Maxent version 3.3.0 released

[Steven Phillips]

Hi everyone,

There's a new version of Maxent available on the download site,
http://www.cs.princeton.edu/~schapire/maxent/. There are quite a few
changes, so we're calling it a "beta" release in case some bugs crept
in. Please feel free to try it out, and let me know if you see anything
amiss. The major changes since version 3.2.19 are:

* Replicated runs added, to allow cross-validation, bootstrapping
and repeated subsampling. After a replicated run, a web page is
made that analyzes and combines the results of the individual runs.
* Clamping pictures have changed. When projecting, the picture
showing the effect of clamping now simply gives the difference
between predictions with and without clamping.
* Parameters are treated more uniformly, and many more are exposed
in the Settings window and described in the Help window.
* Bug fixed in using bias files.
* The feature type buttons have a slightly different meaning, with
"auto features" choosing a subset of the selected types. This
allows you to limit the feature types used by auto features.
* More efficient memory usage, to avoid memory problems with large
grids.
* Pictures of predictions are now created by default.
* Duplicate presence records are now removed by default.
* Projection onto SWD-format files and writing of background
predictions both preserve x and y coordinates of points.
* The html output now gives the command line with all flags needed
to repeat a run.
* A limited API for calling Maxent from other Java code.

-- Steven

[xime velez-liendo]

I wonder if anyone has problem opening the bat file in the new 3.3
version. In my case whenever I click on the bat file to open Maxent,
it just doesn't work. I got the black msdos screen for half second,
and then its gone. I tried with the older version, and starting the
software with bat file works perfectly.

Thanks,
mena

2009/4/23 Steven Phillips <phil...@research.att.com>:

[Julian Ramirez]

Do you have both the .bat and .jar in the same folder?

Julián

[Steven Phillips]

Hi Mena,

Something I should have included in the list of major changes: you need
to have version 1.5 or later of Java installed, so if you're still using
Java 1.4.2, you'll probably get the behaviour you described.

Secondly, I just discovered that there's a way to stop that msdos screen
from disappearing when there's an error: add this line:

if errorlevel 1 pause

to the end of the .bat file. You can edit the .bat file with notepad or
wordpad.

-- Steven

[xime velez-liendo]

Hi Steven,

Attached is the screen with the msdos message.
I checked my java version and I'm running with 1.6, also I've
increased memory to 1300, but still got the same problem.

[Steven Phillips]

Hi Mena,

Not sure what the problem is. What is the "shortcut to maxent" at the
top of the window? What happens if you just click on the jar file?

> ------------------------------------------------------------------------
>

[asha_mc]

Hi Steven

Thanks for the new version, the new option available straight from the
GUI looks great, and it has solved my question regarding single
variable only response data, which I previously could not find.

However, I've tried to rerun my models run from previous versions and
find that they are slightly different. Upon inspection it seems that
there is a large difference in the nunmber of background points used,
10252 in the previous version but only 6904 in the new version. I have
used all other samples/variables/settings the same both times, which
were all default except Jackknife selected, Remove duplicates
selected, Make pictures selected, Create response curves selected (in
the old version anyway).

Whats going on here? What is the reason behind the change and what
effect does it have on my models?

Thanks again for your great work and tireless help,

Asha

On Apr 24, 5:34 am, Steven Phillips <phill...@research.att.com> wrote:
> Hi Mena,
>
> Not sure what the problem is.  What is the "shortcut to maxent" at the
> top of the window?  What happens if you just click on the jar file?
>
> -- Steven
>
>
>
> xime velez-liendo wrote:
> > Hi Steven,
>
> >  Attached is the screen with the msdos message.
> > I checked my java version and I'm running with 1.6, also I've
> > increased memory to 1300, but still got the same problem.
>
> > mena
>

> > 2009/4/23 Steven Phillips <phill...@research.att.com>:

>
> >> Hi Mena,
>
> >> Something I should have included in the list of major changes:  you need
> >> to have version 1.5 or later of Java installed, so if you're still using
> >> Java 1.4.2, you'll probably get the behaviour you described.
>
> >> Secondly, I just discovered that there's a way to stop that msdos screen
> >> from disappearing when there's an error:  add this line:
>
> >>   if errorlevel 1 pause
>
> >> to the end of the .bat file.  You can edit the .bat file with notepad or
> >> wordpad.
>
> >> -- Steven
>
> >> xime velez-liendo wrote:
>
> >>> I wonder if anyone has problem opening the bat file in the new 3.3
> >>> version.  In my case whenever I click on the bat file to open Maxent,
> >>> it just doesn't work. I got the black msdos screen for half second,
> >>> and then its gone. I tried with the older version, and starting the
> >>> software with bat file works perfectly.
>
> >>> Thanks,
> >>> mena
>

> >>> 2009/4/23 Steven Phillips <phill...@research.att.com>:

> > ------------------------------------------------------------------------- Hide quoted text -
>
> - Show quoted text -

[Steven Phillips]

Asha and Bruce,

Some reasons you might get different results:

1. The latest version removes duplicate records by default, whereas
previous version only gave that as an option.

2. If your study area has less than 10000 pixels, versions before 3.2.7
still made 10000 background points, with some points included multiple
times. With newer versions, each pixel is included at most once.

3. Again before 3.2.7, background data were chosen using a different
randomized sampling method.

-- Steven

[Marnin Wolfe]

Additionally, if you are running partitions that involve randomly seeded training presences than each time you run the model you will get slightly different results. The key, then is run the model some 10 or more times and observe the mean and variance in model output before running a final model that uses 100% of your training points. The full model will be the same every time you run it.

Cheers,

M

--
Marnin Wolfe
University of Pittsburgh
Department of Biological Sciences
Ecology & Evolution Program
wol...@gmail.com (or)
md...@pitt.edu
239-595-5081

[semra]

Hi,
I have a problem with opening the new version. I get this error "
'java' is not recognized as an internal or external command, operable
program or batch file."
I checked my java install, and its version. I have recommended version
of java. Also I checked the path variable of computer properties as
mentioned in "readme text". It is ok too.
I can use old version perfectly. What is the missing points?

Thanks for your advice,

Semra

[ColinD]

Hard to say without knowing more about your system and file structure.
All I did was replace the old maxent.jar with the new one in the
folder that I had been using it from and it worked fine (the bat file
is the same). If as you say the old version is working just rename
maxent.jar to maxent.jar.old and place the latest maxent.jar with it
and run the .bat file.