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Re: Integration in gnuplot IS possible!

[Alexandre F. <o.a...@gm...>]

Pieter-Tjerk method is fairly better :D
redefining it this make the same thing but you ask for a maximum integration
distance
instead a maximum
intf(x0,a,h) = (h<=delta) ? f(x0+a/2)*a : ( intf(x0,a/2,delta) +
intf(x0+a/2,a/2,delta) )

when you use gnuplot i think you want to plot something, this version if you
say
plot intf(x0, x - x0, delta)
ensures that any integration interval will be larger than delta, and that
the
recurrence steep will be the minimum (with this function structure)
if you plot with 1024 samples the integration function intf(x0, a, delta) is
called
1397077 times, and the function f(x) will be evaluated 350548 times and the
max
recurrence depth will be 10


to integrate with the same acuracy the Daniel's scheme will call the intf*
functions and f(x) are called about 523 thounsand times. and the max
recurrence deepth is 1024

my scheme calls f(x) 1024 times and intf(x) 1024 times, but use some global
variables.

excuse-me i accidentally replied only to 3snoW

here goes the my scheme.
It's not encouraged the use of global variables, but in such case i think
here we a better solution, not THE better solution

# Characteristic for the integration
n_samps = 100;
a = 0.0;
b = 5.0;
# initialization
aux = 0.0;
h = (b-a)/n_samps;
set samples n_samps
set xrange [a to b]
# the function
f(x) = sin(5*x)/(0.1+x)

#the integrator scheme
intf(x) = (aux = (aux + f(x)*h))
# plot it
plot f(x), intf(x)
# another function
f(x) = sin(x)*x
replot


for the 2D is also possible. the only thing you need is to reinit the aux
variable when x=a
this scheme is as poor as the former, therefore it's O(nsamples) and why to
use recurrence if you can use memorization?
intf can also have other integration schemes, with the advantage that you
have to implement only once
for example simpson's rule or any other method

intf(x) = (aux = (aux + (f(x-h)+4*f(x-0.5*h)+f(x))*h/6))

this example make the h function to be called three times more.
the ideal to generate plots is to derive integration schemes open in
f(x-h) and closed in f(x), but i will not make this now :D

Re: Integration in gnuplot IS possible!

[Alexandre F. <o.a...@gm...>]

The Pieter-Tjerk is fairly better :D
redefining it this make the same thing but you ask for a maximum integration
distance
instead a maximum
intf(x0,a,h) = (h<=delta) ? f(x0+a/2)*a : ( intf(x0,a/2,delta) +
intf(x0+a/2,a/2,delta) )

when you use gnuplot i think you want to plot something, this version if you
say
plot intf(x0, x - x0, delta)
ensures that any integration interval will be larger than delta, and that
the
recurrence steep will be the minimum (with this function structure)
if you plot with 1024 samples the integration function intf(x0, a, delta) is
called
1397077 times, and the function f(x) will be evaluated 350548 times and the
max
recurrence depth will be 10


to integrate with the same acuracy the Daniel's scheme will call the intf*
functions and f(x) are called about 523 thounsand times. and the max
recurrence deepth is 1024

my scheme calls f(x) 1024 times and intf(x) 1024 times, but use some global
variables.

excuse-me i accidentally replied only to 3snoW

here goes the my scheme.
It's not encouraged the use of global variables, but in such case i think
here we a better solution, not THE better solution

# Characteristic for the integration
n_samps = 100;
a = 0.0;
b = 5.0;
# initialization
aux = 0.0;
h = (b-a)/n_samps;
set samples n_samps
set xrange [a to b]
# the function
f(x) = sin(5*x)/(0.1+x)

#the integrator scheme
intf(x) = (aux = (aux + f(x)*h))
# plot it
plot f(x), intf(x)
# another function
f(x) = sin(x)*x
replot

for the 2D is also possible. the only thing you need is to reinit the aux
variable when x=a
this scheme is as poor as the former, therefore it's O(nsamples) and why to
use recurrence if you can use memorization?
intf can also have other integration schemes, with the advantage that you
have to implement only once
for example simpson's rule or any other method

intf(x) = (aux = (aux + (f(x-h)+4*f(x-0.5*h)+f(x))*h/6))

this example make the h function to be called three times more.
the ideal to generate plots is to derive integration schemes open in
f(x-h) and closed in f(x), but i will not make this now :D

Re: Integration in gnuplot IS possible!

