Re: [julia-users] Updated performance tips?

2016-11-23 Thread Douglas Bates
On Tuesday, November 22, 2016 at 1:12:26 PM UTC-6, Harish Kumar wrote: > I found the cause for this ... When i run julia 0.3.2 or 0.5 as standalone > (mix model) it uses all the available cores from my server, so it was fast. Fitting a linear mixed effects model only uses multiple threads for

[julia-users] Re: Unusual amount of storage allocation

2016-11-01 Thread Douglas Bates
I moved this discussion to https://discourse.julialang.org where it is easier to format the code chunks. On Monday, October 31, 2016 at 2:04:02 PM UTC-5, Douglas Bates wrote: > > I am encountering an unexpected amount of storage allocation in the > cfactor!{A::HBlkDia

[julia-users] Unusual amount of storage allocation

2016-10-31 Thread Douglas Bates
I am encountering an unexpected amount of storage allocation in the cfactor!{A::HBlkDiag) method in the MixedModels package. See https://github.com/dmbates/MixedModels.jl/blob/master/src/cfactor.jl for the code. An HBlkDiag matrix is a homogeneous block diagonal matrix where "homogeneous"

[julia-users] Re: ArrayFire.jl - GPU Programming in Julia

2016-08-27 Thread Douglas Bates
On Friday, August 26, 2016 at 6:08:13 PM UTC-5, Min-Woong Sohn wrote: > > Does anybody know of any plan to support ArrayFire in GLM or MixedModels > any time soon? > Do you have a particular application in mind or is this a general question? For MixedModels I would say that, depending upon the

[julia-users] Re: polynomial terms in formula specification

2016-06-25 Thread Douglas Bates
On Friday, June 24, 2016 at 8:39:09 AM UTC-4, Michael Borregaard wrote: > > Sorry for asking a question that should be super-basic, but I have looked > all over the internet for this for an hour now: How does one specify > polynomial terms in glm models? > > In R, I would: > > y ~ x + I(x^2) > >

[julia-users] [JuliaCon] Preferred wireless network?

2016-06-21 Thread Douglas Bates
I don't think there is a separate discussion forum for JuliaCon so I am posting here. I am using the eduroam network in the building and can't use the command line git - the connection times out. I remember this happening a couple of years ago too. It is recommended to use the MIT-Guest

Re: [julia-users] Re: Is passing a function as an argument discouraged?

2016-06-17 Thread Douglas Bates
ote: > >> Specialization of higher-order functions should be much improved in Julia >> 0.5. >> >> On Friday, June 17, 2016 at 1:10:24 PM UTC-7, Douglas Bates wrote: >>> >>> I am writing a simulation function that loops over simulating a data set >

[julia-users] Is passing a function as an argument discouraged?

2016-06-17 Thread Douglas Bates
I am writing a simulation function that loops over simulating a data set and fitting multiple statistical models to the data. The exact form of the output will depend on which characteristics of the fitted models I wish to preserve. My inclination is to pass a callback function to take the

Re: [julia-users] Capture output from a shell command

2016-05-18 Thread Douglas Bates
is is `readstring(`wc -l ratings.dat`)` on 0.5) > > -Jacob > > > On Wed, May 18, 2016 at 11:43 AM, Douglas Bates <dmb...@gmail.com > > wrote: > >> I have forgotten how to capture the output from a shell command. The >> background is that the `wc` program

[julia-users] Capture output from a shell command

2016-05-18 Thread Douglas Bates
I have forgotten how to capture the output from a shell command. The background is that the `wc` program on Linux (and, I assume, OS X) is an incredibly fast way to count the number of lines in a data file, as in julia> run(`wc -l ratings.dat`) 1000209 ratings.dat I want to capture that

[julia-users] Re: Pulling out residuals and fitted values from lmm in MixedModels

2016-04-07 Thread Douglas Bates
On Wednesday, April 6, 2016 at 6:05:04 PM UTC-5, Christina Castellani wrote: > > I am having difficulty figuring out how to pull out the residuals and > fitted values from the result of an lmm in Julia using the package > MixedModels.jl > > In R I would use "residuals(m)" or "fitted(m)", where m

Re: [julia-users] Tools for creating presentation slides with Julia code?

2016-03-22 Thread Douglas Bates
notebook to incorporate both Julia and R cells in a notebook, unless I use the RCall package for Julia. But that solution doesn't highlight R code. On Tue, 2016-03-22 at 16:46, Douglas Bates <dmb...@gmail.com > > wrote: > > This issue comes up in various forms from time t

[julia-users] Tools for creating presentation slides with Julia code?

