Monday, February 28, 2011

How Extremes Change Over Time

From EOS, vol 92, No 2, 11 January 2011:

" Average behavior is often studied, with well developed techniques from the field of statistics allowing for inferences to be readily made. However, in many atmospheric, hydrologic, and other Geophysical problems extremes are often of great interest. .... "

Here a link to the complete article:

from EOS

Here below a link to:

Richard Katz's work

Thursday, February 24, 2011

Where do channels begin ?

It is the title of a famous paper by David Montgomery and Bill Dietrich about channel initiation which appeared in Nature, in 1988, and was followed by a subsequent paper (in 1994 on Water Resources Research): and BTW by many others in the following years to confirm, and using their findings.

So we know much more than then about. However, those pioneering contribution, did refer to what happens in sloped but hilly environments, of Oregon and California. What about the Alps ?

Recent work by Paolo Tarolli brought some quantitative light on the issue. He presented his work at last January Cathy meeting that can be summarized as follows:

-the availability of very detailed laser scanner of topography allows a great opportunity to use objective methods to single out channels' head.
- in a region of the Italian Alps (Dolomites) were surveyed at least two main processes that drive channel initiation: i) channel heads formed essentially by surface runoff (mass wasting, in form of debris flows or "more traditional" erosion), ii) and areas where geology and groundwater seeping upward exercise important controls on channel initiation.
- Wavelet analysis allows to smooth the topography the right way to use in sequence "curvatures" for channels head initiation.

I hope it will not pass to much time before we can bring these tools inside our jgrasstools.

For who is interested, relevant papers are listed below:


David R. Montgomery & William E. Dietrich,Where do channels begin? , Nature 336, 232 - 234 (17 November 1988); doi:10.1038/336232a0

MONTGOMERY and DIETRICH. Source Areas, Drainage Density, and Channel Initiation . Water Resour. Res. (1989) vol. 25 (8) pp. 1907-1918

Orlandini, S., Tarolli, P., Moretti, G., Dalla Fontana, G. (2011). On the prediction of channel heads in a complex alpine terrain using gridded elevation data, Water Resources Research, 47, W02538, doi:10.1029/2010WR009648

Passalacqua, P., Tarolli, P., Foufoula-Georgiou, E. (2010). Testing space-scale methodologies for automatic geomorphic feature extraction from LiDAR in a complex mountainous landscape, Water Resources Research, 46, W11535, ISSN: 0043-1397, doi:10.1029/2009WR008812.

Pirotti and Tarolli. Suitability of LiDAR point density and derived landform curvature maps for channel network extraction. Hydrol. Process. (2010) vol. 24 (9) pp. 1187-1197

Sofia, G., Tarolli, P., Cazorzi, F., Dalla Fontana, G. (under review). Channel heads and channel network identification from high-Resolution DTM: a statistical approach, Hydrol. Earth Syst. Sci., ISSN: 1027-5606.

Tarolli, P., Dalla Fontana, G. (2009). Hillslope-to-valley transition morphology: new opportunities from high resolution DTMs, Geomorphology, 113, 47-56, doi:10.1016/j.geomorph.2009.02.006

Wednesday, February 16, 2011

Using Geopaparazzi

GEOpaparazzi is a very nice tool for doing rapid topographic surveys, taking pictures that are geo-referenced, tracking your walk or excursion, and while walking and looking, taking notes.
This is well explained in the GEOpaparazzi web site.
Obviously it is easy to bring any of the things done into BeeGIS (its larger brother) and JGrass. Connection to Google is provided by exporting .klm files.

Now the wish list:

However, as happens for the good things, using it you would like to have something more. In fact, you can use it only when a GPS satellite is available, that is pretty reasonable thinking for what Geopaparazzi has been created, but the tool is so nice that you would like to use it also for other purposes. For instance, I have a simple app in my iphone where I "twitter-like" annotate what I am doing during the day: especially for helping my memory. A sort of simple diary. It would be great if I could use GEOpaparazzi for doing this. In addition to notes, I could also add picture, and besides, I will have also the location where I did it. This actually would implies that I should like to be able to take notes and picture, when no GPS is available, and let, for instance, the position be taken as soon as a GPS become available. In turn, obviously, this also would imply to have a "Diary viewer". This would make of GEOpaparazzi the insuperable Moleskine of the digital era.

