Friday, February 28, 2014

The final report of the Framework for Interoperable Freshwater Models is out

The aim of the project was to investigate software frameworks for building an interoperable freshwater models in New Zealand, based on existing models. After considering various alternatives, the project chose OMS as base for the work. The informatics was worked out by Gaby Turek who also was one of the speakers of our OMS summer school. One of the characteristics of the project is that it brings under the OMS umbrella some interesting FORTRAN code, according to an example that other can follow.
The wiki of the project can be found here.
The final report of the project can be downloaded from the wiki or from here.

Tuesday, February 25, 2014

Alberto Montanari's view on Hydrology and Hydraulic Constructions

Alberto Montanari (GS) is a distinguished Italian colleague, and the editor in chief of Water Resources Research, one of my favorite hydrological journals. He is also very active in the IAHS especially for what regards this hydrological decades named Panta Rhei.
We do have a different approach on many topics, and different attitudes towards modelling. Nevertheless one cannot deny that his production is important and interesting.

However, this time I was attracted by the fact that he is putting a lot of his material on-line making available to students the videos of his class of advanced hydrology and hydrology construction. Other videos are available on his youtube page.

Eco-hydrology of semi-arid environments: Confronting Mathematical models with ecosystem complexity

In a chain search, regarding the previous post, I also find the videos of the above conference, held last may in Israel.  For who is interested in ecohydrology, is the occasion to listen to some of the protagonists of the revamp  of ecohydrology in the last decade.

The whole conference's videos were uploaded into the Youtube channel, EcoHydrologyConf.

The list of speakers includes : Ignacio Rodriguez-Iturbe (GS), Amilcare Porporato (GS), Paolo D'Odorico (GS), Marc Parlange (GS), Jeffrey McDonnell (GS), Dani Or (GS), and many others very good researchers. A must for who works in the field.  To access the video in order jump here.

Evaporation From Soils

Recently I went back to be interested in evapotranspiration, and I was captured by a thread of publication by Dani Or (GS) and Peter Lehmann and coworkers on the subject. Fortunately, Dany also gave some talk on the same subject that can help to understand the papers.
Some of the main results: 1 - when evaporating from soil the Kelvin effect is not so important. 2 - What is important is the ability of the porous medium to supply water through capillary flows. 3 - The decline of evaporation (a.k.a. stage II evaporation) happens when the vadose zone is made up of disconnected phases. 4 - The latter situation is realised when the evaporating front is at a depth that can be deduced directly from the Soil Water Retention Curves.

Here the talks by Dany:

- The first, longer talk, given at usaskgiws, the University of Saskatchewan (1 h);
- The second one, shorter given at the recent Ecohydrology conference.

Here the papers:

Aminzadeh, M., & Or, D. (2013). Temperature dynamics during nonisothermal evaporation from drying porous surfaces. Water Resources Research, 49(11), 7339–7349. doi:10.1002/2013WR014384

Assouline, S., & Or, D. (2013). Plant Water Use Efficiency over Geological Time – Evolution of Leaf Stomata Configurations Affecting Plant Gas Exchange. PLoS ONE, 8(7), e67757. 

Haghighi, E., Shahraeeni, E., Lehmann, P., & Or, D. (2013). Evaporation rates across a convective air boundary layer are dominated by diffusion. Water Resources Research, 49(3), 1602–1610. doi:10.1002/wrcr.20166

Lehmann, P., & Or, D. (2014). Effect of wetness patchiness on evaporation dynamics from drying porous surfaces, 1–13. doi:10.1002/wrcr.20637

Or, D., Lehmann, P., & Shahraeeni, E. (2014). Advances in soil evaporation Physics - A review. Vadose Zone Journal, 1–16.

Monday, February 24, 2014

JGrass-NewAGE codes

Jgrass-NewAGE is going out from its infantry, and this is signed by its appearance in Github, where the code in development is going to be uploaded. The definitive repository for the code is the JGrasstools Github repository, however, since the requirement to fulfil the jgrasstools standards, were not followed during these first years of development, and because, at the same time, some of the functionalities required for the most recent components are not yet met by the actual version of the uDig Spatial Toolbox, we decided to open a series of new repositories receiving the code in development.
This step was decided also to boost the development of the documentation for the software, that is still kind of missing, at the moment. So here it is the list of the places where the main JGrass-NewAGE components can be found:

All the other components:
  • The Hymod component, 
  • The shortwave radiation component (by Giuseppe Formetta, starting from previous work by Daniele Andreis)
  • The snow water equivalent component (by Giuseppe Formetta)
  • The  evapotranspiration component (by Giuseppe Formetta)
can be found instead here, under the same general repository.