2016-03-22 Thread Douglas Bates
This issue comes up in various forms from time to time. I will be giving a presentation in a few days about mixed-effects models in R and Julia. If it was an R-only presentation I would probably use the the RStudio tools to create slides from .Rmd (R Markdown) sources. I would appreciate

[julia-users] Re: Understanding Dataframes

2016-03-19 Thread Douglas Bates
On Friday, March 18, 2016 at 10:49:37 AM UTC-5, Christina Castellani wrote: > > I apologize for the beginner nature of my question but I am not > understanding the file structure in Julia. > > I am wanting to run lmm on a very large file (47x2000), I would like > to run one lmm on each of

[julia-users] My test is not failing properly

2016-03-12 Thread Douglas Bates
I have been adding more tests to the MixedModels package and encountered a peculiar situation where, AFAICS, a test should produce one type of failure and it doesn't. It fails at a later point but I can't see how it gets there. To reproduce, check out a copy of the MixedModels master branch.

Re: [julia-users] Re: git help needed

2016-03-08 Thread Douglas Bates
On Tuesday, March 8, 2016 at 3:55:03 PM UTC-6, Andreas Noack wrote: > > No problem. When you have made a change like this, i.e. a hard reset or a > rebase and want to push the changes to an existing branch you'll have to > > git push --force origin glmms > > because git is trying to prevent you

[julia-users] Re: git help needed

2016-03-08 Thread Douglas Bates
els.jl/tree/anj/glmms where I've > made exactly these changes or I can open a PR with my version. > > On Tuesday, March 8, 2016 at 1:46:08 PM UTC-5, Douglas Bates wrote: >> >> Having looked closer (nothing like a public post to cause you to read >> again and discover yo

[julia-users] Re: git help needed

2016-03-08 Thread Douglas Bates
Having looked closer (nothing like a public post to cause you to read again and discover you were wrong) I see that I did change all those files in the glmms branch that Andreas changed in his pull request. I hadfixed the issue that Andreas addressed but in a different way and our changes

Re: [julia-users] Re: documentation suggestions

2016-02-12 Thread Douglas Bates
-finance-review.org/ > Editor and Publisher, FAMe, http://www.fame-jagazine.com/ > > On Thu, Feb 11, 2016 at 12:37 PM, Douglas Bates <dmb...@gmail.com > > wrote: > >> Hi Ivo, >> >> Good to hear from you. >> >> On Wednesday, February 10, 2016 at 9:58:37 AM

[julia-users] Re: looking for an equivalent function to "independence_test" in the R coin package

2016-02-12 Thread Douglas Bates
On Thursday, February 11, 2016 at 6:27:26 PM UTC-6, Albert Cardona wrote: > > The formula operator is there via the GLM package [1], but I can't find > the equivalent of the independent_test function [2]. > > [1] https://github.com/JuliaStats/GLM.jl > [2]

[julia-users] Re: documentation suggestions

2016-02-11 Thread Douglas Bates
Hi Ivo, Good to hear from you. On Wednesday, February 10, 2016 at 9:58:37 AM UTC-6, ivo welch wrote: > > > ladies and gents---I am not (yet) a julia user. > > may I suggest adding more examples into two places where julia users will > face starting hurdles? > > [1] the I/O docs of julia. like,

[julia-users] Re: Getting the last match for a regular expression in a string

2015-12-25 Thread Douglas Bates
ts" > "00xyz.ts" > > > Thank you. I was missing the fact that matchall existed. I had a suspicion that there was a function like that but I was unable to navigate the documentation to it. > > El jueves, 24 de diciembre de 2015, 12:30:52 (UTC-6), Douglas B

[julia-users] Getting the last match for a regular expression in a string

2015-12-24 Thread Douglas Bates
Short version: I have a string that contains several instances of names of the form 1.ts, 2.ts, , 00xyz.ts and I want to find the last match. That is, I want to find "00xyz.ts" or, alternatively, find all such names in sequence.. Longer version: These are file names of a series

[julia-users] Looking for a few good algorithms

2015-11-17 Thread Douglas Bates
The short version is: I have a sparse matrix A like julia> m1.R[1,2] 6040x3706 sparse matrix with 1000209 Float64 entries: [1 ,1] = 0.0874371 [6 ,1] = 0.0765784 [8 ,1] = 0.0558497 [9 ,1] = 0.0635299 [10 ,1] = 0.0333554

[julia-users] Re: Looking for a few good algorithms

2015-11-17 Thread Douglas Bates
More careful reading of the spmatmul function in base/sparse/linalg.jl provided a method directly downdates the dense square matrix C (i.e. does not form a sparse A'A then downdate) but I still need to form a transpose. If anyone knows of a fast way of forming A'A without creating the

Re: [julia-users] Got myself in another awkward git situation with Pkg.checkout

2015-10-23 Thread Douglas Bates
f so, the commit >> should be a few steps back in the reflog: `git reflog` >> >> On Fri, Oct 23, 2015 at 5:14 PM, Douglas Bates <dmb...@gmail.com >> > wrote: >> >>> I tagged a new release of one of my packages. Just to ensure that >>> everythi

[julia-users] communicating with a TcpSocket

2015-10-15 Thread Douglas Bates
I have a Tablo over-the-air video recorder (tablotv.com) which communicates via a TCP socket. I almost know enough to be able to write Julia code to communicate with it but not quite. For the sake of illustration let's assume that its IP address on my network is 192.168.1.87. It communicates

[julia-users] Re: C wrapper ReadStat : read files from Stata, SPSS and SAS.