[Alexandre F. <o.a...@gm...>]

The Pieter-Tjerk is fairly better :D
redefining it this make the same thing but you ask for a maximum integration
distance
instead a maximum
intf(x0,a,h) = (h<=delta) ? f(x0+a/2)*a : ( intf(x0,a/2,delta) +
intf(x0+a/2,a/2,delta) )

when you use gnuplot i think you want to plot something, this version if you
say
plot intf(x0, x - x0, delta)
ensures that any integration interval will be larger than delta, and that
the
recurrence steep will be the minimum (with this function structure)
if you plot with 1024 samples the integration function intf(x0, a, delta) is
called
1397077 times, and the function f(x) will be evaluated 350548 times and the
max
recurrence depth will be 10


to integrate with the same acuracy the Daniel's scheme will call the intf*
functions and f(x) are called about 523 thounsand times. and the max
recurrence deepth is 1024

my scheme calls f(x) 1024 times and intf(x) 1024 times, but use some global
variables.

excuse-me i accidentally replied only to 3snoW

here goes the my scheme.
It's not encouraged the use of global variables, but in such case i think
here we a better solution, not THE better solution

# Characteristic for the integration
n_samps = 100;
a = 0.0;
b = 5.0;
# initialization
aux = 0.0;
h = (b-a)/n_samps;
set samples n_samps
set xrange [a to b]
# the function
f(x) = sin(5*x)/(0.1+x)

#the integrator scheme
intf(x) = (aux = (aux + f(x)*h))
# plot it
plot f(x), intf(x)
# another function
f(x) = sin(x)*x
replot

for the 2D is also possible. the only thing you need is to reinit the aux
variable when x=a
this scheme is as poor as the former, therefore it's O(nsamples) and why to
use recurrence if you can use memorization?
intf can also have other integration schemes, with the advantage that you
have to implement only once
for example simpson's rule or any other method

intf(x) = (aux = (aux + (f(x-h)+4*f(x-0.5*h)+f(x))*h/
6))

this example make the h function to be called three times more.
the ideal to generate plots is to derive integration schemes open in
f(x-h) and closed in f(x), but i will not make this now :D

Re: Integration in gnuplot IS possible!

[Alexandre F. <o.a...@gm...>]

Does someone read what i have wrote?

Re: Integration in gnuplot IS possible!

[Pieter-Tjerk de B. <ptd...@cs...>]

Hello,

On Wed, Jun 15, 2011 at 05:35:54PM -0700, 3snoW wrote:

> I've searched the web for ways to integrate in gnuplot and only found people
> saying it is not possible. Unsatisfied, I decided to see if i could make one
> myself. I could :D

Nice!

> Let me know if you have any ideas to make it better

I'd suggest using the recursion not to cover the interval _linearly_,
but using the recursion to _bisect_ the interval, like this:

  intf(a,x,n) = (n==0) ? f((a+x)/2)*(x-a) : ( intf(a,(a+x)/2,n-1) + intf((a+x)/2,x,n-1) )

The last parameter n is the number of recursions, and which equals the
2log of the number of points in which to cut the interval.

This approach should practically avoid stack overflows, since much less
recursion depth is needed for the same accuracy.

Regards,
  Pieter-Tjerk

Re: Integration in gnuplot IS possible!

[Ethan A M. <sf...@us...>]

On Thursday, June 16, 2011 01:06:23 pm Daniel J Sebald wrote:
> The bivariat.dem formula still has the problem of 
> recursion/stack depth, in this case:
> 
>    recursion depth limit exceeded

The depth limit was set rather arbitrary at 250 on the logic that
"nobody would need more than that, right?"

It would be easy enough to make it user-defined.
If you increase it to something much larger and the program
runs out of stack space, then at least you know it's your own
fault.

		Ethan

Re: Integration in gnuplot IS possible!

[Daniel J S. <dan...@ie...>]

On 06/16/2011 01:57 PM, Hans-Bernhard Bröker wrote:
> On 16.06.2011 02:35, 3snoW wrote:
>
>> I'm not sure if this qualifies as "Dev", If it doesn't I'm sorry.
>> I've searched the web for ways to integrate in gnuplot and only found people
>> saying it is not possible.
>
> Strange --- particularly since one of our published/enclosed demos,
> bivariat.dem, has been doing just that since 1998!

I gave those formulas a try.  They behave better than 3snoW's formulas 
in the example I used, because of the parameter delta (i.e., h) rather 
than the fixed number of intervals of 3snoW and because of its use of 
Simpson's rule.  The bivariat.dem formula still has the problem of 
recursion/stack depth, in this case:

   recursion depth limit exceeded

An internal integration function is probably the only solution to that. 
  The tricky part would be interpreting the function name, i.e.,

f(x) = cos(x)
h = 0.2
M = 1
plot intgrt(f(x),h,M)

where f(x) is the function, h is the (initial) stepsize, M is the 
integration method.  The first argument, in this case "f(x)", would need 
special treatment in the parser different from other functions.

Dan

Re: Integration in gnuplot IS possible!

[Hans-Bernhard B. <HBB...@t-...>]

On 16.06.2011 02:35, 3snoW wrote:

> I'm not sure if this qualifies as "Dev", If it doesn't I'm sorry.
> I've searched the web for ways to integrate in gnuplot and only found people
> saying it is not possible.