Monday, February 17, 2014

Again on statistics - P - Values

A Nature paper brings back arguments on what p-values are, and how they should be consider. It also talks about the different positions of Fisher, Neyman and Pearson, on the topic [please notice that the reconstruction of the history gives a little more information than the one I gave in my previous post citing J. Franklin], and I,  quite clearly, vote for Fisher. You can find the article here.

A lot of comments follow. However, the right complements of the Nature paper seems to this "LessWrong blopost" and this other on Prudentia.

Saturday, February 15, 2014

Preferential Flow in Hillslope

This last month was partially spent in reviewing Grigoris Anagnostopoulos Ph.D. thesis about subsurface hillslope modelling and landsliding. Among the topics he faced, one of particular interest is the one of preferential flow. This have been largely debated in literature since the 1982 work by German and Beven (great to address the issue, less fundamental in getting a solution, as well as the 2013 recent effort by the same authors).  Grigoris writes:

“Natural soils normally exhibit a high degree of heterogeneity due to macropores, fissures, cracks and root holes, which are the result of soil forming processes and biological activity. The existence of these structural heterogeneities result in the non- uniformity of the pressure potential making the infiltration front to move faster to greater depths using the macropore space without passing through the soil matrix. 
Several studies showed that the contribution of preferential flow paths to hillslope water regime and catchment response can be substantial [Weiler and Naef , 2003a, b; Jones, 2010]. “

Here I would add the studies by Flury et al, 1990, and other Juris work (e.g  Godhrati, 1990), Jeff McDonnell [e.g McDonnell, 1990], Andreini and Steenhuis, 1990, to name a few.

What has been elusive for years (and still is) is the way to simulate it [e.g. Simunenk, et al, 2003]. Grigoris gives a simple and clear summary:
“The simplest way to describe preferential flow is to use Richards’ equation coupled with piecewise continuous soil water retention and hydraulic conductivity functions that take into account the increase in hydraulic conductivity near saturation, due to the existence of macropores [Mohanty et al., 1997; Schaap and van Genuchten, 2005; Børgesen et al., 2006]. “

He also comments:

“This approach, although it is very easy to implement and takes into account successfully the substantial increase in the hydraulic conductivity near saturation, cannot describe the non-equilibrium mechanisms of flow that the existence of macropores implies.
Furthermore … more rigorous approaches for modelling preferential flow through soil have been proposed the last decades, ranging from single-porosity non equilibrium flow models to dual-porosity and dual-permeability models. 
Single porosity non equilibrium models [Ross and Smettem, 2000; Diamantopoulos et al., 2012] make the assumption that water content in not a function of the pressure head and the SWRC in not used any more for its computation. Instead, a kinematic approach is used to describe the water content’s evolution towards equilibrium. 
The implementation of the aforementioned approach in existing numerical codes based on the mixed form of Richards’ equation is easy and straightforward. (N.o.B. - straightforward is usually not so)
Dual-porosity models [Philip, 1968; van Genuchten and Wierenga, 1976] divide the soil media into two distinct domains: the macropore domain and the soil matrix domain. Water is assumed to flow only through the macropores and the soil matrix is used to store and exchange water with the macropore domain without permitting the development of convective flow. 
In dual-permeability models, two separate Richard’s equation are used to simulate water flow through the two distinct pore regions described above [Gerke and van Genuchten, 1993a, b, 1996]. 
The basic drawback of this approach is that it requires the determination of many parameters because of the fact that sepa- rate soil water retention and hydraulic conductivity functions are used for the two pore regions and the interface between them.
During the last decades many hillslope-scale experiments were carried out in several places around the world [Tsuboyama et al., 1994; Uchida et al., 2002; Weiler and Naef, 2003a; Uchida et al., 2005] trying to shed light on many qualitative and quantitative characteristics of preferential flow phenomena and their implications in subsurface flow and catchment response. Several researchers [Beckers and Alila, 2004; Weiler, 2005; Weiler and McDonnell, 2007] proposed simple models for the description of preferential flow, trying to incorporate all the knowledge acquired from the observed characteristics from the field experiments. 
The problem of this kind of approaches arises from their lack of generality, because they are founded and tested with the data from a specific test site, making them not easily transferable to other locations.”