2015-10-12 Thread Douglas Bates
On Monday, October 12, 2015 at 11:24:06 AM UTC-5, Matt wrote: > > ReadStat is an excellent C library by Evan Millers that allows to read > files from Stata, SPSS and SAS. > Evan wrote a wrapper for ReadStat in the Dataread.jl package > https://github.com/WizardMac/DataRead.jl > However, the

[julia-users] Is there a function in Base or Base.LinAlg that behaves like A_mul_B! with multipliers α and β?

2015-09-14 Thread Douglas Bates
I want to perform an operation like the BLAS.gemm! operation with multipliers α and β but for my own custom matrix type. The name gemm! is unsuitable because the ge part indicates general matrices. I can, of course, choose my own name for the generic but I thought I would ask if there was

[julia-users] Re: How to evaluate variable inside Formula type? (Linear Mixed Models)

2015-09-11 Thread Douglas Bates
On Friday, September 11, 2015 at 8:18:39 AM UTC-5, Megan Smith wrote: > > For a statistical analysis in genomics, I need to evaluate a linear mixed > effects model hundreds of thousands of times. I want to fit the model > > mod=fit(lmm(Y ~ X + (1|PatientID),Data)) > > repeatedly in a loop with

[julia-users] Sparse matrix with elements that are fixed-size dense matrices

2015-08-15 Thread Douglas Bates
I want to use sparse matrices in which the nonzeros are fixed-sized dense matrices. The matrix is of size m*p by n*q with nz nonzero blocks, each of size p by q. Generally p and q are very small but m, n and nz can be large. In a CSC representation of such a matrix, A, the A.colptr and

[julia-users] Iterate over the possible values of an enum?

2015-07-31 Thread Douglas Bates
In a FLAC (as in Free Lossless Audio Codec) package for version 0.4 I used @enum to create a type to pass to calls to the C library libflac. Metadata for a flac stream object. Used in both encoding and decoding of a stream. Each type of metadata object contains an indicator of its `typ`, an

[julia-users] Re: Iterate over the possible values of an enum?

2015-07-31 Thread Douglas Bates
To answer my own question for typ in instances(MetadataType) ... end On Friday, July 31, 2015 at 9:41:13 AM UTC-5, Douglas Bates wrote: In a FLAC (as in Free Lossless Audio Codec) package for version 0.4 I used @enum to create a type to pass to calls to the C library libflac. Metadata

[julia-users] Re: [Slightly OT] Creating JuliaCon presentation slides as a Jupyter notebook

2015-06-22 Thread Douglas Bates
Thanks for the suggestion, David. I am using RISE. On Monday, June 22, 2015 at 10:08:08 AM UTC-5, David P. Sanders wrote: El jueves, 4 de junio de 2015, 9:49:15 (UTC-5), Douglas Bates escribió: The JuliaCon2015 organizers have suggested preparing conference proceedings in the form

[julia-users] Unexpected bottleneck in v0.4-dev sub() call

2015-06-21 Thread Douglas Bates
After profiling some code that I will discuss in a lightning talk at JuliaCon I found a bottleneck in an unexpected place. (I guess I should know by now that profiling always shows that the bottleneck is in an unexpected place - that's why we do it.) I have a matrix of matrices, some of which

[julia-users] [Slightly OT] Creating JuliaCon presentation slides as a Jupyter notebook

2015-06-04 Thread Douglas Bates
The JuliaCon2015 organizers have suggested preparing conference proceedings in the form of Jupyter notebooks, which I think is a great idea. I have considered going further and preparing presentation slides using Jupyter. I know this can be done but many of the search engine hits on the topic

[julia-users] Determine if an array is memory-mapped?

2015-05-13 Thread Douglas Bates
Is there a way to determine if an array is memory-mapped? I know that if the file was opened read-only then trying to write to the array throws an error but that seems a rather heavy-handed approach. Perhaps this is not possible because the memory-mapped file behaves just like a chunk of

[julia-users] Re: how to compute the maximum value of an object's attribute

2015-05-07 Thread Douglas Bates
On Thursday, May 7, 2015 at 11:55:59 AM UTC-5, Kristoffer Carlsson wrote: Boring but non allocating like list comprehension and anonymous function: m = typemin(Int16) for TUnit in TUnitS m = max(m,TUnit.tau_max) end Even more compact is to use a function as the first argument to

[julia-users] Re: Does sizehint! make sense for sparse matrices?