Dreaming too much ?

Tuesday, February 15, 2011

Indexing the water table position: Lanni, McDonnell and Rigon

The paper deals with the introduction of a new topographic index, i.e. an indicator of water table depth in a hillslope.
We need a simplified index for this job, since we are required to analyze large dataset at large resolution (i.e. an entire basin of thousands of square kilometers, or so, at 1 m or so of resolution). This is obviously an issue since many years, and many researchers tried to get solutions.
The first is the one based on the topographic index (TWI in our paper) by Beven and Kirby (1979), but also by O'Loughlin (1986), and used both in rainfall-runoff models (i.e. TOPMODEL) and hillslope stability analysis (i.e SHALSTAB, 1992 and 1994 and SINMAP, 1994). This index, is laregely applied (for instance in D'Odorico and Rigon, 2003, and in our software Peakflow, named after one other paper mentioned in this blog) but reveled insufficient mainly for three reasons:
1 - Barling and Grayson (1994), on the basis of kinematic concepts showed that seldom rainfall are long enough to bring a hillslope to the stationarity condition which is at the base of the derivation of the TWI. -
2 - Donwhill conditions count, as Jeff McDonnel l, and Jan Seibert, among others, showed in their papers;
3 - TWI also contains the assumption of the identification of topographical gradients with hydraulic head gradients: which is clearly not correct when there are discountinuos or so variations of slope from one pixel to a next-neighbor, since hydraulic potential tends to be continuous by definition.

We introduce here a new index that correspond to the complete perceptual model, and compare it to previous indexes and with simulation performed with a Boussinesq equation solver, used as the truth.

Having such an index would be profitable for rainfall-runoff models like Peakflow, or for modifying models like SHALSTAB and SINMAP in estimating hillslope instability.

Who is interested to know more can ask me or co-authors for copy of the draft.

References of the paper

Barling, R. D., Moore, I. D., Grayson, R. B., 1994. A quasi-dynamic wetness index for characterizing the spatial distribution of zones of surface saturation and soil water content. Water Resour. Res., 30, 4, doi:

Beven KJ, Kirkby MJ. 1979. A physically based variable contributing area model of basin hydrology. Hydrology Science Bulletin 24(1):43–69.

Beven, K. and Freer, J. (2001), A dynamic TOPMODEL. Hydrological Processes, 15: 1993–2011. doi: 10.1002/hyp.252.

Beven, K. J., Lamb, R., Quinn, P. F., Romanowicz, R. & Freer, J. (1995) TOPMODEL (Chapter 18, pp. 627-668). In: Singh, V. P. (ed.) Computer models of watershed hydrology, Water Resources Publications, Highlands Ranch, Colorado, U.S.A., 1130 pp.

Borga M, Dalla Fontana G, Cazorzi F (2002) Analysis of topographic and climatologic control on rainfall-triggered shallow landsliding using a quasi-dynamic wetness index. J Hydrol 268:56–71.

Burt TP. Butcher DP. 1986. Development of topographic indices for use in semi-distributed hillslope runoff models. Zeitschift für Geomorphologue 58: 1–19.

Carson, M. A. and Kirkby, M. J. Cambridge, Hillslope form and process, England : University Press , 1972, 475 p.

Casadei, M., Dietrich, W. E. and Miller, N. L. (2003), Testing a model for predicting the timing and location of shallow landslide initiation in soil-mantled landscapes. Earth Surface Processes and Landforms, 28: 925–950. doi: 10.1002/esp.470.

Casulli, V. (2009), A high-resolution wetting and drying algorithm for free-surface hydrodynamics. International Journal for Numerical Methods in Fluids, 60: 391–408. doi: 10.1002/fld.1896

Cohen, J. (1960). A coefficient of agreement for nominal scales. Educational and Psychological Measurement, 20, pp. 37- 46.

Cordano, E., Rigon, R. A mass-conservative method for the integration of the two-dimensional
groundwater (Boussinesq) equation. Submitted Water Resour. Res.

Crave A, Gascuel-Odoux C. 1997. The influence of topography on time and space distribution of soil surface water content.Hydrological Processes 11: 203–210.

