+0
Phil Steitz wrote:
There have been no problems reported with math 1.1 RC4, other than some
small javadoc fixes, which have been applied to the release branch.
Assuming a positive vote, I will cut a new signed release, including
these fixes.
Release notes are here:
Ok, that means that the patches for Min and Max should be as follows:
For class Max:
public void increment(final double d)
{
if (!Double.isNaN(d))
value = (d value) ? d : value;
n++;
}
public double evaluate(final double[] values, final int begin,
Hi,
Would it be possible to add the method .getDataRef() to the interface
RealMatrix? This facilitates the usage of RealMatrix greatly.
Cheers,\
Kim
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Hi Phil and Al,
Thanks for the advise. I have digged through it, and the code seems fine
with many matrices.
Kim
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Ok, I think I have a bunch of classes available:
(- what it overrides)
DotProduct
Covariance (storeless)
CorrelationCoefficient (storeless)
abstract LinearRegression (storeless) - CC
LeastSqaresRegression (storeless) - linear
MajorAxisRegression (with correct R^2 (minimizing x AND y direction,
Hi All,
In the past, I have plugged the JAMA SVD class to the matrix class of
commons.math. I do now want to run a test in it, so, the questio
becomes, does someone has a known test case for me?
Cheers,
Kim
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In the past, I have made matrix based distance and special Matrices
classes that can be adapted to do just these things. It contains SSCP,
covariance and correlation matrices and rowbased Euclidian and Mahalanobis
distances. An idea?
Cheers,
Kim
John Gant said:
What exactly does column-wise
Ok, what the hell is an incubater project. I have integrated the
different decompositions already to the RealMatrix and they work fine.
So, just go ahead I would say.
kim
Mark Diggory wrote:
Even if we have to go through the incubator, I'm convinced that adding
the JAMA codebase into the math
I think it might be wise to use the JAMA implementation for this, they
are completly free of copyright and related stuff and they are easy
implemented (as I have done) in commons.math
Kim
Tzvika Barenholz wrote:
The formulas that you cite look correct mathematically, but
unfortunately not the
Phil Steitz wrote:
I agree with Kim that we can probably grab the QR decomp algorithm
from JAMA (have not looked recently, but I vaguely recall it being
there). I will work on making sure that this does not present any
copyright problems. Any suggestions / straw men for what the
interface
Just go ahead, no objections from me
Phil Steitz wrote:
I was about to close this vote as passed when I got a private email
indicating a small but functionally important bug, which I have now
fixed (PR #32531, ChiSquareTestImpl was incorrectly rejecting tables
containing 0's). Do we need to
+0 as I can not help not having any cvs system set up.
Cheers,
Kim
---
[ ] +1 I support this release and am willing to help
[ ] +0 I support this release but am unable to help
[ ] -0 I do not support this release
[ ] -1 I do not
Well, here is my +1!
Phil Steitz wrote:
This vote is to approve the public release of commons math 1.0-RC2. This
release candidate incorporates community feedback on RC1. Like RC1, this
will be a publicly announced RC to enable full feedback for a final
1.0 release in about two weeks if all is
+1 for after version 1.0
No issue wtith that. I think the whole
(miltiple)(non-linear)regression/ANOVA/GLM area needs to be dealt with
in a consistent manner, and that will ask a lot of work and thinking.
Cheers,
Kim
Phil Steitz wrote:
Kim van der Linde wrote:
Hi All,
I have made three
Hi All,
I have made three regression classes based on the Bivariateregression
class. The base class is an abstract LinearRegression class, with two
derived classes, LSRegression and RMARegression. Is there interest to
include these in the math package?
I have changed some things, such as
Hi,
Small question. Implementation like TTest, RealMatrix etc do have the
structure of an interface with an implementation. SimpleRegression does
not? Any particular reason?
Cheers,
Kim
--
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-
To
Phil Steitz wrote:
Frank,
After reading carefully again and thinking about some practical
examples, I agree that the current framework has a fundamental and
unecessary limitation. The point mass at 0, continuous beyond 0
example below does occur in practical applications (e.g. component
Phil Steitz wrote:
Good point. I am +0 for dropping ChiSquaredDistributionImpl, but -1 for
exponential (because of efficiency). Unless others object, I will make
that change. Thanks for pointing this out.