2015-02-24 Thread Douglas Bates
On Tuesday, February 24, 2015 at 3:47:12 PM UTC-6, Seth wrote: I was surprised to find that there is no method on sizehint! for sparse matrices: ERROR: MethodError: `sizehint!` has no method matching sizehint!(::Base. SparseMatrix.SparseMatrixCSC{Int64,Int64}, ::Int64) Is this

Re: [julia-users] Linked list. Julia -- C

2015-02-16 Thread Douglas Bates
On Monday, February 16, 2015 at 10:30:36 AM UTC-6, Jameson wrote: Gtk.jl has a rather substantial example (I think it's in src/GLib/glists.jl, but I'm on an iPhone) If Fermat were alive today his famous enigmatic note would be I have discovered a wonderful proof of this but I'm on an

[julia-users] Re: why does findn for sparse matrices check for nzval != 0?

2015-02-13 Thread Douglas Bates
On Thursday, February 12, 2015 at 10:03:04 PM UTC-6, Zouhair Mahboubi wrote: I'm trying to find the column indices of non-zero elements of a given row in a sparse matrix A I figured using findn would be a fast way to do that, but I was curious to see how the implementation was done since

[julia-users] exemplar package for 0.4-style documentation

2015-01-13 Thread Douglas Bates
I'm having difficulty navigating my way around documentation standards for v0.4-, and whether the Docile or Lexicon or Markdown packages are needed. What would be a good package to study to see how @doc, etc. should be used?

Re: [julia-users] exemplar package for 0.4-style documentation

2015-01-13 Thread Douglas Bates
/CSVReaders.jl * https://tshort.github.io/Sims.jl/ In Sims.jl, I used Mkdocs (mkdocs.org) along with Docile/Lexicon to create that documentation site. On Tue, Jan 13, 2015 at 4:59 PM, Douglas Bates dmb...@gmail.com javascript: wrote: I'm having difficulty navigating my way around

[julia-users] in-place substitution for an array?

2015-01-12 Thread Douglas Bates
This is trivial to write myself but I wanted to check that I am not missing an already-defined function. I need to scan an Int32 array replacing all instances of typemin(Int32), which is the missing value sentinel used by R, with zero(Int32). Is such substitution implemented by a function in

Re: [julia-users] Re: flip sparse matrices slow

2015-01-07 Thread Douglas Bates
On Wednesday, January 7, 2015 1:48:31 PM UTC-6, Christoph Ortner wrote: Thanks for your replies - I will write a short piece of code that shows the performance problem, and then submit an issue. Christoph P.S: I do use sparse(I,J,V) to construct the matrix, but I am then unable to

[julia-users] Re: Package name for embedding R within Julia

2015-01-06 Thread Douglas Bates
. Please let me know how I could be helping in the development of the package. Best Randy On Friday, January 2, 2015 11:59:04 AM UTC-8, Douglas Bates wrote: For many statistics-oriented Julia users there is a great advantage in being able to piggy-back on R development and to use at least

Re: [julia-users] Re: Package name for embedding R within Julia

2015-01-06 Thread Douglas Bates
issue. // T On Monday, January 5, 2015 10:50:04 PM UTC+1, Douglas Bates wrote: The (unregistered) [RCall](https://github.com/JuliaStats/RCall.jl) package is an initial cut at the interface. I am not happy with all the names that I chose and welcome suggestions of improvements. For some

Re: [julia-users] Re: Package name for embedding R within Julia

2015-01-05 Thread Douglas Bates
...@iastate.edu wrote: That sounds great! Rcall.jl or RCall.jl are fine names; RStats.jl may be slightly more search-friendly for people coming from R, since they may not know about PyCall. On Friday, January 2, 2015 1:59:04 PM UTC-6, Douglas Bates wrote: For many statistics-oriented Julia

[julia-users] Package name for embedding R within Julia

2015-01-02 Thread Douglas Bates
For many statistics-oriented Julia users there is a great advantage in being able to piggy-back on R development and to use at least the data sets from R packages. Hence the RDatasets package and the read_rda function in the DataFrames package for reading saved R data. Over the last couple of

Re: [julia-users] Re: Package name for embedding R within Julia

2015-01-02 Thread Douglas Bates
and recipient of the derived work without a valid license for the GPL code, leaving them open to legal action by the copyright holders of the GPL code. On Fri, Jan 2, 2015 at 4:54 PM, Simon Kornblith si...@simonster.com javascript: wrote: On Friday, January 2, 2015 2:59:04 PM UTC-5, Douglas

