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Spencer Graves | 17 May 05:12

new version of fda fixes bug in pca.fd and supports library(Matrix)

Hello, All:

	  fda_2.2.8 (functional data analysis) is now available on CRAN.  This 
revision includes the following improvements:

		    1.  A bug in pca.fd has been fixed.

		    2.  Many functions have a new argument "returnMatrix", which if 
TRUE allows the function to use the sparse matrix representations in 
library(Matrix).  This should allow users to solve some larger problems 
and provides a speed advantage in a few cases.

		    3.  A few other minor bugs have been fixed including problems with 
some of the script files in system.files('scripts', package='fda').

	  A package using the returnMatrix argument will also need Matrix in 
the dependencies in DESCRIPTION and something like import(Matrix) in 
NAMESPACE.  Each use will require adding returnMatrix = TRUE to an 
appropriate fda function call.

       Best Wishes,
Jim Ramsay, Giles Hooker, Spencer Graves
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Justin Donaldson | 9 May 00:46
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ANN: bigml package for R bigml_0.1.tar.gz

The "bigml" package is an R wrapper for the BigML API:
https://bigml.com/developers

It contains straightforward methods for most of the relevant API end
points, as well as some fancier methods that allow for direct translations
from R dataframes directly into datasets appropriate for BigML.

Excerpt from an upcoming blog post, which describes the package in more
detail:

Today BigML releases the bigml package for R.  R is already well known for
> its capabilities in statistics and data analysis, and we use it internally
> for a number of different day-to-day tasks.  The bigml package enables the
> R community to easily take advantage of our highly scalable cloud based
> machine learning infrastructure, while using familiar R data structures and
> workflows.

Apologies for sending this e-mail a bit late.

Best,
-Justin

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Tobias Sing | 5 May 20:25
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ROCR source code now available on github

Dear all,

the commented source code for the ROCR package
(http://cran.r-project.org/web/packages/ROCR) is now available on
github -- feel free to fork, add improvements, and contribute back!
https://github.com/ipa-tys/ROCR

Kind regards,
  Tobias
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Yihui Xie | 2 May 23:31
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New version of the knitr package (0.5)

The knitr package version 0.5 is on CRAN now. It has gone through
extensive development in the past few months, and about 200 issues
were solved (https://github.com/yihui/knitr/issues) thanks to the
feedback of users, which greatly improved the quality and usefulness
of this package. For a complete list of changes, see
https://github.com/yihui/knitr/blob/master/NEWS

Most notable new features are:

- chunk options can be arbitrary valid R code, e.g. <<echo=!TRUE,
results=ifelse(x, 'asis', 'markup')>>=; this makes a document really
programmable, and the syntax is also consistent with normal R code;
http://yihui.name/knitr/demo/sweave/
- the listings package is supported via render_listings(), and the
styles are based on Sweavel.sty (courtesy of Frank Harrell);
http://yihui.name/knitr/demo/listings/
- for HTML/markdown documents, R plots can be automatically uploaded
to Imgur to make sure the output is self-contained (no need to copy
images when publishing the output);
http://yihui.name/knitr/demo/upload/
- arbitrary recursive references of code chunks with <<label>> (e.g.
chunk A can call chunk B which in turn calls C);
http://yihui.name/knitr/demo/reference/
- for cached chunks, their dependencies can be automatically figured
out by analyzing the R code for global and local variables (see the
'autodep' option)
- new chunk options fig.cap and fig.scap to create figure environments
with captions in LaTeX;
- Sweave concordance was implemented and integrated with RStudio so
that error navigation and PDF/Rnw sync become easy
(Continue reading)

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Michael Sweeting | 2 May 09:24
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bcrm package update

Dear all,

Version 0.3 of the bcrm package is now available on CRAN. The package 
allows users to fit Bayesian Continuous Reassessment Method Phase I 
trial designs. This version has the following new developments from 
version 0.1:

* Stopping rules have been added, allowing stopping to be based on a 
maximum sample size, the maximum number to be treated at the final MTD 
estimate, the precision of the MTD estimate, and a minumum sample size.
* Implementation of escalation based on posterior toxicity intervals 
using loss functions.
* Posterior summaries after each recruited cohort can now be plotted 
using the "each" argument of plot.bcrm.
* When simulating, operating characteristics are also now presented by 
true regions of toxicity risk.
* Simulations now run faster, as they use information from identical 
previous simulations to choose next dose. This is only implemented if 
nsims<=1000, otherwise the computation time to search previous 
simulations becomes unmanageable.
* Plot and print commands now refer to actual dose labels when they have 
been given by the user
* Output from simulations can now be plotted as histograms using the 
function plot.bcrm.sim

Best wishes
Mike

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Jon Clayden | 30 Apr 18:17
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New package for morphology and smoothing in any number of dimensions: mmand

Dear all,

I'm pleased to announce the release on CRAN of the "mmand" package
(for Mathematical Morphology in Any Number of Dimensions). It provides
functions for performing mathematical morphology (erode, dilate,
etc.), smoothing, and other kernel-based operations on array-like
objects of any dimensionality. The package is centred around a
flexible function called morph(), which can apply any kernel to array
elements, optionally conditioned on their value or number of nonzero
neighbours.