Strange --- particularly since one of our published/enclosed demos, 
bivariat.dem, has been doing just that since 1998!

Re: Integration in gnuplot IS possible!

[3snoW <vas...@gm...>]

Daniel J Sebald wrote:
> 
> On 06/15/2011 07:35 PM, 3snoW wrote:
>>
>> Hello,
>> I'm not sure if this qualifies as "Dev", If it doesn't I'm sorry.
> [snip]
>> Let me know if you have any ideas to make it better or if you find any
>> bug
>> using it! I hope this was helpful!
> 
> Very creative.  Of course, this is straightforward rectangular 
> approximation to integration.  It will have problems with functions that 
> change quickly near discontinuities and so on so won't have the 
> precision of, say, adaptive integral techniques.  Nonetheless, it works 
> (sort of, see note at end), assuming the initial condition is that the 
> integral passes through zero at a.
> 
> [snip]
> 
> Notice how accuracy is lost moving outward.  So you might want to 
> experiment with making h another parameter in the function.  Generalizing, 
> 
> intf(a,x,N)=x>a?intfAux1(a,x-(x-a)/N/2,(x-a)/N)*(x-a)/N:intfAux2(a,x+(a-x)/N/2,(a-x)/N)*(x-a)/N; 
> 
> I can't push N high enough to get good resolution before a stack 
> overflow occurs. 
> 
> An internal integration feature is probably the only good way to address 
> this sort of thing. 
> 
> Dan 
> 
Hi Dan,

The reason I was using f(x)-f(a) in the intfAux functions and then add
f(a)*(x-a) is because I originally was using a fixed small step h instead of
dividing the interval in 90 small parts. That way, if f(a) was not 0, the
integral would have a discontinuity every time x was a multiple of h, so, as
a workaround to this problem, I set it to integrate f(x)-f(a), and
compensated adding f(a)*(x-a). But since I switched to dividing into 90
equal parts, this is no longer a problem. 

I didn't make the integration method more sophisticated because of the
'stack overflow' issue. Adaptive integral techniques would most likely
consume 'stacks' at a much higher rate, and in the end you would have a
worse integration because of the lack of resolution. I'm thinking of maybe
upgrading this to the trapezoidal integration or even a superior order
technique, but for now I think this works fine for any 'well behaved'
function.

Lastly, the generalized function that includes N as a parameter is a good
idea, but I'll call it Nintf instead of intf, because that way I can have
both functions. Thank you for your contribution, it was really constructive!
I'll update the config.ini file with your changes.

3snoW
-- 
View this message in context: http://old.nabble.com/Integration-in-gnuplot-IS-possible%21-tp31856137p31859432.html
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Re: Integration in gnuplot IS possible!

[Daniel J S. <dan...@ie...>]

On 06/15/2011 07:35 PM, 3snoW wrote:
>
> Hello,
> I'm not sure if this qualifies as "Dev", If it doesn't I'm sorry.
[snip]
> Let me know if you have any ideas to make it better or if you find any bug
> using it! I hope this was helpful!

Very creative.  Of course, this is straightforward rectangular 
approximation to integration.  It will have problems with functions that 
change quickly near discontinuities and so on so won't have the 
precision of, say, adaptive integral techniques.  Nonetheless, it works 
(sort of, see note at end), assuming the initial condition is that the 
integral passes through zero at a.

Let's see if we can simplify your formulas slightly for efficiency. 
Starting with

intfAux1(a,x,h)=(x>a?(f(x)-f(a))*h+intfAux1(a,x-h,h):0);
intfAux2(a,x,h)=(x<a?(f(x)-f(a))*h+intfAux2(a,x+h,h):0);
intf(a,x)=x>a?intfAux1(a,x-abs(x-a)/90./2,abs(x-a)/90.)+f(a)*(x-a):-intfAux2(a,x+abs(x-a)/90./2,abs(x-a)/90.)+f(a)*(x-a);

Note that the abs() function call is extraneous because we know that

If x>a, then abs(x-a) = x-a
If x<=a, then abs(x-a) = a-x

Therefore, substituting the above

intf(a,x)=x>a?intfAux1(a,x-(x-a)/90./2,(x-a)/90.)+f(a)*(x-a):-intfAux2(a,x+(a-x)/90./2,(a-x)/90.)+f(a)*(x-a);

It's possible to factor out the h from the auxiliary formulas and simply 
multiply it with the auxiliary formula, knowing that h=(x-a)/90 in the 
one case and h=(a-x)/90 in the other case:

intfAux1(a,x,h)=(x>a?(f(x)-f(a))+intfAux1(a,x-h,h):0);
intfAux2(a,x,h)=(x<a?(f(x)-f(a))+intfAux2(a,x+h,h):0);
intf(a,x)=x>a?intfAux1(a,x-(x-a)/90./2,(x-a)/90.)*(x-a)/90.+f(a)*(x-a):-intfAux2(a,x+(a-x)/90./2,(a-x)/90.)*(a-x)/90.+f(a)*(x-a);