[julia-users] Re: JULIA code performance help

2014-12-24 Thread Douglas Bates
Type consistency will help. R has the unusual convention that 0 is a floating-point constant. In Julia 0 is an integer. Use '0.0' for a floating point value in places like if R = r0 F0 = log10(r0/R) else F0 = 0 end which could be rewritten F0 = R = r0 ? log10(r0/R) : 0.0 Then

[julia-users] R version of microbenchmarks

2014-12-19 Thread Douglas Bates
Perhaps the R version of the microbenchmarks could be run on Revolution R Open, http://mran.revolutionanalytics.com/download/. The major difference between RRO and other versions is that RRO incorporates MKL. For one or two of the benchmarks this could make a difference. By the way, I was

[julia-users] Packages for handling pedigrees?

2014-12-16 Thread Douglas Bates
Is anyone working on a Julia package or packages to work with pedigrees, in the sense used in animal breeding? Ana Vazquez and I are developing such a package which we plan to call Pedigrees. Its principle type will be Pedigree, which is constructed from two Integer vectors representing the

[julia-users] Re: Packages for handling pedigrees?

2014-12-16 Thread Douglas Bates
the recommended Matrix package for R that Martin Mӓchler and I wrote). I have the suspicion that the ideas are the same, it's just the names that are different. On Tuesday, December 16, 2014 10:03:06 AM UTC-7, Douglas Bates wrote: Is anyone working on a Julia package or packages to work with pedigrees

[julia-users] Is there a function that performs (1:length(v))[v] for v a Vector{Bool} or a BitArray?

2014-12-11 Thread Douglas Bates
I realize it would be a one-liner to write one but, in the interests of not reinventing the wheel, I wanted to ask if I had missed a function that does this. In R there is such a function called which but that name is already taken in Julia for something else.

Re: [julia-users] Is there a function that performs (1:length(v))[v] for v a Vector{Bool} or a BitArray?

2014-12-11 Thread Douglas Bates
On Thursday, December 11, 2014 3:21:07 PM UTC-6, John Myles White wrote: Does find() work? Yes. Thanks. -- John On Dec 11, 2014, at 4:19 PM, Douglas Bates dmb...@gmail.com javascript: wrote: I realize it would be a one-liner to write one but, in the interests

[julia-users] SharedArray from a memory-mapped array

2014-12-06 Thread Douglas Bates
If I have a memory-mapped array, say an uncompressed dataset in a HDF5 file, can I convert it to a SharedArray directly? From my, admittedly inexpert, reading of base/sharedarray.jl it seems that a SharedArray will end up being memory-mapped. Is there a way to avoid creating a new

[julia-users] Decreasing rate of return on number of blas threads

2014-12-04 Thread Douglas Bates
I have been working on a package https://github.com/dmbates/ParalllelGLM.jl and noticed some peculiarities in the timings on a couple of shared-memory servers, each with 32 cores. In particular changing from 16 workers to 32 workers actually slowed down the fitting process. So I decided to

Re: [julia-users] Decreasing rate of return on number of blas threads

2014-12-04 Thread Douglas Bates
On Thursday, December 4, 2014 1:50:06 PM UTC-6, Viral Shah wrote: On 05-Dec-2014, at 1:16 am, Douglas Bates dmb...@gmail.com javascript: wrote: Thanks, I'll try that. I'm still curious as to why there is so little difference between 8 and 16 threads. peakflops() just performs

Re: [julia-users] Decreasing rate of return on number of blas threads

2014-12-04 Thread Douglas Bates
}: 1.65354e11 1.7099e11 1.70911e11 1.71407e11 1.71238e11 1.70983e11 On Dec 4, 2014, at 3:24 PM, Viral Shah vi...@mayin.org javascript: wrote: On 05-Dec-2014, at 1:32 am, Douglas Bates dmb...@gmail.com javascript: wrote: On Thursday, December 4, 2014 1:50:06 PM UTC-6

Re: [julia-users] Decreasing rate of return on number of blas threads

2014-12-04 Thread Douglas Bates
. That helps to explain a lot. On Thursday, December 4, 2014 11:13:38 PM UTC+2, Douglas Bates wrote: On Thursday, December 4, 2014 2:32:01 PM UTC-6, Stefan Karpinski wrote: Hyperthreading? Of the threshold is 16 but you're really only getting 8 cores, you might only get scaling up to 8

Re: [julia-users] SymTridiagonal

2014-11-17 Thread Douglas Bates
On Monday, November 17, 2014 12:02:07 PM UTC-6, Eka Palamadai wrote: I don't know what matlab does. As a user, ones(n,1) and ones(n) both return me a vector, and it is confusing to find that ones(n,1) != ones(n). As Andreas and Tim have tried to say, your claim that ones(n,1) and

