Re: A new R package for soils investigations, and some ideas [Dec 2012 updates]

[Dylan Beaudette]

Greetings,

This is a quick follow-up to an email that I sent out 2 years ago on
the topic of a new R package for quantitative soils analysis. I am
happy to announce that the 'aqp' package has now been through rigorous
testing over the last 2 years, and put into production work within
several academic circles and government agencies. The stable version
is available on CRAN [1] and the development version is available on
R-Forge [2]. The details of several components of the packages are
described in detail as part of this recent paper [3]. All functions,
classes (S4), and sample datasets are documented within the package
manual pages. Further examples and tutorials can be found on the
R-Forge site [2].

Links:
1. http://cran.at.r-project.org/web/packages/aqp/index.html
2. http://aqp.r-forge.r-project.org/
3. http://dx.doi.org/10.1016/j.cageo.2012.10.020

Since the last email a stable concept and implementation of a
soils-specific data structure has been integrated into the 'aqp'
package. Largely through the work of Pierre Roudier, the
'SoilProfileCollection' class was defined to accommodate the complex
hierarchy of common soil databases. This is still a work in progress,
so please feel free to comment on, or suggest improvements or
bug-fixes.

Cheers,
Dylan


--
Dylan E. Beaudette
USDA-NRCS Soil Scientist
California Soil Resource Lab
http://casoilresource.lawr.ucdavis.edu/



On Thu, Jul 8, 2010 at 11:58 AM, Dylan Beaudette
<debea...@ucdavis.edu> wrote:
> Greetings,
>
> I would like to announce a project that may be of interest to the
> Pedometrics / DSM groups. The Algorithms for Quantitative Pedology (AQP)
> project was started as a place to put some of the functions I used on a daily
> basis. It slowly grew into a collection of algorithms that support studies
> related to soil genesis, taxonomy, and mapping. The short list of
> functionality includes:
>
> - classes for storing and manipulating soil profile data
> - functions for plotting soil profile sketches
> - color conversion functions (Munsell to RGB)
> - plotting functions for groups of soil profiles
> - plotting functions for depth-functions + uncertainty estimates
> - functions for re-sampling genetic horizons to regular sequences
> - profile aggregation functions
> - an implementation of between-profile dissimilarity calculation
> - functions for re-sampling XRD patterns to a common basis
> - functions for performing full-pattern matching of XRD patterns
>
> Obviously, this project is far from an exhaustive implementation of what the
> name might otherwise suggest. In addition,
>
> My reasoning for putting this package together is based on the premise that
> methods used by pedologists have grown with our understanding of natural
> systems and our ability to work with larger and larger datasets-- however,
> coupling of theory and practice to modern numerical methods is rare outside
> of academic circles. That is not to say that federal agencies and the soil
> science community are not catching up. Rather, it seems like the adoption of
> these new approaches can by hindered by a lack of an implementation that is
> more accessible than an article in a scientific journal. I am speaking from
> my experience in the western United States, therefore I apologies if I have
> not adequately described corresponding conditions in other parts of the
> world.
>
> The naming of the package. It is currently named "Algorithms for Quantitative
> Pedology", inspired by Jenny's treatise on the topic. It could be argued that
> most modern pedologic studies (i.e. on the topic of soil genesis, morphology,
> classification, and mapping) are by and large a quantitative effort-- so this
> name may be more of a convenient acronym than descriptive label. In naming
> this package I was hoping to encapsulate the idea of how modern numerical
> methods might be applied to the field of pedology. Well, the
> word "Pedometrics" does a pretty good job of conveying that idea. In
> particular, it falls well in line with Alex's initial description of
> Pedometrics:
>
> “the application of mathematical and statistical methods for the study of the
> distribution and genesis of soils.”
>
> On the other hand, the potential for a diffuse interpretation of the
> word "Pedometrics" could lead to a package that lacks focus and ultimately
> critical mass. In that case, an entire suite of related R packages would
> likely work. There are several cases on CRAN / R-Forge where large efforts
> are split into several, related packages. In addition, the term 'Pedometrics'
> means many different things to many different people.
>
> I would like to present a couple ideas on how this project, and extensions of
> it, might function as a liaison between rapid advances in the realm of
> Pedometrics and those interested in the application of these methods.
>
> 1. R is an ideal environment for working with soils information and the
> packaging system is a robust approach to encapsulating code, documentation,
> and discussion.
>
> 2. A suite of R packages, each geared towards a specific realm of what most
> soil scientists do (or would like to do) with their data, may be one way in
> which common work flows can be streamlined and better documented. These
> packages would be the vehicle by which theory, defined in academic journals,
> could be translated into well-documented tools for a wider range of
> practitioners.
>
> 3. Within this suite, a master package (why not call it "pedometrics") could
> contain classes and utility functions for describing and manipulating objects
> that represent the complex structure of a soil profile. The companion
> packages would build on these common data structures and methods, making the
> implementation of newly discovered or experimental methods much simpler.
>
> 4. The R-Forge system would facilitate concurrent access to the source code
> and documentation through the use of revision control. In this way, changes
> would be documented, and versions could be seamlessly forked or merged so
> that rapid development would not result in an unstable product.
>
>
> Ultimately, I am interested in getting modern tools into the hands of current
> pedologists, and making it simpler for the adoption of these tools by new
> pedologists. If you are interested in these efforts, have comments or
> criticisms please don't hesitate to contact me. There is a mini-manual with
> an extended discussion on the AQP package, included in the source. I would
> encourage anyone that is interested to check the R-Forge site:
>
> http://aqp.r-forge.r-project.org/
>
> A slightly older version is available on CRAN:
> http://cran.r-project.org/web/packages/aqp/
>
>
>
>
> Cheers,
> Dylan
>