to a File with Java 8 II and III (YouTube video)

6 - Working with Git

• From command line 
• Part I
• Part II
• from Eclipse (EGit)

-----Not yet implemented: ----

7 - Programming the heat diffusion equation

8 - Making the heat diffusion an OMS3 components

9 - Building Java projects with Ant, Maven and GRADLE

8 - GEOtools essentials

9 - Commenting the programming of the GEOframe-ET

10 - The Java REPL

11 - A little on Java Modules in Java 9

12 - Setting the continuous integration in GIT (using Travis)

The source code is available for download to from GitHub.

References

Please go to this blogpost.


^* - From the links you can quite understand the I rely very much on Lars Vogel site for the basic stuff. It is not obviously the only good resource available (stackoverflow is another one, for instance, and many others will be addressed).

An introduction to Forecast, Errors, Uncertainty in Models, and Forecast Correction

Following the link below, you can find  the presentation I gave at the Pensa Trasversale initiative. I talked about modelling and its uncertainty, and I had, obviously, in mind my experience as a hydro-geomorpho-logical modeler.
The last topic in the title, forecast correction, is not as deep investigated as I would have. But in writing I realised that I had to speak to High School Students.
The presentation is in Italian, but I can translate it in English if someone is interested.  In the case, I should do a further investment in making some parts more technical and add some examples.

The presentation can be found, as usual, on slideshare. A companion of the presentation, also in Italian, of this presentation can be this paper that I wrote more than twenty years ago about modelling, entitled: Introduction to the Mathematical Models of Environment.  I dedicated this small contribution to Sandro Marani with whom I discussed a lot the topic.