[julia-users] Re: Experience with PythonTeX and usefamily=jl

2014-11-12 Thread Douglas Bates
On Tuesday, November 11, 2014 5:16:35 PM UTC-6, Douglas Bates wrote: PythonTeX (https://github.com/gpoore/pythontex) now supports Julia with the package option usefamily=jl or usefamily={julia,jl} I am still flailing around trying to get both the expression that is evaluated and its

Re: [julia-users] Help optimizing sparse matrix code

2014-11-12 Thread Douglas Bates
Also, there is a disadvantage in leaning too hard on CHOLMOD or UMFPACK or CSparse code in that the licenses are GPL or LGPL. The goal is eventually to eliminate those dependencies. On Wednesday, November 12, 2014 2:37:28 PM UTC-6, Tony Kelman wrote: Virtually all operations on sparse

[julia-users] Experience with PythonTeX and usefamily=jl

2014-11-11 Thread Douglas Bates
PythonTeX (https://github.com/gpoore/pythontex) now supports Julia with the package option usefamily=jl or usefamily={julia,jl} I am still flailing around trying to get both the expression that is evaluated and its value shown in the compiled LaTeX document. Does anyone have experience

Re: [julia-users] Compressing .jld files

2014-11-10 Thread Douglas Bates
On Monday, November 10, 2014 12:55:24 PM UTC-6, Steven G. Johnson wrote: On Tuesday, September 2, 2014 3:58:25 PM UTC-4, Jake Bolewski wrote: It would be best to incorporate it into the HDF5 package. A julia package would be useful if you wanted to do the same sort of compression on

[julia-users] Re: row-wise dot product

2014-11-06 Thread Douglas Bates
On Thursday, November 6, 2014 9:14:10 AM UTC-6, Sebastian Good wrote: Working through the excellent coursera machine-learning course, I found myself using the row-wise (axis-wise) dot product in Octave, but found there was no obvious equivalent in Julia. In Octave/Matlab, one can call

[julia-users] Re: row-wise dot product

2014-11-06 Thread Douglas Bates
. On Thursday, November 6, 2014 10:42:26 AM UTC-5, Douglas Bates wrote: On Thursday, November 6, 2014 9:14:10 AM UTC-6, Sebastian Good wrote: Working through the excellent coursera machine-learning course, I found myself using the row-wise (axis-wise) dot product in Octave, but found

Re: [julia-users] Re: row-wise dot product

2014-11-06 Thread Douglas Bates
Good* On Thu, Nov 6, 2014 at 1:10 PM, Douglas Bates dmb...@gmail.com javascript: wrote: On Thursday, November 6, 2014 10:48:26 AM UTC-6, Sebastian Good wrote: A good solution for this particular problem, though presumably uses more memory than a dedicated axis-aware dot product method

[julia-users] Re: installing julia stable on ubuntu 14.10?

2014-11-03 Thread Douglas Bates
Did you add the PPA for julia-deps in addition to juliareleases? Elliot has versions of dependencies that are compatible with the Julia packages. On Monday, November 3, 2014 11:20:53 AM UTC-6, a. kramer wrote: I recently upgraded to Xubuntu 14.10. On 14.04 I was using the PPA

[julia-users] Unexpected heavy memory allocation

2014-10-30 Thread Douglas Bates
I haven't finished with the notebook http://nbviewer.ipython.org/github/dmbates/JuliaWorkshop/blob/master/ParallelGLM.ipynb but, unfortunately, must turn my attention to something else. I'll get back to it tomorrow. In the meantime, if someone has a hint as to where the memory allocation is

[julia-users] julia version 0.4.0-dev+1249 throwing an error on ArrayViews

2014-10-23 Thread Douglas Bates
I think this is due to a recent change in 0.4.0. The declaration # use ContiguousView when contiguousness can be determined statically immutable ContiguousView{T,N,Arr:Array{T}} : ArrayView{T,N,N} arr::Arr offset::Int len::Int shp::NTuple{N,Int} end throws an ERROR: T not

[julia-users] Re: How can I get allocation information in Julia?

2014-10-22 Thread Douglas Bates
Those coming to Julia from languages like Python, R, Matlab/Octave, etc. have it ingrained in them to fear the loop and to perform loop-like calculations in verbose and convoluted ways. It is actually quite easy to do this calculation in Julia with very little storage allocation by writing

[julia-users] Re: Modified Gram-Schmidt: getting the best out of Julia

2014-10-21 Thread Douglas Bates
Also, in your Julia code you have used *nvars* without defining it. You probably intended n,nvars=size(X)

[julia-users] Re: How to get the p-value in GLM?