Swap the order of x and a in the second formula:

intf(a,x)=x>a?intfAux1(a,x-(x-a)/90./2,(x-a)/90.)*(x-a)/90.+f(a)*(x-a):intfAux2(a,x+(a-x)/90./2,(a-x)/90.)*(x-a)/90.+f(a)*(x-a);

Note that f(a) is subtracted 90 times, so that can be removed from the 
auxiliary formulas and lumped in the main formula:

intfAux1(a,x,h)=(x>a?f(x)+intfAux1(a,x-h,h):0);
intfAux2(a,x,h)=(x<a?f(x)+intfAux2(a,x+h,h):0);
intf(a,x)=x>a?intfAux1(a,x-(x-a)/90./2,(x-a)/90.)*(x-a)/90.-90.*f(a)*(x-a)/90.+f(a)*(x-a):intfAux2(a,x+(a-x)/90./2,(a-x)/90.)*(x-a)/90.-90.*f(a)*(x-a)/90.+f(a)*(x-a);

at which point a couple terms cancel.  So we have

intfAux1(a,x,h)=(x>a?f(x)+intfAux1(a,x-h,h):0);
intfAux2(a,x,h)=(x<a?f(x)+intfAux2(a,x+h,h):0);
intf(a,x)=x>a?intfAux1(a,x-(x-a)/90./2,(x-a)/90.)*(x-a)/90.:intfAux2(a,x+(a-x)/90./2,(a-x)/90.)*(x-a)/90.;

Seems to work the same.  It's not drastically shorter, but the 
arithmetic operations are reduced.

The thing one has to be aware of is that as x gets further and further 
away from a, the resolution effectively decreases because element 
h=(x-a)/90 becomes larger.  This is a problem for functions that appear 
to be high frequency.  For example, try your cosine example, but with

set sample 1000
set xrange [-200:200]

Notice how accuracy is lost moving outward.  So you might want to 
experiment with making h another parameter in the function.  Generalizing,

intf(a,x,N)=x>a?intfAux1(a,x-(x-a)/N/2,(x-a)/N)*(x-a)/N:intfAux2(a,x+(a-x)/N/2,(a-x)/N)*(x-a)/N;

I can't push N high enough to get good resolution before a stack 
overflow occurs.

An internal integration feature is probably the only good way to address 
this sort of thing.

Dan

Integration in gnuplot IS possible!

[3snoW <vas...@gm...>]

Hello,
I'm not sure if this qualifies as "Dev", If it doesn't I'm sorry.
I've searched the web for ways to integrate in gnuplot and only found people
saying it is not possible. Unsatisfied, I decided to see if i could make one
myself. I could :D
This was the result:

intfAux1(a,x,h)=(x>a?(f(x)-f(a))*h+intfAux1(a,x-h,h):0);
intfAux2(a,x,h)=(x<a?(f(x)-f(a))*h+intfAux2(a,x+h,h):0);
intf(a,x)=x>a?intfAux1(a,x-abs(x-a)/90./2,abs(x-a)/90.)+f(a)*(x-a):-intfAux2(a,x+abs(x-a)/90./2,abs(x-a)/90.)+f(a)*(x-a);

Basically, intfAux 1 and 2 are just functions for this thing to work, and
intf(a,b) integrates f(x) from a to b. You can just type this in every time
you want to integrate f(x), or you can download the gnuplot.ini that i made
with this function and put it into your binary folder:
http://old.nabble.com/file/p31856137/gnuplot.ini gnuplot.ini 

Here is also a demonstration of using this:
http://old.nabble.com/file/p31856137/Integrate%2B.png 

There are two problems with this function (that I know of):
-It will most likely not work with self recursive functions because this
function itself is self recursive, and gnuplot has a "stack overflow" limit.
This makes it impossible to double integrate using this function. I made it
so it was not at the limit, it is almost there, so, for example having a
function g(x)=h(intf(0,x)) should not be a problem. By the way, if anyone
knows of a way to set the stack overflow limit higher, I'd appreciate
posting it here.
-The other problem is that it will integrate specifically f(x), so if you
want to integrate another function, g(x) for example, you would have to
create an intg(a,b). To make this task easier, I made it so that if you
replace in those 3 lines of code all the f's with the name of your function,
g for example (again), you would have your intg made. This way you can just
open notepad, use the "replace" command and copy the result to gnuplot.

Let me know if you have any ideas to make it better or if you find any bug
using it! I hope this was helpful!