I do not mind HOW it is in the package, but I would argue against an
option where the
[EMAIL PROTECTED] wrote:
Hi
4. Since the chi-squared and exponential distributions are just special cases
of the gamma distribution, there is no need to have separate implementation
classes for these. In my opinion, one should avoid having multiple
implementations of the same distribution
I think I learned this morning the hard way of making test cases,
something I do often, but not always...
public static void main(String args[])
{
double[][] data = {{1, 2, 3, 4},
{1.5, 2.5, 3.5, 4.5},
{2, 4, 6, 8},
{4, 5, 6,
Hi Phil,
I discovered this morning that I messed up the bug fix, it just created
another. The correct code is here under:
RealMatrix getSubMatrix (int startRow, int endRow, int startColumn,
int endColumn)
/**
* Get a submatrix. Rows and columns are indicated
* counting from 0 to n-1.
*
Phil Steitz wrote:
I agree here as well. Do you see use cases where you will want to start
with a double[][] array, perform matrix operations on it (say some
decomposition) and then run stats on the resulting matrix? Will it be
too onerous to make copies of the double[][] at each stage? If
Ok, my question then becomes: why this structure?
Cheers,
Kim
Phil Steitz wrote:
Kim van der Linde wrote:
Hi All,
I have a question. All evaluate methods are non-static, but they do
not depend on information stored already in the class. That would
suggest for me to make them static So, I
Hi Phil,
As I do not have any CVS set up, so I do it this way:
4) Add the following new methods to both RealMatrix and BigMatrix
interfaces:
RealMatrix getSubMatrix (int startRow, int endRow, int startColumn,
int endColumn)
RealMatrix getSubMatrix (int[] rows, int[] columns)
RealMatrix
O, the code I gave in the bug-report contains a bug, the code I just
send has been tested in actuall applications.
Cheers,
Kim
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Hi Phil,
I have been thinking for a few days on the Matrix classes.
I think the Matrix class itself should contain all those methods that do
matrix calculations (add, subtract, multiply) that either a Matrix
themselfs or proporties of the Matrix (isSingular for example). The mean
methods
Hi Phil,
I guess my inclination at this point is to make the property
boolean-valued for Variance, StandardDeviation and omit it altogether
(for now) for Skewness and Kurtosis. Is everyone OK with this?
I can live with this. For the time being, I have no good examples in
which anything else than
Kim van der Linde wrote:
Mark R. Diggory wrote:
This is the sort of thing that defeats the purpose of having the
RealMatrix package. Such computations could be used to abuse the
contents of the internal data structure effectively breaking the
original Matrix.
We need a more OO strategy
Yup, see here under (although it is a bit long). What I do is wait with
generating the matrix till it is needed, and I still do use the
getData() method, but do not need the getDataRef() anymore. If you want
to get rid of that too, I would be less happy with that.
This routine takles about 30
that we need to maintain it?
-Original Message-
From: Kim van der Linde [mailto:[EMAIL PROTECTED]
Sent: Mon 9/27/2004 11:21 AM
To: Jakarta Commons Developers List
Cc:
Subject: Re: [math] API changes for RC2
Phil Steitz wrote:
Spooky -- delightful word
Phil Steitz wrote:
No, you are not missing anything. What you are suggesting should
work fine, with similar change for getResult.
A little nit -- I would prefer to use a boolean for the property
(unless there are more than two values) and not rely on the *value*
of the int constant (flag) in
Mark R. Diggory wrote:
This is the sort of thing that defeats the purpose of having the
RealMatrix package. Such computations could be used to abuse the
contents of the internal data structure effectively breaking the
original Matrix.
We need a more OO strategy for capturing the requirements
Phil Steitz wrote:
These are new feature
requests that came in after RC1 was cut and they can be accomodated in
1.1 without breaking backward compatability. I see no reason to hold the
release for this.
I have requested these weeks before the RC1 was cut.
Kim
--
http://www.kimvdlinde.com
Phil Steitz wrote:
Kim van der Linde wrote:
Phil Steitz wrote:
These are new feature requests that came in after RC1 was cut and
they can be accomodated in 1.1 without breaking backward
compatability. I see no reason to hold the release for this.
I have requested these weeks before the RC1
You are right. Blur of the mind.
Kim
Phil Steitz wrote:
Kim van der Linde wrote:
Phil Steitz wrote:
These are new feature requests that came in after RC1 was cut and
they can be accomodated in 1.1 without breaking backward
compatability. I see no reason to hold the release for this.