Detty, J. M., McGuire, K. J., 2010. Threshold changes in storm runoff generation at a till-mantled headwater catchment. Water Resour. Res., 46, 7, doi: 10.1029/2009WR008102.

Franchini M, Wendling J, Obled C, Todini E. 1996. Physical interpretation and sensitivity analysis of the TOPMODEL. Journal of Hydrology 175(1–4): 293–338.

Freer, J., J.J. McDonnell, K. J. Beven, N. E. Peters, D. A. Burns, R. P. Hooper, B. Aulenbach, and C. Kendall (2002).  The role of bedrock topography on subsurface storm flow.  Water Resources Research, 38(12): 5-1 - 5-16.

Grabs, T., J. Seibert, K. Bishop, H. Laudon, 2009. Modeling spatial patterns of saturated areas: A comparison of the topographic wetness index and a dynamic distributed model, Journal of Hydrology, 373 (1-2), 15-23

Grayson, R. B., Terrain-based hydrologic modelling for erosion studies, Ph.D. thesis, 375 pp., Dept. of Civ. and Agric. Eng., The Univ. of Melbourne, Australia, 1990.

Grayson, R. B., I. D. Moore, and T. A. McMahon, Physically based hydrologic modeling, 1, A terrain-based model for investigative purposes, Water Resour. Res., 28(10), 2639-2658, 1992.

Grayson, R. and Western, A. (2001), Terrain and the distribution of soil moisture. Hydrological Processes, 15: 2689–2690. doi: 10.1002/hyp.479.

Güntner, A., J. Seibert, and S. Uhlenbrook, 2004. Modeling spatial patterns of saturated areas: An evaluation of different terrain indices, Water Resour. Res., 40, W05114, doi:10.1029/2003WR002864.

Haitjema, H.M., Mitchell-Bruker, S., Are water tables a subdued replica of the topography?, Ground Water 43 (6) (2005), pp. 781–786

Hjerdt, K. N., J. J. McDonnell, J. Seibert, and A. Rodhe, 2004. A new topographic index to quantify downslope controls on local drainage, Water Resour. Res., 40, W05602, doi:10.1029/2004WR003130.

I. Iorgulescu, J.-P. Jordan, Validation of TOPMODEL on a small Swiss catchment, Journal of Hydrology, Volume 159, Issues 1-4, July 1994, Pages 255-273, ISSN 0022-1694, DOI: 10.1016/0022-1694(94)90260-7.

J.P. Jordan, Spatial and temporal variability of stormflow generation processes on a Swiss catchment, Journal of Hydrology, Volume 153, Issues 1-4, January 1994, Pages 357-382, ISSN 0022-1694, DOI: 10.1016/0022-1694(94)90199-6.

Lane SN, Brookes CJ, Kirkby MJ, Holden J, 2004. A network-index-based version of TOPMODEL for use with high-resolution digital topographic data. Hydrological Processes 18: 191–201.

McDonnell, J.J., J. Freer, R. Hooper, C. Kendall, D. Burns and K. Beven (1996). New method developed for studying flow on hillslopes. EOS, 77(47): 465-472.

O'Callaghan, J. F., Mark, D. M., The extraction of drainage networks from digital elevation data, Computer Vision, Graphics, and Image Processing, Volume 28, Issue 3, December 1984, Pages 323-344, ISSN 0734-189X, DOI: 10.1016/S0734-189X(84)80011-0.

Orlandini, S., Moretti, G., 2009. Determination of surface flow paths from gridded elevation data, Water Resour. Res., 45, 3, doi: 10.1029/2008WR007099.

Orlandini, S., G. Moretti, M. Franchini, B. Aldighieri, and B. Testa (2003), Path-based methods for the determination of nondispersive drainage directions in grid-based digital elevation models, Water Resour. Res., 39(6), 1144, doi:10.1029/2002WR001639.

Quinn, P. F., K. J. Beven, P. Chevallier, and O. Planchon (1991), The prediction of hillslope flowpaths for distributed modelling using digital terrain models, Hydrol. Processes, 5, 59– 80.

Rodhe, A. and Seibert, J., 1999, Wetland occurrence in relation to topography - a test of topographic indices as moisture indicators, Agricultural and Forest Meteorology 98-99: 325-340.