Operations such as erode and dilate are provided for 2D data by the
EBImage Bioconductor package, but mmand can be used for higher (and
lower!) dimensional data, can produce and apply anisotropic kernels,
and does not have external dependencies--except for the small, pure R
package "reportr" (also on CRAN), which is used for message reporting.

Owing to its more general, dimensionality-independent implementation,
mmand is a little slower than EBImage; but due to various performance
optimisations, run time is still very reasonable. For example:

> x <- EBImage::readImage(system.file("images", "shapes.png", package="EBImage"))
> k <- matrix(1,3,3)
>
> y1 <- EBImage::erode(x,k)
> y2 <- mmand::erode(x,k)
> identical(EBImage::imageData(y1),y2)
[1] TRUE
>
> system.time(for(i in 1:100) EBImage::closing(x,k))
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Neuwirth Erich | 30 Apr 09:07
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RExcelInstaller update

New version RExcel 3.2.7-1
Download wrapper for new version of RExcel.
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Barnet Wagman | 24 Apr 17:31

New version of rreval: Remote R Evaluator

rreval 1.1 is now available on CRAN.

This release fixes a Window specific bug. It is required for cloudRmpi 
1.1 (which is also now available on CRAN).

rreval is a means for using R on a remote system from within a local R 
session. Any R expression can be evaluated on the remote server. All 
non-graphical results are returned to the local R session: this includes 
the results of remote evaluations and (nearly) all textual output, 
including errors and warnings. rreval uses socket level communication 
via ssh port forwarding. It supports uploading and downloading R objects 
and scp file tranfers.

Cheers,

Barnet Wagman
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Carlos M. Martinez Manrique | 27 Apr 06:32
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New package TestSurvRec_1.01


Dear all, 

Recurrent events are common in many areas: psychology, engineering, medicine, physics, astronomy,
biology, economics and so on . 
Such events are very common in the real world: viral diseases, carcinogenic tumors, machinery and
equipment failures, births, murders, 
rain, industrial accidents, car accidents and so on . The availability of computerized tools for the
analysis is indispensable. 
The development of tools for the statistical analysis of recurrent events is relatively recent and is not
fully known. 
The purpose of this package is to present statistical tests for the analysis of recurrent event data. 

Now, a new package called “ TestSurvRec_1.01 ” is available. 

“ TestSurvRec_1.01 ” computes the p-values of tests to compare two survival curves of groups
with recurrent events. 

Function for plotting of survival curves [estimates by PHS, Peña et al. ( 2001 )] of the groups is also
available. 

The recurrent events of the units are plotted. Counting process are powerful tools in survival analysis. 
These processes consider two scale time, a calendar time scale and a gap time scale. 
This idea originated from Gill ( 1981 ) and has been extended in Peña et al. ( 2001 ). 
Martínez et. al ( 2009 ) published these weighted tests for survival analysis with recurrent events. 

Visit: http://cran.r-project. org/web/packages/TestSurvRec/ 

Regards,
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Adrian Duşa | 23 Apr 11:38
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new version of QCAGUI

Dear All,

I have just submitted a new version of the QCAGUI package on CRAN, it
should be propagated in a couple of days.
This version is nothing but a quick update to the latest Rcmdr base
package, and works (as usual) with the QCA package up to version 0.6-5

For the later versions of the QCA package, I will start adapting the
GUI in the shortest time possible.

Best wishes,
Adrian

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Romanian Social Data Archive
1, Schitu Magureanu Bd.
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Tel.:+40 21 3126618 \
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Fax: +40 21 3158391

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Mauricio Zambrano-Bigiarini | 18 Apr 10:12
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new package: hydroPSO 0.1-54-1

Dear R and hydrological/environmental community,

I would like to draw your attention to hydroPSO, a newly developed R 
package for the calibration/optimisation of (complex) environmental models.

hydroPSO implements a state-of-the-art Particle Swarm Optimisation (PSO) 
algorithm, which is a global optimisation technique with a surge of 
attention given its flexibility, ease of implementation and efficiency.

Key features of hydroPSO are:

1) Model-independent calibration engine
2) Minimal user intervention to define I/O functions for interfacing 
hydroPSO with the model code
3) Several fine-tuning options to customise the calibration engine (for 
advanced PSO users)
4) Sensitivity analysis included, using the Latin Hypercube 
One-factor-At-a-Time (LH-OAT)
5) Several functions for post-processing of the calibration results

hydroPSO is already available on CRAN:

http://cran.r-project.org/web/packages/hydroPSO/

you can install it with:

 > install.packages("hydroPSO")

This package includes a vignette (tutorial) showing how to calibrate 
SWAT-2005 (http://swatmodel.tamu.edu/software/swat-model/) and
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Gmane