So I thanks Grigoris of the little review and I hope he does not blame me if I reproduced here part of his thesis, and added some bibliography.  With a good luck for his carrier.


Beven, K.J., Germann, P F. 1982. Macropores and water flow in soils, Water Resources Research, 18(5), 1311‐1325.

Beven, K., and P. Germann (2013), Macropores and water flow in soils revisited, Water Resour. Res.,49, 3071–3092, doi:10.1002/wrcr.20156

Børgesen, C. D., O. H. Jacobsen, S. r. Hansen, and M. G. Schaap, Soil hydraulic properties near saturation, an improved conductivity model, Journal of Hydrology, 324, 40–50, 2006.

Diamantopoulos, E., S. C. Iden, and W. Durner, Inverse modeling of dynamic nonequilibrium in water flow with an effective approach, Water Resources Research, 48, 1–16, 2012.

Flury, M., H. Flühler, W. A. Jury, and J. Leuenberger (1994), Susceptibility of soils to preferential flow of water: A field study, Water Resour. Res., 30(7), 1945–1954, doi:10.1029/94WR00871.

Gerke, H., and M. T. van Genuchten, A dual-porosity model for simulating the preferential movement of water and solutes in structured porous media, Water Resources Research, 29, 305–319, 1993a.

Gerke, H. H., and M. T. van Genuchten, Evaluation of a First-Order Water Tranfer Term for Variably Saturated Dual-Porosity flow Models, Water Resources Research, 29, 1225–1238, 1993b.

Gerke, H. H., and M. T. van Genuchten, Macroscopic representation of structural geometry for simulating water and solute movement in dual-porosity media, Advances in Water Resources, 19, 343–351, 1996

Ghodrati, M. and Jury, William A.  A Field Study Using Dyes to Characterize Preferential Flow of Water, SSSAJ, Vol. 54 No. 6, p. 1558-1563, Nov, 1990, doi:10.2136/sssaj1990.03615995005400060008x

Hencher, S. R., Preferential flow paths through soil and rock and their association with landslides, Hydrological Processes, 24, 1610–1630, 2010.

Jones, J. A. A., Soil piping and catchment response, Hydrological Processes, 24, 1548– 1566, 2010.

McDonnell, J. J. (1990), A Rationale for Old Water Discharge Through Macropores in a Steep, Humid Catchment, Water Resour. Res., 26(11), 2821–2832, doi:10.1029/WR026i011p02821. 

Mohanty, B., R. Bowman, J. M. H. Hendrickx, and M. T. van Genuchten, New piecewise-continuous hydraulic functions for modeling preferential flow in an intermittent-flood-irrigated field, Water Resources Research, 33, 2049–2063, 1997.

Philip, J., The theory of absorption in aggregated media, Australian Journal of Soil Research, 6, 1–19, 1968.

Ross, P., and K. Smettem, A Simple Treatment of Physical Nonequilibrium Water Flow in Soils, Soil Science Society of America Journal, 64, 1926–1930, 2000.

Schaap, M. G., and M. T. van Genuchten, A Modified Mualem-van Genuchten For- mulation for Improved Description of the Hydraulic Conductivity Near Saturaion, Vadose Zone Journal, 5, 27–34, 2005.

Simunek, J., Jarvis, N.J., van Genuchten, M.Th. , and Gardena, A., Review and comparison of models for describing non-equilibrium and preferential flow and transport in the vadose zone, Journal of Hydrology 272 (2003) 14–35

Uchida, T., I. T.-v. Meerveld, and J. J. Mcdonnell, The role of lateral pipe flow in hillslope runoff response : an intercomparison of non-linear hillslope response, Journal of Hydrology, 311, 117–133, 2005.

van Genuchten, M., and P. Wierenga, Mass Tranfer Studies in Sorbing Porous Media I. Analytical Solutions, Soil Science Society of America Journal, 40, 473–480, 1976.