Schmidt, F., and Persson, A, 2003, Comparison of DEM Data Capture and Topographic Wetness Indices, Precision Agricolture, 4, 179-192.

Seibert, J. 1999. On TOPMODEL's ability to simulate groundwater dynamics. In Regionalization in Hydrology (Proc. Conf. at Braunschweig, March 1997) . IAHS Publication 254: 211-220.

Seibert, J., and McGlynn, B.L., 2007. A new triangular multiple flow-direction algorithm for computing upslope areas from gridded digital elevation models, Water Resour. Res., 43, W04501, doi:10.1029/2006WR005128.

Seibert, J., A.Rodhe, K.Bishop, 2003. Simulating interactions between saturated and unsaturated storage in a conceptual runoff model, Hydrological Processes, 17: 379-390.

Seibert, J., Stendahl, J. and Sørensen, R., 2007. Topographical influences on soil properties in boreal forests, Geoderma, 141(1-2): 139-148.

Sørensen, R. and Seibert, J., 2007. Effects of DEM resolution on the calculation of topographical indices: TWI and its components, Journal of Hydrology, 347: 79-89.

Spearman, C., 1904, The proof and measurement of association between two things, Amer. J. Psychol., 15, pp. 72–101

Tarboton, D. G. (1997), A new method for the determination of flow directions and upslope areas in grid digital elevation models, Water Resour. Res., 33(2), 309– 319.

Tetzlaff, D., McDonnell, J. J., Uhlenbrook, S., McGuire, K. J., Bogaart, P. W., Naef, F., Baird,
A. J., Dunn, S. M. and Soulsby, C. (2008), Conceptualizing catchment processes: simply too complex?. Hydrological Processes, 22: 1727–1730. doi: 10.1002/hyp.7069.

Tromp-van Meerveld, H. J., and McDonnell, J. J., 2006, Threshold relations in subsurface stormflow: 2. The fill and spill hypothesis, Water Resour. Res., 42, 2, doi: 10.1029/2004WR003800

Western, A. W., Bloschl, G., On the spatial scaling of soil moisture, Journal of Hydrology, Volume 217, Issues 3-4, 30 April 1999, Pages 203-224, ISSN 0022-1694, DOI: 10.1016/S0022-1694(98)00232-7.

Wolock, D. M., Price, C. V., 1994. Effects of digital elevation model map scale and data resolution on a topography-based watershed model, Water Resour. Res., 30, 11, doi: 10.1029/94WR01971.

Friday, February 11, 2011

H index - G - index - Research and all of this

You can have a nice summary (in Italian) here.

It is in Italian, however, most of the links refer to English sources (and one points to these Einstein and Pitagorean Index). So, from this point of view, it is useful also for English readers.

I confess I did know most of the physicists in Einstein's ranking figure, but I did not know before Juan Maldacena. As usual, it is always exciting to come to know the work of outstanding scientists, even if Strings were one of the reasons that made me abandon theoretical physics.

Thursday, February 10, 2011

Writing good papers

Writing good papers is matter of having the contents before ("rem tene, verba sequentur").   So I give for granted that you chose a topic which is important (not just because fashionable, but because you humbly assimilated what your community of scientists, and the best among them, thinks it is important) and you have done the right amount of work with solid methods.

However, here, I want to support the idea that a scientific paper has its own structure. The Nature journal has a page with several useful references (here, last accessed February, 9, 2011, as well as all the links below). Other and many resources can be easily found googling "scientific writing" or similar keywords (and you find, for instance this).
However, I am summarizing here a contribution brought to us a few years ago by our friend  Julie Campbell.
She reminded that the general organization of a scientific paper has some standard parts:

Introduction and Literature Review (Previous Studies)
Approach and Method(s)
Results and Analysis**

Stanley Malloy wrote a small guide where he defines the previous parts as:

"Abstract: An abstract is a succinct (one paragraph) summary of the entire paper. The abstract should briefly describe the question posed in the paper, the methods used to answer this question the results obtained, and the conclusions. It should be possible to determine the major points of a paper by reading the abstract. Although it is located at the beginning of the paper, it is easiest to write the abstract after the paper is completed.