3snoW
-- 
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Re: Citation of gnuplot in a scientific publication

[<pl...@pi...>]

On 06/08/11 04:50, Ethan Merritt wrote:
> On Tuesday, June 07, 2011 06:05:40 pm Clark Gaylord wrote:
>> I have always felt the gnuplot.info name should be canonical. It points
> to sf for v4 and vt for v6 and is much more portable.
>
> But what is it that one is citing, exactly?
>
> The source is not (so far as I know) available on gnuplot.info,
> So if the idea is to cite the location of the program source, then *·info
> may not be the correct URL.
>
> If the idea is to cite the manual, say, then that's another issue.
> Perhaps we should register the manual with a repository that would
> issue a permanent DOI.  arXiv.org?
>
>
> 	Ethan
>
Hi,

What is the aim here? The fact that you are having to do contortions to 
fit this into the reference citation format for the publications 
suggests you are misusing it. That may not go down well with the publisher.

While it is nice to recognise the software in a paper using it , it is 
after all only a plotting tool and there is no reason to cite it as a 
reference since it should not affect the results in any way.

The only exception I can think of is if your are using it to do linear 
regression or something in which case you should probably understand how 
it does that and comment on what methods *you* have adopted to fit 
straight lines , functions, whatever, in choosing to do that with a 
particular tool that automates the process.


To recognise gnuplot and help the reader reproduce your work it would be 
sufficient to name gnuplot  as an open source plotting tool. Anyone 
capable of using it should be able to find without further help.

Mentioning gnuplot as the tool used to produce any graphics seems like a 
good idea. I doubt citing it as a reference is appropriate.

best regards.

Re: Citation of gnuplot in a scientific publication

[Ethan M. <merritt@u.washington.edu>]

On Tuesday, June 07, 2011 06:05:40 pm Clark Gaylord wrote:
> I have always felt the gnuplot.info name should be canonical. It points 
to sf for v4 and vt for v6 and is much more portable.

But what is it that one is citing, exactly?

The source is not (so far as I know) available on gnuplot.info,
So if the idea is to cite the location of the program source, then *·info 
may not be the correct URL.

If the idea is to cite the manual, say, then that's another issue.
Perhaps we should register the manual with a repository that would
issue a permanent DOI.  arXiv.org?


	Ethan

Re: Citation of gnuplot in a scientific publication

[Ethan M. <merritt@u.washington.edu>]

On Tuesday, June 07, 2011 06:05:40 pm Clark Gaylord wrote:
> I have always felt the gnuplot.info name should be canonical. It points 
to sf for v4 and vt for v6 and is much more portable.

What's "v6"?

	Ethan

> 
> --
> Clark Gaylord
> cga...@vt...

Re: Citation of gnuplot in a scientific publication

[C. G. <cga...@vt...>]

I have always felt the gnuplot.info name should be canonical. It points to sf for v4 and vt for v6 and is much more portable.

--
Clark Gaylord
cga...@vt...
... sent from HTC Android
    auto-correct is not always my friend ...

----- Reply message -----
From: "Ethan Merritt" <merritt@u.washington.edu>
Date: Tue, Jun 7, 2011 12:29
Subject: Citation of gnuplot in a scientific publication
To: <gnu...@li...>

On Tuesday, June 07, 2011 06:18:18 am Peter Juhasz wrote:
> Dear gnuplot-beta list,
> 
> I want to cite gnuplot in my publication. Is the following reference OK?
> 
> Williams, T. and Kelley, C. (2011). Gnuplot 4.5: an interactive
> plotting program. URL http://gnuplot.info. (Last accessed: 2011 June
> 7)

I have used the following BibTeX entry:


@MISC{Gnuplot_4.4,
 author = {Thomas Williams and Colin Kelley and {many others}},
 title = {Gnuplot 4.4: an interactive plotting program},
 month = {March},
 year = {2010},
 howpublished={\url{http://gnuplot.sourceforge.net/}}
}

	Ethan

-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
University of Washington, Seattle 98195-7742

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Re: Citation of gnuplot in a scientific publication

[Daniel J S. <dan...@ie...>]

On 06/07/2011 01:37 PM, Juhász Péter wrote:
> I agree, but the journal I'm submitting to has a strict policy on
> reference format: it's either "Author1, X and Author2, Y", or "Author1
> et al.", and I have to cite as "Author, year" in the text.

Citing the originators names only is fair.  Try running "T. Williams, C. 
Kelly, et al." through and see if they accept it.  That's slightly 
re-interpreting "et al.", but it makes sense.