2014-10-14 Thread Douglas Bates
On Tuesday, October 14, 2014 6:57:57 AM UTC-5, David Gonzales wrote: The thing with julia is that most of the language is written in julia, so getting answers means just reading more julia code. So in GLM/src/lm.jl there is a function coeftable(..) that generates the above table. Taking the

[julia-users] Solving sparse triangular systems

2014-10-06 Thread Douglas Bates
Is there an existing method for solving sparse triangular systems - taking advantage of the sparseness and the triangularity? It seems that with the templated Triangular type taking the matrix type as well as the element type it should be straightforward to create a

Re: [julia-users] Solving sparse triangular systems

2014-10-06 Thread Douglas Bates
them somewhere but I was looking for such methods in the base/sparse directory instead of base/linalg. Med venlig hilsen Andreas Noack 2014-10-06 13:06 GMT-04:00 Douglas Bates dmb...@gmail.com javascript:: Is there an existing method for solving sparse triangular systems - taking advantage

[julia-users] Re: Why lufact() is faster than my code?

2014-09-26 Thread Douglas Bates
On Friday, September 26, 2014 2:50:51 AM UTC-5, Staro Pickle wrote: Thank you all. On Friday, September 26, 2014 2:50:56 AM UTC+8, Jason Riedy wrote: Others have given some reasons... If you want to see contortions that were (perhaps still are) necessary to be competitive, see:

Re: [julia-users] Moving/stepen average without loop ? Is posible ?any command ?

2014-09-18 Thread Douglas Bates
On Thursday, September 18, 2014 2:36:53 PM UTC-5, paul analyst wrote: No idea ? W dniu 2014-09-18 o 13:26, paul analyst pisze: I have a vector x = int (randbool (100)) a / how quickly (without the loop?) receive 10 vectors of length 10, in each field the average of the next 10 fields

Re: [julia-users] Matlab bench in Julia

2014-09-18 Thread Douglas Bates
Part of the problem is the definition of benchmark. If all you are doing is solving a linear system or evaluating a decomposition then you are just benchmarking the BLAS/LAPACK implementation. It doesn't really matter if user-facing language is Matlab or Octave or R or Julia. They are just a

[julia-users] Re: Trouble with `permute!`

2014-09-17 Thread Douglas Bates
On Wednesday, September 17, 2014 1:36:16 PM UTC-5, Douglas Bates wrote: On Wednesday, September 17, 2014 1:03:25 PM UTC-5, DumpsterDoofus wrote: I am having trouble with `permute!`, the in-place version of `permutedims`. I tried the following: A = rand(Float32, 20, 30, 40, 2); permute

Re: [julia-users] Comprehension Produces Any

2014-09-12 Thread Douglas Bates
On Friday, September 12, 2014 12:41:49 AM UTC-5, Christoph Ortner wrote: That did work - thank you, see code below. To explain: this came from a bottleneck in a bigger code, so my problem there must be a different one. -- Christoph function testtime() a1 = rand(10, 10, 100, 100)

[julia-users] Re: create a matrix dynamically with Julia

2014-09-11 Thread Douglas Bates
The short answer is vcat, as in julia A = Array(Int,(0,2)) 0x2 Array{Int64,2} julia vcat(A,[1,2]') 1x2 Array{Int64,2}: 1 2 Note that the ' is important as it cause the column vector [1,2] to be reshaped into a 1 by 2 matrix. You may find it more effective to create the columns separately

[julia-users] Re: self dot product of all columns in a matrix: Julia vs. Octave

2014-09-08 Thread Douglas Bates
On Monday, September 8, 2014 11:18:02 AM UTC-5, Jeff Waller wrote: On Monday, September 8, 2014 7:37:52 AM UTC-4, Mohammed El-Beltagy wrote: Octave seems to be doing a pretty good job for this type of calculation. If you want to squeeze a bit more performance out of Julia, you can try to

[julia-users] Compressing .jld files

2014-09-02 Thread Douglas Bates
Now that the JLD format can handle DataFrame objects I would like to switch from storing data sets in .RData format to .jld format. Datasets stored in .RData format are compressed after they are written. The default compression is gzip. Bzip2 and xz compression are also available. The

Re: [julia-users] Compressing .jld files

2014-09-02 Thread Douglas Bates
/fileexchange/39721-save-mat-files -more-quickly). But perhaps there's a good middle ground. It would take someone doing a little experimentation to see what the compromises are. --Tim On Tuesday, September 02, 2014 08:30:39 AM Douglas Bates wrote: Now that the JLD

Re: [julia-users] Has anyone successfully performed probit or logit regression in Julia?