Introduction: The Introduction should (i) describe the question tested by the experiments described in the paper, (ii) explain why this is an interesting or important question, (iii) describe the approach used in sufficient detail that a reader who is not familiar with the technique will understand what was done and why, and (iv) very briefly mention the conclusion of the paper.

Approach and Methods: Or the Materials and Methods section should succinctly describe what was actually done. It should include description of the techniques used so someone could figure out what experiments were actually done. The details of a published protocol do not need to be reproduced in the text but an appropriate reference should be cited – e.g., simply indicate “were done as described by Hughes et al. (4)”. Any changes from the published protocol should be described. It is not appropriate to indicate volumes of solutions added – instead indicate the relevant information about the experiment such as final concentrations used, etc.

Results: Begin each paragraph with an opening sentence that tells the reader what question is being tested in the experiments described in that paragraph. Write the opening sentence in bold font for emphasis. (Sometimes a complete sentence is used and sometimes a short phrase is used – either style is OK but the style should be used consistently throughout the manuscript.) Any results that include multiple data points that are critical for the reader to evaluate the experiment should be shown in tables or figures. However, the results should be summarized in accompanying text. When referring to a particular table or figure, they should be capitalized (e.g., Table 1, Figure 6, etc.) The text of the Results section should be succinct but should provide the reader with a summary of the results of each table or figure.
Not all results deserve a separate table or figure. As a rule of thumb, if there are only a few numerical results or a simple conclusion describe the results in the text instead of in a table or figure. Your paper should focus on what worked, not things that did not work (unless they didn’t work for reasons that are interesting and provide insights).

Analysis (Discussion): Do not simply restate the results — explain your conclusions and interpretations of the Results section. How did your results compare with the expected results? What further predictions can be gleaned from the results?

Acknowledgments:  Projects or Institution that financed the research, reviewers that helped. People with whom the topics treated were discussed appear cited here.

Reference lists: Like citations, a variety of reference formats are used by different journals. For an example of a commonly used example, see “Instructions to authors” on ASM web site ( or examples from published manuscripts. "

Citations: It is essential to credit published papers for work mentioned in your manuscript. - RR Note: There are no many other rewards than being cited. So as you like to be cited, do not forget those from whom you learned something - There are a variety of ways of citing references in the text – the style used depends upon the policy of the journal. In text citations should refer to reference list. Do not rewrite title of references in text. "

Julie provided a nice hand-out in her lecture and here it is an excerpt regarding figures: create Tables and Figures that stand-alone.

"The tables and figures that you place in a scientific paper should be able to be understood mostly, if not completely, whether or not your reader reads the accompanying text. Therefore, contents should be clearly labeled and units of measure specified. Use only abbreviations of terms that will be clearly understood by your readers; otherwise, spell out terms. Keep in mind that even though you have defined abbreviations of terms in your text, including equation variables, the table or figure will not stand alone unless you redefine them in your table or figure, being consistent with the abbreviations that you have used in your text.

For figures, specifically plots, there should be a key for symbols used. Also, there should be fully explanatory axis labels that include the units of measure. Recall that the y axis
often begins at zero, but it if does not, you should consider, depending upon who your readers are and the nature of the quantity, calling that fact to your readers’ attention in your caption."

Example: From Gutierrez-Magness and McCuen.

(Notice that the graphic key is easier to comprehend than a verbal description of the line types and/or symbol types would be. Regarding the issue of standing alone, this figure basically satisfies some of the requirements for standing alone. It does, however, need further notation explaining what kind of data has been analyzed, as well as the region, the year(s), and the type of instrument used.)

Example: From “Distributions-Oriented Verification of Ensemble Streamflow Predictions” by A. Allen Bradley, Stuart S. Schwartz, and Tempei Hashino, Journal of Hydrometeorology 5 (2004): 532-545.

(Note the key for the symbols, as well as the notation that provides information about the data in question and its units, as well as the year. Note also the somewhat unusual abbreviation of September, which is traditionally abbreviated, Sept. In this case, the logarithmic scale must start at 1000. In general, this figure satisfies the requirements for standing alone.)

Example: From “Heavy Rainstorms in Chicago: Increasing Frequency, Altered Impacts, and Future Implications,” by Stanley A. Changnon and Nancy E. Wescott, Journal of the American Water Resources Association 38.5 (2002): 1467-1475.