I have
1) +1 (although I can see that some statistics (like PCA, factorial,
cluster analysis and so) might end up in a multivariate package).
2) +1
3) +0 (I can see that it might be more logical to implement it after
1.0, but them I would be in favour of dropping PNRG all together in this
release.)
4)
it as is. Again, it might mean an API change in the
future, but I doubt anyone knows the perfect solution so let's see how
this one goes.
So the only one I'd advise as really being worth the effort is 1.
Hen
On Sat, 25 Sep 2004 21:41:31 -0400, Kim van der Linde
[EMAIL PROTECTED] wrote:
1) +1 (although
For the same reasons as before, -1
Phil Steitz wrote:
RC1 has been out for almost 2 weeks now and there has been just one bug
reported, which has been fixed in CVS. I propose, therefore, that we
move forward with the official 1.0 release. An updated release candidate
is available here:
Phil,
Phil Steitz wrote:
Kim,
Can you be more explicit? Most of your objections were addressed in RC1.
Some of my objections were resolved. The matrix stuff was partially
resolved, as is the name of the regression, which is still in the wrong
package. Furthermore, the different types of
Phil,
Phil Steitz wrote:
the regression, which is still in the wrong package.
We discussed this and concluded that it did not make sense to combine
univariate and multivariate statistics into one package and by any
reasonable definition regression (even with just one independent
variable) is a
Mark,
Open source principles.
I agree with the principles, but IMHO, there are several issues with
this release that are to fundamental to be released.
Furthermore, the different types of variances remains unsolved, as
they are variant's of each other and should be in one single
class.
Consensus
Phil Steitz wrote:
No other binding votes. Kim Van Der Linde voted +1, then changed to -1
(then back again?)
No, she remains that -1 for the remaining points as mentioned.
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Interestingly, as of 1.2 at least, the JDK-supplied PRNG is Knuth's 3.2.1
(linear congruential). I am +1 for adding additional PRNGs, but I would
also recommend that if we do that we also include benchmark tests (like
the ones here: http://csrc.nist.gov/rng/SP800-22b.pdf), performance
Phil Steitz wrote:
That depends entirely on what you mean by serious scientific work.
Different PRNGs have different properties that make them better (or
worse) for specific purposes. Most practical applications require
neither astronomical periods nor cryptographic security, so I would be
Hi,
Brent Worden wrote:
1) Change the RealMatrix getEntry, getRow, getColumn methods to use
0-based indexing.
Looking at the implementation, I believe the current indexing is
satisfactory and I can't think of where using it with native arrays would be
overly burdensome or confusing.
Well, so you
For the people who are interested in some extensions to the commons.math
package such as 0-based Matrix class and population variances
implemented within the variances class can look here:
http://www.kimvdlinde.com/professional/programming/commonSense/
or download the jar file:
Well, I had a discussion with several collegues (type science users, we
went snorkeling) on several of these issues. The score of the day was
the idea that the simple linear LS regression was considered a
multvariate statistics.
Phil Steitz wrote:
Nothing has been put aside. We make decisions
Phil Steitz wrote:
Kim van der Linde wrote:
Well, I had a discussion with several collegues (type science users,
we went snorkeling) on several of these issues. The score of the day
was the idea that the simple linear LS regression was considered a
multvariate statistics.
So it should stay
Hi Phil,
With the 1 base system, I keep casting back and forth between the 0
based underlying java system and the 1 based matrix system. But only in
selected cases, not as a general rule. It also requires me to make
specific methods just to increase the row number by one, as the method
returns
Phil,
Honestly, I think that if you make the argument that you want to use
Mathematical correct notations, you should start any array at 1. If
everything (commons-math and JAVA itself) would be like that, fine, but
reality is that java is 0 based.
As long as you use only one system (Matrices
Phil Steitz wrote:
No, an array is not a mathematical object.
If you are a purist, yes, but for many people, they are roughly equivalent.
Here again, the point is that the math object should expose
properties consistent with its definition -- like any other Java
object. What is actually wrong
Mark R. Diggory wrote:
I agree entirely with your argument. I would feel more comfortable with
0 to n-1.