2014-09-01 Thread Douglas Bates
On Monday, September 1, 2014 9:48:46 AM UTC-5, Bradley Setzler wrote: Thanks Taylor, added predict method to documentation. It may be useful to clarify the scale of the values returned by predict. Is it the scale of the linear predictor or the scale of the mean response? For the Normal

[julia-users] Re: reference for the Formula language used in MixedModels

2014-08-22 Thread Douglas Bates
, 2014 4:35:05 PM UTC-5, Douglas Bates wrote: On Thursday, August 21, 2014 4:20:46 PM UTC-5, Thomas Covert wrote: Is there a reference somewhere for the formula language specified in DataFrames and used in MixedModels? In particular, I'm confused about how fixed- and random-effects

[julia-users] Re: reference for the Formula language used in MixedModels

2014-08-21 Thread Douglas Bates
On Thursday, August 21, 2014 4:20:46 PM UTC-5, Thomas Covert wrote: Is there a reference somewhere for the formula language specified in DataFrames and used in MixedModels? In particular, I'm confused about how fixed- and random-effects are separately specified. For example, suppose I've

[julia-users] Is there a REPL shortcut for a subscript numeral?

2014-08-20 Thread Douglas Bates
I find it convenient to use identifiers like julia a₁ = 2 2 In the iESS emacs mode for a Julia session I can set the input-mode to TeX and type a_1 to create this identifier. Is there a key sequence in the REPL to create such an identifier?

Re: [julia-users] Is there a REPL shortcut for a subscript numeral?

2014-08-20 Thread Douglas Bates
On Wednesday, August 20, 2014 10:10:15 AM UTC-5, John Myles White wrote: Try typing the sequence \_1TAB Thanks.

[julia-users] table of UTF8 operator symbols

2014-08-14 Thread Douglas Bates
It may be due to a because it's there syndrome but I feel that code is easier to understand when I use ≠ instead of !=. Now I am trying to remember the UTF8 symbols and TeX-like names for == and ===. I know there is a table of these somewhere but perfunctory searches of

[julia-users] unsure about an error message from ccall

2014-08-14 Thread Douglas Bates
I'm getting an error from ccall when the first argument is a tuple of a symbol and a string. julia libwsmp /home/bates/.julia/v0.4/WSMP/deps/usr/lib/libwsmp julia ccall((:wkktord_,libwsmp),Void,(Ptr{Cint},Ptr{Cint},Ptr{Cint},Ptr{Cint},Ptr{Cint},

[julia-users] Re: unsure about an error message from ccall

2014-08-14 Thread Douglas Bates
On Thursday, August 14, 2014 2:06:06 PM UTC-5, Ivar Nesje wrote: Does it help to declare libwsmp as const? Now the problem seems to have cured itself. I'm not sure what I am doing differently.

[julia-users] Segfault when looking up a symbol in a dynamic library

2014-08-08 Thread Douglas Bates
I am experimenting with calling IBM's Watson Sparse Matrix Package (WSMP) from Julia. This is not Open Source software. It is shipped as a library. The evaluation version is a static library but the author was kind enough to send me a dynamic library for Linux. I was able to compile, link

[julia-users] Re: Segfault when looking up a symbol in a dynamic library

2014-08-08 Thread Douglas Bates
Strangely, I can get the symbol if I first get a handle with dlopen julia const libwsmp = Pkg.dir(MixedModels,deps, usr, lib, libwsmp64.so) /home/bates/.julia/v0.3/MixedModels/deps/usr/lib/libwsmp64.so julia tt = dlopen(libwsmp) Ptr{Void} @0x03488090 julia typeof(tt) Ptr{None} julia

[julia-users] Re: Segfault when looking up a symbol in a dynamic library

2014-08-08 Thread Douglas Bates
Now that I have read the documentation it is not really so strange because that docs say that the first argument should be a handle. So never mind.

Re: [julia-users] Re: emacs ess julia trouble

2014-08-02 Thread Douglas Bates
Yes.

[julia-users] Re: Julia equivalent of MATLAB colamd

2014-08-01 Thread Douglas Bates
and education. Regards, Don On Thursday, July 31, 2014 4:49:21 PM UTC-4, Douglas Bates wrote: Rats, I had a reply with code and examples then Google groups croaked and when it reloaded my draft reply was gone. On Thursday, July 31, 2014 2:13:36 PM UTC-5, Donald Lacombe wrote: Dear Doug

[julia-users] Re: JuliaLang questions posted on #StackOverflow by month from January 2012 to end of July 2014.

2014-08-01 Thread Douglas Bates
What are the lines on the plot? I am assuming that the magenta color is the raw counts and the green is some kind of smoothed values (moving averages?). On Friday, August 1, 2014 3:03:36 PM UTC-5, Stu Thompson wrote: Hi folks, I wanted to share a graph with everyone: JuliaLang questions

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