(Note the detailed information in the title that aids the table in standing alone. Note that in the labels, the numbers 2 through 10 have been spelled out, while those numbers greater than ten are given in their numeric form. Many style guides request this differentiation. In general, the rule goes as follows: “Technical quantities of any amount are expressed in numerals. Nontechnical quantities of fewer than 10 are expressed in words. Nontechnical quantities of more than 10 are expressed in numerals” [Markel p. 644]. Needing clarification, however, are the last two rows—the third row indicates the maximum number of storms in a year, and the fourth row indicates that the specific year in question is 2001, but this information is essentially part of row three.)

For more information, see Ch. 14 in Markel on “Creating Graphics,” especially, “Creating Effective Tables,” pp. 333-335.

And more from Julie's handout

I. Notes from Article Excerpts: “Advances in the Use of Observed Spatial Patterns of Catchment Hydrological Response,” by Rodger B. Grayson et al, Advances in Water Resources 25 (2002): 1313-1334.

--Collective nouns—use a singular verb when the parts of the group act as one unit; use a plural verb when the parts of the group act individually. Example: the jury have/has reached a verdict. Note: the expression “a number of” means “several” and needs a plural verb.

--Parallelism—the repetition of a grammatical structure. It suggests similarity between ideas and creates symmetry and balance. A parallel construction repeats an identical grammatical pattern within the same sentence, paragraph, or passage. Sentence examples: a) In this study we will focus on examining the parameters of . . . , calculating the difference between . . . , and explaining how the different patterns signify . . . .
b) The first goal is to acquire the necessary data. The second goal is to calculate . . . . Finally, we hope to show . . . . c) Our study encompasses the derivation of . . . , the illustration of . . . , and the conclusions that we draw . . . .

--Revision of Second Sentence, Intro. Paragraph:
Original—“But these have served more to consolidate the work of the 1990s and propose new methodological advances, rather than focus on new data sources.”
Revision—“These, however, have served more to consolidate the work of the 1990s and (to) propose new methodological advances than to focus on new data sources.”

--Revision of Third Sentence, Intro. Paragraph:
Note: the comma is required before “and” in this case because the author is combining two “independent clauses” with a conjunction.
“Nevertheless, the calls of the 1980s and early 1990s for more research into representing spatial heterogeneity, the collection of data sets for the testing and development of distributed models, and methods how to best deal with issues of scale, have to some extent been heeded, and it is these on which we will focus in this paper.”

--Revision of Results Paragraph:
--See “trade-off”
--Why is it incorrect to place a comma before “and” in the last sentence?

--Revision of Summary Paragraph:
--How could we rewrite for parallelism here?

II. Punctuation Review, American English

--Most common punctuation errors:
A) The comma splice—links two independent clauses (clauses that could stand alone as sentences) with only a comma.
Incorrect: This report was distributed widely in the U.S., its findings were considered groundbreaking.
Correct: This report was distributed widely in the U.S., and its findings were considered groundbreaking.
This report was distributed widely in the U.S.; its findings were considered groundbreaking.
This report was distributed widely in the U.S.: its findings were considered groundbreaking.

B) The run-on or fused sentence—contains two independent clauses with no dividing punctuation.
Incorrect: The internal temperature reached 30 degrees we stopped the experiment at that point.
Correct: The internal temperature reached 30 degrees, so we stopped the experiment at that point.
The internal temperature reached 30 degrees; therefore, we stopped the experiment at that point.
The internal temperature reached 30 degrees. We stopped the experiment at that point.
Also: When the internal temperature reached 30 degrees, we stopped the experiment.

C) The sentence fragment—is an incomplete sentence; some grammatically necessary part is missing.
Incorrect: The drop in temperature caused by a leak in the canister.
Correct: The drop in temperature was caused by a leak in the canister.

Note: In the “Appendix: Reference Handbook,” in Markel (see bibliography below), there is an excellent section on “Editing Your Documents” that covers most aspects of punctuation and grammar.

III. Use of Acronyms and Initial Abbreviations

--An acronym is a word consisting of initials and pronounced as a word, for example, NATO—North Atlantic Treaty Organization, SAR—Synthetic Aperture Radar, or GRASS—Geographic Resources Analysis Support System

--An initial abbreviation consists of the first letter of each word in a phrase or name, for example, GPS—global positioning system or GIS—geographic information system.