Weiler, M., and F. Naef, An experimental tracer study of the role of macropores in infiltration in grassland soils, Hydrological Processes, 17, 477–493, 2003a.

Weiler, M., and F. Naef, Simulating surface and subsurface initiation of macropore flow, Journal of Hydrology, 273, 139–154, 2003b.

Tuesday, February 11, 2014

Evolution and selection of river networks: Statics, dynamics, and complexity

This is a review paper published on PNAS, that I co-authored. Actually a review with some new results that were the outcome of my recent efforts with Java.  OCN stands for Optimal Channel Networks, a theory I co-authored with Ignacio Rodriguez-Iturbe (also here), Andrea Rinaldo, Raphael Bras, Ede Ijjasz-Vasquez (also here), and that produced a thread of papers of mine that are mentioned in a previous post, here.
This is the reunion of a old group of guys that made some good thing together, and hopefully not the last paper together.  The list of co-author of this specific paper also includes Amos Maritan (also here) and Jayanth Banavar (also here).  OCNs revealed a very interesting metaphor for many other networks, including blood vessels, and could be a key to explain the ratio between form and structure of living being. Browsing Rinaldo's production you can find several applications of the concept.

Here below, the abstract of the paper that you can preview here (or clicking under the figure):

"Moving from the exact result that drainage network configurations minimizing total energy dissipation are stationary solutions of the general equation describing landscape evolution, we review the static properties and the dynamic origins of the scale-invariant structure of optimal river patterns. Optimal channel networks (OCNs) are feasible optimal configurations of a spanning network mimicking landscape evolution and network selection through imperfect searches for dynamically accessible states. OCNs are spanning loopless configurations, however, only under precise physical requirements that arise under the constraints imposed by river dynamics—every spanning tree is exactly a local minimum of total energy dissipation. It is re- markable that dynamically accessible configurations, the local optima, stabilize into diverse metastable forms that are nevertheless characterized by universal statistical features. Such universal features ex- plain very well the statistics of, and the linkages among, the scaling features measured for fluvial landforms across a broad range of scales regardless of geology, exposed lithology, vegetation, or climate, and differ significantly from those of the ground state, known exactly. Results are provided on the emergence of criticality through adaptative evolution and on the yet-unexplored range of applications of the OCN concept."

Some geomorphologist do not understand OCNs and tend to overlook them. However, I bet OCNs will resist for many and many years as a sound theory, and sooner or later, someone will close the open issues we left behind.

The Virtual Luna Project

Luna Leopold wrote some of the papers that delighted my early research years (together with those by Ronald Shreve, Ignacio-Rodriguez-Iturbe and V.K. Gupta/Ed Waymire).

"On February 23, 2006, Luna Leopold died at the age of 90.  Luna was a vital force, a man of extraordinary creativity and originality, whose passion about science and the natural world permeated all he did.  He wrote with a clarity, simplicity, and insightfulness that inspired generations of researchers.  Nearly all of Luna’s papers precede the time when publishing houses make pdf’s available.  In order to avoid Luna’s seminal papers becoming “classics” (papers often cited but never read), we have created a web page where the majority of Luna’s papers have been scanned and made available on line as pdf’s.    Luna assisted with this work, reviewing the publication list and helping us find originals of papers. "

     The Luna Leopold Virtual Project  "contains a list of Luna’s publications. For those papers for which we could find copies, we (the web site curators) have made pdf’s.  There are some gaps (which we -they- hope to close soon) and some wonderful inclusions."

The Luna Lepold Virtual Page, can be found here.

Monday, February 10, 2014

River Networks as Ecological Corridors for Species Populations and Water borne Diseases

This was the talk given by Andrea Rinaldo for the opening day of the 2013-2014 Doctoral Academic year of our doctoral School. Andrea is possibly the most influential Italian hydrologist ever (if we do not count as proto-hydrologist Leonardo da Vinci).  

 It was a fascinating and passionate travel through river networks structure (their topology, their physical origin), a research of which I was a active witness for some period, and the spreading of diseases or populations (but without loosing appropriate generality in the description of the phenomena) along the networks. 

