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Are there any R-project packages that facilitate asynchronous network IO?
I'm think here along the lines of Ruby's Eventmachine or Python's Twisted.
If there are several such packages/libraries which is the best in terms of:
- performance
- features
First of all, R is single-threaded, so typically people try to use parallel computing approaches (see, for instance, the snow package). I don't think there's anything quite like Eventmachine or Twisted.
Check out the following:
The "State of the Art in Parallel Computing with R" paper describes most of the approaches to parallel computing in R (http://www.jstatsoft.org/v31/i01/paper). There are many useful packages in the HighPerformanceComputing view: http://cran.r-project.org/web/views/HighPerformanceComputing.html.
Check out svSocket: http://cran.r-project.org/web/packages/svSocket/
You can try using NetWorkSpaces with R: http://cran.r-project.org/web/packages/nws/.
There are several examples of R servers. RServe: http://www.rforge.net/Rserve/
The iBrokers packages is one of the only ones that I know which uses asynchonous requests. Have a look at the source code for that package (you can download it off R-Forge) and the related vignette: http://cran.r-project.org/web/packages/IBrokers/vignettes/RealTime.pdf
The biocep project also includes many relevant features: http://biocep-distrib.r-forge.r-project.org/
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I am looking for an R implemention of the excellent Glicko-2 algorithm of Mark Glickman. Thusfar I found this one. Although this is a very nice piece of code I am particularly looking for a code that is able to deal with large data frames with match scores (meaning that it is capable of ranking all the players in the data frame in one go). A bit like the way the PlayerRatings package does the trick with e.g. Elo, Glicko. Unfortenately this package doesn't haven an implementation of the Glicko-2 algorithm.
Does anyone have an idea?
Glicko2 and few other algorithms are available in R package sport. Possible for two-player and multi-player matchups. Available on cran and github. Vignette included, standarized syntax, supported by C++.
Quick snippet
# install.packages("sport")
library(sport)
glicko2 <- glicko2_run(formula = rank|id ~ rider, data = gpheats)
# computation results
print(glicko2)
summary(glicko2)
tail(glicko2$r)
tail(glicko2$pairs)
If you had noticed the fine print at the bottom of Mark Glickman's page you would have seen (in tiny text admittedly)
PlayerRatings, an R package implementation of Glicko, as well as a
few other rating systems
with the link being: https://cran.r-project.org/web/packages/PlayerRatings/
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I'm trying use linear regression with elastic net penalties for a mixed model. In the past I have used the R glmnet package with the penalty.factors parameter to accomplish this, but R is no longer an option for my project. I have found several implementations of elastic net in different languages, but none which allow for different penalty factors for each feature the way that the R glmnet package does.
Does a true translation of the R glmnet function exist in any other language? Thanks!
EDIT: Note that the R code is actually a wrapper of the FORTRAN code written for the R package. A few other wrappers exist in other languages, but I am looking for an new implementation of the full algorithm, not just an alternative wrapper. I want to be able to edit the code a bit, but I am not at all familiar with FORTRAN.
I would have put this in comments if I had enough points, but there is an implementation in Matlab, written by a few members of the team that wrote the original glmnet package:
http://web.stanford.edu/~hastie/glmnet_matlab/
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I'm looking for an integration of ImageJ and R. There was a package called RImageJ as referenced in [1][2] for previous versions of R (I'm using R 3.1.2 (2014-10-31) -- "Pumpkin Helmet" ) but it isn't available anymore.
Basically what I'd like to try is a region growing algorithm over an image in R. Does anybody know about an updated version of RImageJ or another package allowing this algorithm?.
Thanks ;)
[1] http://romainfrancois.blog.free.fr/index.php?category/R-package/RImageJ
[2] http://cmci.embl.de/documents/101105ij_r_jython#using_imagej_from_r
The Bio7 project is a version of ImageJ which features integration with R, among other improvements.
It is also worth mentioning that the ImageJ2 project has a project under development called scripting-r, which seeks to provide a JSR-223-compliant scripting language built on top of RServe. However, it is not yet functional. Once it is, it will be possible to execute R code as a script from within ImageJ's Script Editor.
Edit 2016-09-26: As of this writing, the SciJava scripting-r project is now built on Renjin, an implementation of R on top of the JVM. Huzzah!
I've used the pixmap package to do image processing in the past, but it's pretty bare-bones. It might also be worth looking into the package geomorph.
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I just searched on google and r-project.org but couldn't find anything.
Is there a package in R for statistical relational learning?
Link to wikipedia:
http://en.wikipedia.org/wiki/Statistical_relational_learning
Yes, there are quite a few actually.
On CRAN, look at the gRaphical Models Task View.
Under each header is a listing of R Packages subsumed under that subject header--the first being Representation, manipulation and display of graphs.
Scroll down this page to the last three section headers:
Miscellaneous: Model search, specialized types of models etc.,
Bayesian Networks/Probabilistic expert systems; and
BUGS models, just below it.
Under these three headers are a total of 16 R Packages (seven, three and six packages, respectively). Within these nine, you should have no trouble finding a couple most suited for your project.
The only one I have personally used is bnlearn, a Package for Bayesian network structure learning. This is not my field, so I recall that the Package documentation (Manual and Vignette) are excellent and include working code examples.
Finally, for visualizing these models, I recommend highly the R bindings to the excellent Graphviz Library; the R bindings are gathered in the R Package, RGraphviz. RGraphviz is not available on CRAN but rather on Bioconductor; it depends on GraphViz.
Not yet, actually. Doug's answer is inherently misleading. If someone's looking for non-R implementation of the requested models, I may provide this link.
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I'm interesting in evolutionary algorithms. I have tested genetic algorithms with R but has someone tried with genetic programming? Do you know, if there are code somewhere written in R.
I'm not aware of anything on CRAN for genetic programming in particular, although there is some work being done on the problem. In particular, have a look at the RGP package that is still in development.
Otherwise, have a look at the RFreak package, which is a wrapper for the "Free Evolutionary Algorithm Kit".
You might want to have a look at genalg, at GA and at galgo
There is a new package available:gramEvol: Grammatical Evolution for R
A native R implementation of grammatical evolution (GE). GE
facilitates the discovery of programs that can achieve a desired goal.
This is done by performing an evolutionary optimisation over a
population of R expressions generated via a user-defined context-free
grammar (CFG) and cost function.
You can find the vignette here:Grammatical Evolution: A Tutorial using gramEvol
UPDATE: I posted an article on my blog about it:
Symbolic Regression, Genetic Programming… or if Kepler had R.