IV. Use of Prepositions

-- Prepositions are the words that link and establish specific relations among words or group of words. In some cases, usage is highly idiomatic—in other words, there are few clear rules!
A. Prepositions of Place (literal and figurative)
a. in—in the picture, in the photo, in the paragraph, in the sentence, in the equation, in front (of), in the process (of), in New York, in fact, in place (of), in existence
b. on—on the map, on the page, on the subject, on the edge, on purpose, on top (of), on site, on the contrary
c. at—at the corner, at the intersection, at a glance, at least, at these coordinates, at one time, at work

B. Prepositions of Duration
a. for—for a while, for three days, for a week
(also: a need for, a desire for, for that reason, for instance)
b. while—while we calibrated the...., while I was watching...., while we measured....
c. during—during class, during the experiment, during the day

C. Prepositions of Time and Date
a. in—in a couple of weeks, in February, in time (for)
b. at—at seven o’clock, at Christmas, at sundown, at first
c. on—on Christmas day, on Tuesday, on schedule

Common Words and Phrases Used as Prepositions: about, above, according to, across, after, against, ahead of, along with, among, around, as, as for, at away from, because of, before, behind below, beneath, beside, between, beyond, by, concerning, due to, except, except for, for, from, in, in addition to, in back of, in case of, including, inside, inside of, in spite of, next to, of, off, on, onto, on top of, other than, out, out of, outside, over, past, regarding, through, to, toward, until, unlike, upon, up to, with, within, without

Note: See sections on prepositions in books listed in the bibliography below.

V. Use of Idiomatic Expressions

--Idioms are words, phrases, or expressions that are either grammatically unusual or they convey a meaning that is different from the literal meaning of the term or phrase. Examples: “the big picture”, “to warm up to someone”, “a cold fish”...

Note: A convenient source for help with idiomatic expressions in English may be found at

These sorts of expressions are interesting and useful to know in general, but have limited use in scientific and technical writing because of their lack of univocal meaning in some cases.

VI. Use of Capitalization
--For help with standard practices of capitalization in English, see one of the recommended handbooks in the bibliography below.

VII. Use of Precise Terms to Avoid Ambiguity
--When writing a technical paper, it is critically important to be as specific as possible. Avoid using imprecise words and terms (e.g., a lot, some, a few, an insignificant amount), and if you must use them, be sure to follow them with the precise explanation of what you mean. Use precise words and terms (e.g., 300 meters to the west, 40 degrees warmer than the previous measurement, two key points) whenever possible.
--See pp. 251-251 and pp. 625-627 in Markel, as noted in the bibliography below.

VIII. (Addendum) Writing “Mathematical English”
--When you incorporate an equation into your writing, you should remember that the parts of the equation function as parts of speech. Therefore, the equation and its parts require appropriate use of punctuation, as well as grammatical consideration.

--Variables used in the equation all need to be defined.

Typical errors include the following:
-- Misuse of the colon (:) to introduce every inset equation, no matter the grammatical structure of the sentence which incorporates the equation.
--Capitalization of linking words following the equation that are actually already in the middle of a sentence, such as where, therefore, thus, so, if, and that.
--Failure to follow the equation with a comma preceding the “where...” phrase because in this case, the “where...” phrase is a nonrestrictive element of the sentence.

Example: From “Recent Developments in Statistical Time Series Analysis: Examples of Use in Climate Research” by F. Godtliebsen, L.R. Olsen, and J.-G. Winther, Geophysical Research Letters 30.12 (2003): 56-1—56-4.

A relevant nonparametric regression problem for this is to attempt to use data of the form
where m(x) is the target curve. Here, we assume that the xi are equally spaced on the range of x, that m is smooth and that the εi are independent Gaussian variables with mean 0 (which makes m the regression curve of yi on xi) and variance Var (εi) = .

(Note that there is no colon introducing the equation, and “where” is not capitalized. A comma, however, should be placed after the equation.)

Example: From “Accuracy Evaluation of Rainfall Disaggregation Methods” by
Angelica L. Gutierrez-Magness and Richard H. McCuen, Journal of Hydrologic Engineering ASCE 9.2 (2004): 71-78.