Please find clicking on the figure the presentation.

Cited References (The ones I could reconstruct)

Ammerman & Cavalli Sforza, The Neolithic transition and the Genetics of population in Europe, Princeton Univ. Press 1984^1

Bertuzzo, E., A. Maritan, M. Gatto, I. Rodriguez-Iturbe, and A. Rinaldo (2007), River networks and ecological corridors:Reactive transport on fractals, migration fronts, hydrochory, Water Resour. Res., 43, W04419, doi:10.1029/2006WR005533. 

Bertuzzo, E., S. Azaele, A. Maritan, M. Gatto, I. Rodriguez-Iturbe, and A. Rinaldo (2008), On the space-time evolution of a cholera epidemic, Water Resour. Res., 44, W01424, doi:10.1029/2007WR006211. 

E. Bertuzzo,Casagrandi  R. , Gatto M. ,Rodriguez-Iturbe  I., 
and Rinaldo A. , On spatially explicit models of cholera epidemics, J. R. Soc. Interface (2010) 7, 321–333 doi:10.1098/rsif.2009.0204

E Bertuzzo, L Mari, L Righetto, M Gatto, R Casagrandi, M Blokesch, I Rodriguez‐Iturbe, A Rinaldo, Prediction of the spatial evolution and effects of control measures for the unfolding Haiti cholera outbreak, Geophysical Research Letters, Vol 38, No 6, 2011

Campos, D., Fort, J., & Méndez, V. (2006). Transport on fractal river networks: Application to migration fronts. Theoretical Population Biology, 69(1), 88–93. doi:10.1016/j.tpb.2005.09.001

Carrara, F., Altermatt, F., Rodriguez-Iturbe, & Rinaldo, A. (2012). Dendritic connectivity controls biodiversity patterns in experimental metacommunities, 1–6. doi:10.1073/pnas.1119651109/-/DCSupplemental/pnas.201119651SI.pdf

F. Carrara, A. Rinaldo, A. Giometto and F. Altermatt. Complex Interaction of Dendritic Connectivity and Hierarchical Patch Size on Biodiversity in River-Like Landscapes, in The American Naturalist, vol. 183, num. 1, p. 13-25, 2014.

Chao, D., Halloran, M. E., & Longini, I. M. (2011). Vaccination strategies for epidemic cholera in Haiti with implications for the developing world. Pnas, 1–5. doi:10.1073/pnas.1102149108/-/DCSupplemental/sapp.pdf

 Codeço, C. T. (2001). Endemic and epidemic dynamics of cholera: the role of the aquatic reservoir. BMC Infectious Disease, 1–14. 

Capasso V, Paveri-Fontana SL., A mathematical model for the 1973 cholera epidemic in the European Mediterranean region, Rev Epidemiol Sante Publique. 1979 Sep 18;27(2):121-32.

Colaiori et al., PRE, 2003 ?

Gatto, M., Mari, L., Bertuzzo, E., Casagrandi, R., Righetto, L., Rodriguez-Iturbe, I., & Rinaldo, A. (2012). Generalized reproduction numbers and the prediction of patterns in waterborne disease. PNAS, 1–6. doi:10.1073/pnas.1217567109/-/DCSupplemental

M Gatto, L Mari, E Bertuzzo, R Casagrandi, L Righetto, I Rodriguez-Iturbe, and A. Rinaldo, Spatially explicit conditions for waterborne pathogen invasion, The American Naturalist 182 (3), 328-346

A Giometto, F Altermatt, F Carrara, A Maritan, A Rinaldo, Scaling body size fluctuations
Proceedings of the National Academy of Sciences 110 (12), 4646-4650

Hartley et al, PNAS, 2006

Hubbel, 2001

Greg Huber, Scheidegger's rivers, Takayasu's aggregates and continued fractions, Physica A: Statistical Mechanics and its Applications, Volume 170, Issue 3, 15 January 1991, Pages 463–470

A Kolmogorov, L Petrovsky, N Piskunov, An investigation of the diffusion equation combined with an increase in mass and its application to a biological problem - Bull. Uni. Moscow Ser. Int. A, 1937

Leopold, L. B.; Langbein, W. B., The concept of entropy in landscape evolution
1962,  USGS Professional Paper: 500-A 

Marani, A., R. Rigon and A. Rinaldo, A Note on fractal channel networks,Water Resources Research, (27)5, 3041-3049, 1991.