Dan

PS: For BibTeX, using commas can help with abbreviations for those 
styles that do so, i.e.,

  author = {Williams, Thomas and Kelley, Colin and {many others}},


>
> Perhaps I should take a leaf out of R's book? They have a recommendation
> for citation, in which they list the author as "R Development Core
> Team".
>
> In our case "gnuplot development team" would be neutral and it would
> reflect reality as well.
>
> Péter Juhász.
>
> On Tue, 2011-06-07 at 08:39 -0700, Ralf Juengling wrote:
>> That only the originators get credit does not seem fair. Perhaps
>> don't name any authors?
>>
>> Ralf
>>
>>
>> On Tue, 7 Jun 2011, Peter Juhasz wrote:
>>
>>> Dear gnuplot-beta list,
>>>
>>> I want to cite gnuplot in my publication. Is the following reference OK?
>>>
>>> Williams, T. and Kelley, C. (2011). Gnuplot 4.5: an interactive
>>> plotting program. URL http://gnuplot.info. (Last accessed: 2011 June
>>> 7)
>>>
>>> (I've found one instance of this question in the list archives, that's
>>> where the above comes from.)
>>>
>>> Péter Juhász
>>>
>>> ------------------------------------------------------------------------------
>>> EditLive Enterprise is the world's most technically advanced content
>>> authoring tool. Experience the power of Track Changes, Inline Image
>>> Editing and ensure content is compliant with Accessibility Checking.
>>> http://p.sf.net/sfu/ephox-dev2dev
>>> _______________________________________________
>>> gnuplot-beta mailing list
>>> gnu...@li...
>>> https://lists.sourceforge.net/lists/listinfo/gnuplot-beta
>>>
>
>
>
> ------------------------------------------------------------------------------
> EditLive Enterprise is the world's most technically advanced content
> authoring tool. Experience the power of Track Changes, Inline Image
> Editing and ensure content is compliant with Accessibility Checking.
> http://p.sf.net/sfu/ephox-dev2dev
> _______________________________________________
> gnuplot-beta mailing list
> gnu...@li...
> https://lists.sourceforge.net/lists/listinfo/gnuplot-beta


-- 

Dan Sebald
email: daniel(DOT)sebald(AT)ieee(DOT)org
URL: http://www(DOT)dansebald(DOT)com

Re: Citation of gnuplot in a scientific publication

[Juhász P. <pet...@gm...>]

I agree, but the journal I'm submitting to has a strict policy on
reference format: it's either "Author1, X and Author2, Y", or "Author1
et al.", and I have to cite as "Author, year" in the text.

Perhaps I should take a leaf out of R's book? They have a recommendation
for citation, in which they list the author as "R Development Core
Team".

In our case "gnuplot development team" would be neutral and it would
reflect reality as well.

Péter Juhász.

On Tue, 2011-06-07 at 08:39 -0700, Ralf Juengling wrote:
> That only the originators get credit does not seem fair. Perhaps
> don't name any authors?
> 
> Ralf
> 
> 
> On Tue, 7 Jun 2011, Peter Juhasz wrote:
> 
> > Dear gnuplot-beta list,
> >
> > I want to cite gnuplot in my publication. Is the following reference OK?
> >
> > Williams, T. and Kelley, C. (2011). Gnuplot 4.5: an interactive
> > plotting program. URL http://gnuplot.info. (Last accessed: 2011 June
> > 7)
> >
> > (I've found one instance of this question in the list archives, that's
> > where the above comes from.)
> >
> > Péter Juhász
> >
> > ------------------------------------------------------------------------------
> > EditLive Enterprise is the world's most technically advanced content
> > authoring tool. Experience the power of Track Changes, Inline Image
> > Editing and ensure content is compliant with Accessibility Checking.
> > http://p.sf.net/sfu/ephox-dev2dev
> > _______________________________________________
> > gnuplot-beta mailing list
> > gnu...@li...
> > https://lists.sourceforge.net/lists/listinfo/gnuplot-beta
> >

Re: Citation of gnuplot in a scientific publication

[Ethan M. <merritt@u.washington.edu>]

On Tuesday, June 07, 2011 06:18:18 am Peter Juhasz wrote:
> Dear gnuplot-beta list,
> 
> I want to cite gnuplot in my publication. Is the following reference OK?
> 
> Williams, T. and Kelley, C. (2011). Gnuplot 4.5: an interactive
> plotting program. URL http://gnuplot.info. (Last accessed: 2011 June
> 7)

I have used the following BibTeX entry:


@MISC{Gnuplot_4.4,
 author = {Thomas Williams and Colin Kelley and {many others}},
 title = {Gnuplot 4.4: an interactive plotting program},
 month = {March},
 year = {2010},
 howpublished={\url{http://gnuplot.sourceforge.net/}}
}

	Ethan

-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
University of Washington, Seattle 98195-7742

Citation of gnuplot in a scientific publication

[Peter J. <pet...@gm...>]

Dear gnuplot-beta list,

I want to cite gnuplot in my publication. Is the following reference OK?

Williams, T. and Kelley, C. (2011). Gnuplot 4.5: an interactive
plotting program. URL http://gnuplot.info. (Last accessed: 2011 June
7)

(I've found one instance of this question in the list archives, that's
where the above comes from.)