Ok, how do I update the inproved class, as I did that already yesterday
evening. I would also like to add several new methods:
RealMatrix getSubMatrix (int startRow, int endRow, int
Hi All,
I ran into a problem with the RealMatrixImpl class. The class is
designed such that it uses the default 1 to n counting for the rows and
columns. However, JAVA has as a default the 0 tot n-1 system. i now run
into the problem that some standard methods return an array of n (0 tot
n-1)
-
[x] +1 Go ahead and release 1.0-RC1
[ ] +0
[ ] -0
[ ] -1 Don't release 1.0-RC1, because...
-
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--- Phil Steitz [EMAIL PROTECTED] wrote:
Kim van der Linde wrote:
I generally use the RandomX package that you can
find here.
Where is here?
Oeps, I forgot the link:
http://www.fourmilab.ch/hotbits/source/randomX/randomX.html
--- Mark R. Diggory [EMAIL PROTECTED]
wrote:
Well, I think should step back and ask a few design
questions concerning the objects that will use these
Sample/Population variances and that will assist us
in their own design.
1.) Is it the case that a covariance matrix could be
built off
Hi All,
I just digged in and found that you use the standard
random generator of SUN. Is that an inproved version
of the 1.0.2 version, which is a very very basic
pseudo-pseudo-pseudo random generator. Any help?
Kim
__
Do you Yahoo!?
Read only
Hi,
I just looked through the variance class, and saw that
it only supports sample vasriance (N-1) but not
population variances (N). Any reason for this, and can
it be added?
Cheers,
Kim
__
Do you Yahoo!?
Yahoo! Mail - 50x more storage than
stuff) so that will not do.
cheers,
Kim
--- Phil Steitz [EMAIL PROTECTED] wrote:
Kim van der Linde wrote:
Hi All,
I just digged in and found that you use the
standard
random generator of SUN. Is that an inproved
version
of the 1.0.2 version, which is a very very basic
pseudo
--- Brent Worden [EMAIL PROTECTED] wrote:
Any objection to tracking these and future feature
requests using the wiki?
Yes, because I am not one of those hard core
developers.
Kim
__
Do you Yahoo!?
Yahoo! Mail - 50x more storage than other
Besides that, there is no maths part there (yet?)
__
Do you Yahoo!?
Yahoo! Mail Address AutoComplete - You start. We finish.
http://promotions.yahoo.com/new_mail
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To
--- matthew.hawthorne [EMAIL PROTECTED] wrote:
Kim van der Linde wrote:
I think I am a typical math only user and
developer
and I just joined the e-mail lists. The last days,
I
seriously contemplated on leaving both lists
because
of the use amout of completly irrelevant bullshit
--- Martin Cooper [EMAIL PROTECTED] wrote:
It seems that you are missing the single most
important facet of Jakarta Commons here - community.
Commons is one community,
A community from whom? Whom are in it? Only hard-core
developers? Or the developers and users at large?
Apparently, I have
Hi All,
I think I am a typical math only user and developer
and I just joined the e-mail lists. The last days, I
seriously contemplated on leaving both lists because
of the use amout of completly irrelevant bullshit that
passes by every morning and during the day on my
computer. I have better
I just downloaded it, so if anyone wants a copy, let
me know
Theory and Methods
The Remedian: A Robust Averaging Method for Large Data
Sets
Peter J. Rousseeuw; Gilbert W. Bassett, Jr.
Journal of the American Statistical Association, Vol.
85, No. 409. (Mar., 1990), pp. 97-104.
Stable URL:
--- Eric MacAdie [EMAIL PROTECTED] wrote:
Phil Steitz wrote:
Kim,
Sorry for the response latency. Thanks in advance
for any contributions that you can make to [math].
One thing to keep in mind is that we are trying to
focus on commonly used stuff. So, e.g. a basic GLM
package would
implementation be based on the existing library architecture
as well, so goal might be to see if these could be easily modified to
work with the existing Matrix/Statistics classes in our api.
thanks,
Mark
Kim van der Linde wrote:
Hi Phil,
Thanks for the answer, and I was talking about numerical
,
multivariate euclidian and mahalanobis distances and maybe some other
classes as model 2 regressions (RMA: Reduced Major Axis). Interested?
Kim
Phil Steitz wrote:
Kim van der Linde wrote:
Hi All,
I have a question. How stable are the matrix classes as implemented?
Cheers,
Kim
Hi Kim,
If your question is about
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