L Mari, E Bertuzzo, L Righetto, R Casagrandi, M Gatto, I Rodriguez-Iturbe, and A. Rinaldo,
Journal of The Royal Society Interface 9 (67), 376-388

L Mari, E Bertuzzo, R Casagrandi, M Gatto, SA Levin, I Rodriguez‐Iturbe, and A. Rinaldo, Hydrologic controls and anthropogenic drivers of the zebra mussel invasion of the Mississippi‐Missouri river system
Water Resources Research 47 (3) 

L Mari, R Casagrandi, E Bertuzzo, A Rinaldo, M Gatto,
Metapopulation persistence and species spread in river networks
Ecology letters

R Muneepeerakul, JS Weitz, SA Levin, A Rinaldo, I Rodriguez-Iturbe,
Journal of Theoretical Biology 245 (2), 351-363 2007

Water Resources Research 43 (12)

Water Resources Research 43 (7)

R Muneepeerakul, E Bertuzzo, HJ Lynch, WF Fagan, A Rinaldo, ...
Neutral metacommunity models predict fish diversity patterns in Mississippi–Missouri basin,
Nature 453 (7192), 220-222, 2008

DW Murray, AJ Carr et al., Survival analysis of joint replacements,  Journal of Bone & Joint …, 1993 -
Pascual M, Bouma MJ, Dobson AP (2002) Cholera and climate: Revisiting the quantitative evidence. Microbes Infect 4: 237–245

Pascual, M. and  Dobson A., Seasonal Patterns of Infectious Diseases, 2005, DOI: 10.1371/journal.pmed.0020005

Renaud Piarroux, Robert Barrais, Benoît Faucher, Rachel Haus, Martine Piarroux, Jean Gaudart, Roc Magloire, and Didier Raoult, Understanding the Cholera Epidemic, Haiti, Emerg Infect Dis. 2011 July; 17(7): 1161–1168. doi:  10.3201/eid1707.110059
PMCID: PMC3381400

Rinaldo et al., PNAS, in press

Rodriguez-Iturbe, I. , A. Rinaldo, R. Rigon, R. L. Bras, A. Marani and E.J. Ijjasz-Vasquez, Energy dissipation, runoff production, and the 3-dimensional structure of river basin, Water Resources Research, (28)4, 1095-1103, 1992.

Rinaldo, A., I. Rodriguez-Iturbe, R. Rigon, R.L. Bras, E. J. Ijjasz-Vasquez e A. Marani, Minimum energy and fractal structures of drainage networks, Water Resources Research, (28), 2183, 1992.

Rodriguez-Iturbe, I. , A. Rinaldo, R. Rigon, R. L. Bras, A. Marani and E.J. Ijjasz-Vasquez, Fractal structure as least energy patterns: The case of river networks, Geophysical Res. Letters, (19)9, 889-892, 1992.

Rodriguez-Iturbe & Rinaldo, Fractal River Basins: Chance and Self-Organization, Cambridge Univ, Press, 2007

M Takayasu, A Provata, G Huber,  Statistical models of river networks, J. Stat. Phys 65, 725-745, 1991
^1 - See also: M. Gkiasta, T. Russell, S.Shennan, and James Steele, Neolithic transiti on in Europe: the radiocarbon record revisited - UCL

Tuesday, February 4, 2014

Notes from a panel on reviewing

I take from one of the blog I follow Living on an Ivory basement, a post on reviewing papers:
My notes for a panel presentation on reviewing papers and grants. Talking on reviewing is always an excuse to talk about science, and the way scientists think to it.  Jump to the blog for reading it.

Directly from the post above: Env. Micro. referee comments:

Some examples:
- "It is sad to see so much enthusiasm and effort go into analyzing a dataset that is just not big enough."
- "You call the sample fresh water, this is confusing as it is saline water."
- "The biggest problem with this manuscript, which has nearly sucked the will to live out of me, is the terrible writing style."

These is absolutely not how you should write reviews. But they are funny.