Péter Juhász

Re: compiling Qt on Mac

[Mojca M. <moj...@gm...>]

On Fri, May 27, 2011 at 18:31, Ethan A Merritt wrote:
>
>> However I have
>>     /Library/Frameworks/QtCore.framework
>> and others present and I'm able to compile and use other Qt applications.
>
> Aha. Sounds promising.
> Can you see how the Make files for those other Qt applications
> refer to Qt, and borrow equivalent commands for gnuplot's configure script?

I just checked the source code of Geant4
(http://geant4.cern.ch/support/download.shtml). The configure script
includes 500 lines of code devoted to Qt only.

At the end it sets the following variables (which are later used as
flags to compiler):

QTFLAGS=-I/Library/Frameworks/QtCore.framework/Headers
-I/Library/Frameworks/QtGui.framework/Headers
-I/Library/Frameworks/QtOpenGl.framework/Headers
QTLIBS=-F/Library/Frameworks -framework QtCore -framework QtGui

I now commented out a few lines in gnuplot's configure script and ran

export QT_CFLAGS="-I/Library/Frameworks/QtCore.framework/Headers
-I/Library/Frameworks/QtGui.framework/Headers
-I/Library/Frameworks/QtNetwork.framework/Headers
-I/Library/Frameworks/QtSvg.framework/Headers"
export QT_LIBS="-F/Library/Frameworks -framework QtCore -framework
QtGui -framework QtNetwork -framework QtSvg"

./configure --enable-qt

which ended up building gnuplot, but complaining about
qtterminal/QtGnuplotWidget.cpp:280:34: error: ui_QtGnuplotSettings.h:
No such file or directory

which seems to be a valid complaint. I cannot find such file in
gnuplot sources either.

Mojca

Re: compiling Qt on Mac

[Ethan A M. <sf...@us...>]

On Friday, May 27, 2011 12:20:26 am Mojca Miklavec wrote:
> Hello,
> 
> I wanted to test Qt compilation, but I cannot even start it.

The configure script is assuming that a pkg-config files exists to 
describe the local installation of Qt.  I think we've been through 
this before that OSX does not [typically] use pkg-config.  So you
may have to modify the autoconf scripts to deal with the OSX way 
of doing things.  Here's a start:

> configure scripts asks for lrelease-qt4, but the name of binary on mac
> seems to be lrelease-4.7 (it probably depends on version).

Modify the following line
configure.in:1189:AC_CHECK_PROGS(LRELEASE, lrelease-qt4 lrelease, no)

> On top of that it complains about
> 
> No package 'QtCore' found
> No package 'QtGui' found
> No package 'QtNetwork' found
> No package 'QtSvg' found

Those would have been picked up in the pkgconfig files, I think.
But on OSX they may well be defined in a system header that needs to
be included.  The linux libqt4 distribution includes header files for
a surprising number of other systems. I see, for example:
/usr/lib/qt4/mkspecs/common/mac-g++.conf
/usr/lib/qt4/mkspecs/common/mac-llvm.conf
/usr/lib/qt4/mkspecs/common/mac.conf
/usr/lib/qt4/mkspecs/cygwin-g++
/usr/lib/qt4/mkspecs/cygwin-g++/qmake.conf
/usr/lib/qt4/mkspecs/cygwin-g++/qplatformdefs.h
/usr/lib/qt4/mkspecs/darwin-g++
/usr/lib/qt4/mkspecs/darwin-g++/qmake.conf
/usr/lib/qt4/mkspecs/darwin-g++/qplatformdefs.h
/usr/lib/qt4/mkspecs/macx-xcode
/usr/lib/qt4/mkspecs/macx-xcode/Info.plist.app
/usr/lib/qt4/mkspecs/macx-xcode/Info.plist.lib
/usr/lib/qt4/mkspecs/macx-xcode/qmake.conf
/usr/lib/qt4/mkspecs/macx-xcode/qplatformdefs.h
/usr/lib/qt4/mkspecs/macx-xlc
/usr/lib/qt4/mkspecs/macx-xlc/qmake.conf
/usr/lib/qt4/mkspecs/macx-xlc/qplatformdefs.h

It seems likely that among those (and many more I didn't list) are
the definitions and configuration information you need.

> However I have
>     /Library/Frameworks/QtCore.framework
> and others present and I'm able to compile and use other Qt applications.

Aha. Sounds promising.
Can you see how the Make files for those other Qt applications
refer to Qt, and borrow equivalent commands for gnuplot's configure script?

compiling Qt on Mac

[Mojca M. <moj...@gm...>]

Hello,

I wanted to test Qt compilation, but I cannot even start it. The
configure scripts asks for lrelease-qt4, but the name of binary on mac
seems to be lrelease-4.7 (it probably depends on version).