(Note that there is no colon after “by.” Note also that elements which could stand alone as “mathmatical sentences” are set off with semicolons.)

For more information on “Mathematical English,” see the American Institute of Physics Style Manual at


--Anderson, Paul V. Technical Communication: A Reader-Centered Approach. 5th ed. Thompson/ Heinle, 2002.
--Fulwiler, Toby and Alan R. Hayakawa. The Blair Handbook. 4th ed. Upper Saddle River, NJ: Prentice Hall, 2003.
--Hacker, Diana. A Writer’s Reference. Bedford Books, 2003.
--Hacker, Diana. A Pocket Style Manual. Bedford Books, 2003.
--Markel, Mike. Technical Communication. 7th ed. Boston: Bedford-St. Martin’s, 2004.
--Strunk, William and E.B. White. The Elements of Style. 4th ed. Pearson Higher Education, 2000. See also:

External links

See the beautiful presentation by Jeffrey McDonnell

And find here the clarification of co-authorship responsability

Here the Thomas Hengl guide to write a paper

The mononota song as a paradigm for writing a good paper

Thursday, February 3, 2011

Characteristics of good modeling software

Making good models is just one part of the whole job of a hydrologist. It is a tradition in our research field to make good research with not very good computer codes. Please do not misunderstand me. I do not mean that the algorithms used are wrong: I mean that the overall simulations machinery is usually not very well engineered, and using the code produced by researchers is not as easy as it could be (and actually is for many   industrial programs). This eventually makes scientists (and users too) loose a lot of time in redoing the same things, even when the original codes are available, simply because these codes are not well documented or do not provide those  functionalities that make them usable. The following paper (that was addressed to me by the Author of the Csparse library, T. Davis) covers some of the topics of making a good and usable code, and is a must to read for who does modeling.

Please follow the link below for getting the paper (last accessed February 3rd, 2011)
Characteristics of Industrial strength software.

The main conclusions by the Authors are summarized, and a little edited below for the laziest.

" … It is important to design a ... software to be easy to use and robust. Often it is better to assume that the user is not an expert in … algorithms, but someone who has a problem to solve and wishes to solve it accurately and efficiently with minimal effort. After all, even experienced users were once novices and a user’s initial experiences of using a solver are likely to determine whether he or she goes on to become an expert user. Based on our experiences …., in addition to the requirements of good performance (in terms of memory and speed) and the availability of comprehensive well-written documentation, in our opinion the following features characterize an ideal …. solver.

• Simplicity: the interface should be simple and enable the user to be shielded from algorithmic details (note: this is called in OO information hiding). The code should be easy to build and install, with no compiler warning messages. During the building of the software from supplied source, minimum effort and intervention by the user should be required. …. dynamic memory allocation should be used so that the user need not preallocate memory. In fact, the software developer needs very good reasons for not selecting a language that includes dynamic memory allocation.

The software developer should consider providing interfaces to popular high-level programming environments, such as Matlab, Mathematica, and Maple (note: and I add R, because Open Source is an add value.. Besides offering an appropriate interface is also behind the whole JGrass Project).

• Clarity: …. Furthermore, to allow repeated solves and iterative refinement there should be a clear distinction between (note by RR:) preprocessing and solve phases. … Developers should consider offering simple (all-in-one) interface as well as an interface with the greater flexibility of access to the different phases of modeling.

• Smartness: good choices for the default parameters and of the algorithms to be used should be automatically made without the user having to understand the algorithms and to read a large amount of detailed technical documentation. There should be an option to check the user-supplied input data, particularly for any assumptions that the code relies on. (Note by RR:) Parameters of the models should be as much as possible explained in documentation and code.

• Flexibility: for more experienced users and those with specific applications in mind, the solver should offer a wide range of options, ….. There should also be options for the user to specify the information that he or she requires …. The software should …. support 64-bit architectures, (note by RR) and be platform independent.

• Persistence: the solver should be able to recover from failure. For example, if it is found that there is not enough memory, a code that contains both in-core and out-of-core algorithms should automatically switch to out-of-core mode. Reverse communication should be designed to allow corrections to the input data.

• Threadsafety: The code should be threadsafe to enable the user to safely run multiple instances of the package simultaneously in different threads or on different processors.