Blog Archives

R Package for Hierarchical Bayesian species distribution models now available

December 6, 2012
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 hSDM: hierarchical Bayesian species distribution models Ghislain Vieilledent, Andrew M. Latimer, Alan E. Gelfand, Cory Merow, Adam M. Wilson, Frederic Mortier and John A. Silander Jr hSDM is an R package for estimating parameters of hierarchic...

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Speeding up R with Intel’s Math Kernel Library (MKL)

May 2, 2012
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I did some comparisons of the generic BLAS with Intel's MKL (both sequential and parallel) on a Dell PowerEdge 610 server with dual hyperthreading 6-core 3.06GHz Xeon X5675 processors.  Here are the results from an R benchmarking script (Normal R indicates the generic BLAS,  sMKL is the sequential (single core Intel MKL, and pMKL is the parallel Intel MKL using...

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Speeding up R with Intel’s Math Kernel Library (MKL)

May 2, 2012
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Speeding up R with Intel’s Math Kernel Library (MKL)

I did some comparisons of the generic BLAS with Intel's MKL (both sequential and parallel) on a Dell PowerEdge 610 server with dual hyperthreading 6-core 3.06GHz Xeon X5675 processors.  Here are the results from an R benchmarking script (Normal R ...

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Installing R’s maps package on Ubuntu

April 16, 2012
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I recently ran into trouble trying to install the R maps package on Ubuntu 10.04.  Here's the error I was getting: ** arch - gcc -std=gnu99 -O3 -pipe  -g    Gmake.c   -o GmakeGmake.c: In function ‘get_lh’:Gmake.c:111: warning: cast from pointer to integer of different sizeGmake.c:113: warning: cast from pointer to integer of different sizeGmake.c: In function ‘main’:Gmake.c:211: warning: cast from...

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Installing R’s maps package on Ubuntu

April 16, 2012
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Installing R’s maps package on Ubuntu

I recently ran into trouble trying to install the R maps package on Ubuntu 10.04.  Here's the error I was getting: ** arch - gcc -std=gnu99 -O3 -pipe  -g    Gmake.c   -o GmakeGmake.c: In function ‘get_lh’:Gmake.c:...

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Slow R graphics via SSH

March 30, 2012
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Slow R graphics via SSH

I do most of my R work on a server via SSH.  Viewing graphics (i.e. plot()) can be excruciatingly slow through the SSH pipe, but it's easy to make it fast.  Simply run:        X11.options(type="Xlib")once in the R session....

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Slow R graphics via SSH

March 30, 2012
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I do most of my R work on a server via SSH.  Viewing graphics (i.e. plot()) can be excruciatingly slow through the SSH pipe, but it's easy to make it fast.  Simply run:        X11.options(type="Xlib")once in the R session.  Tags: linuxgraphicsR

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Copy all the files in a directory to a new directory using R

October 27, 2011
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Someone asked me how to move a directory full of files from one place to another using R.  The easiest way I've found is as follows (where "oldpath" is the existing directory and "newpath" is the new directory):file.copy(list.files(oldpath),newpath) Tags: R

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Copy all the files in a directory to a new directory using R

October 27, 2011
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Copy all the files in a directory to a new directory using R

Someone asked me how to move a directory full of files from one place to another using R.  The easiest way I've found is as follows (where "oldpath" is the existing directory and "newpath" is the new directory):file.copy(list.files(oldpath),newpath)

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Extracting reflectance data from SpectraSuite JCAMP files in R

May 6, 2011
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Extracting reflectance data from SpectraSuite JCAMP files in R

I've been using an OceanOptics USB4000 spectrometer in research on biomass accumulation and climate in South Africa.This post presents a R function that will read in JCAMP files from the SpectraSuite software and output a vector of reflectance values.&...

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