On top of that it complains about

No package 'QtCore' found
No package 'QtGui' found
No package 'QtNetwork' found
No package 'QtSvg' found

However I have
    /Library/Frameworks/QtCore.framework
and others present and I'm able to compile and use other Qt applications.

Mojca

Re: Transparent background with pdfcairo

[Ethan M. <merritt@u.washington.edu>]

On Tuesday, May 24, 2011 12:52:52 am Christoph Bersch wrote:
> On 24.05.2011 05:35, sfeam (Ethan Merritt) wrote:
> > Christoph Bersch<us...@be...>  wrote>
> >>
> >> is there a specific reason why the 'transparent' terminal option 
applies
> >> only to the pngcairo and not to the pdfcairo terminal?
> >>
> >
> > So far as I know, pdf and PostScript files have no "background" to be
> > set transparent or opaque.
> 
> Correct, but in cairo.trm the background of the pdf is explicitely set 
> to white. This can be avoided with the 'transparent' option which is 
> used only by the pngcairo terminal

You are right. 
The default for PDF output should be transparent.  It already accepts an
explicit background command to override this, but I'll add your patch to
allow the {no}transparent keywords also.

	cheers,

		Ethan 

Re: Transparent background with pdfcairo

[Christoph B. <us...@be...>]

On 24.05.2011 05:35, sfeam (Ethan Merritt) wrote:
> Christoph Bersch<us...@be...>  wrote>
>>
>> is there a specific reason why the 'transparent' terminal option applies
>> only to the pngcairo and not to the pdfcairo terminal?
>>
>
> So far as I know, pdf and PostScript files have no "background" to be
> set transparent or opaque.

Correct, but in cairo.trm the background of the pdf is explicitely set 
to white. This can be avoided with the 'transparent' option which is 
used only by the pngcairo terminal

> Do you actually see a difference in the output file after your patch?

Yes.
I came to this problem when I tried to combine the epslatex and the 
pdfcairo terminal. I could not use the pdf file unless all text was set 
to front.

> Using what tool to view it?

To show the problem, consider the following code:


set terminal pdfcairo transparent
set output 'test-inc.pdf'
set tics lc rgbcolor 'white'
plot sin(x) lw 4


\documentclass{minimal}
\usepackage{graphicx}
\begin{document}
\rule{3cm}{3cm}\hspace*{-3cm}\includegraphics{test-inc}
\end{document}


Without my patch, the file test-inc.pdf completely covers the black 
square. Only with my patch the background of the pdf file is transparent 
to show the black square behind.

Christoph

Re: fit, NLLS and Levenberg–Marquardt

[<pl...@pi...>]

On 05/24/11 02:08, Ethan Merritt wrote:
> On Monday, May 23, 2011 01:12:23 am pl...@pi... wrote:
>>> if there is an alternative approach for the case when x
>>> uncertainty can't be ignored, keep the discussion going and maybe we can
>>> add such a feature to the list of items we'd like to add in the future.
>>>
>>> Dan
>>
>> Yes , I would love to propose that. Some kind of total least squares may
>> be an option I don't know enough about that to make a concrete proposal.
>
> It is standard in my field to use instead a maximum likelihood residual
> that allows for separate error distributions on x and y.  The maximum
> likelihood treatment reduces to a weighted least squares treatment
> if and only if the distribution of errors on both x and y are
> (1) Gaussian and (2) of equal magnitude.
>
> Gnuplot allows for input of precalculated non-uniform weights on y,
> which partially addresses (2).  But there is no provision for non-Gaussian
> errors on y, and no provision for any error model at all on x.
>
> If the errors in your data do not follow the simple Gaussian model,
> then almost certainly you would be better off using maximum likelihood
> rather than least-squares.  But in order to do so you need first a model
> for the error distributions.  That may be obvious for any particular
> experiment or source of data, but it's difficult to impossible for a
> general-purpose program to figure it out for you. You're the one who
> knows the source of the data, so it's up to you to provide an appropriate
> explicit error model along with the data.
>
> The point is that switching to a better minimization residual is more
> than just a matter of changing the internal code.  It would require a
> more complex description of your data that includes error models for
> both the independent and dependent variables.
>
> NB:  When I say "x", I really mean the full set of independent variables
> [x1,x2,x3,...].   "y" is the single dependent variable estimated by
> f(x1,x2,x3,...)
>
> 	Ethan
>

Thanks for all that detail Ethan.

It seems likely that this may be the job for external processing by some 
stats capable package rather than a job for a plotting tool.

That brings us back to the original point of this thread : the idea of 
putting a specific warning about the limitations of least squares 
techniques used by gnuplot into the help text for "fit".

I won't bore everyone with anecdotes but I never cease to be amazed by 
the widespread ignorance of this issue , even at PhD level.

For the cost of a couple of lines it would be good if at least gnuplot 
user were made aware of it.

best regards.Peter.