rainman

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  • in reply to: Variance explained by ordination axes #505
    rainman
    Member

    Yes, thanks. That’s what I thought, but it was making my head hurt 🙂

    in reply to: Variance explained by ordination axes #503
    rainman
    Member

    Hi Lee,

    I’m still a bit concerned about this topic.

    Apparently in the DOS version one was able to get this stat when running the varimax rotation procedure.

    Obviously it would be great to obtain this stat in the windows version too. I mean, if you’re looking at axis y, which shows the most meaningful result for your experiment (given your a priori groups etc…), you could be missing what is ‘actually’ happening in your dataset. That is, axis x could be accounting for more of the variability – in a way which you may not have previously considered.

    Does PATN automatically employ varimax rotation and present that result? And, if so, does VR move the data points relative to the axes themselves, or merely spin the ordination (as one can do in the current windows version 3.11)?

    Many thanks in advance,
    Tom.

    in reply to: save dendogram image question #489
    rainman
    Member

    mmmm interesting. I have just tried this, for the first time.

    I had similar problems. When I tried to save it as a *.bmp, there was a file error. Then when I saved it as a reduced bmp, PATN automatically changed it to a emf file.

    Seems very buggy to me, so I guess you’re not alone :), but I don’t have a solution…

    in reply to: Uniform ordination axes scales #487
    rainman
    Member

    Thanks for that Lee.

    While I understand that the relationship between the points in the plot is the most important feature, as you explain above, I am still a little confused.

    Why are the scales on the axes different, but the actual length of the axes the same on the screen? Doesn’t this essentially squash the plot?

    For example, in the following analysis I ordinated the [mean abundance of] aquatic invertebrate communities at four sites over five sampling rounds (i.e. Site 1, Round 2 = 12 etc…).

    This is the patn plot. Note the nice-ish division between the dry season samples on the left (numbers ending in 1 or 4), and the wet season samples on the right (numbers ending in 2, 3 or 5).

    http://tomandzoe.com/broadband/analyses/aquatic_inverts.jpg

    The x axis covers a range of 1.695, while the y axis covers a range of 2.128. However, the actual axes themselves are the same length.

    Exported into sigmaplot, the ordination looks like this (note the even axes). The relationship between the points (which you stress above) has changed because the axes are no longer squashed.

    http://tomandzoe.com/broadband/analyses/aquatic_inverts_sigmaplot.JPG

    Is this a bug in patn, or am I missing the ‘point’ 😉 (i.e. are the axes actually measuring different things (therefore actually different scales)?

    Or, is it because as you state here (http://patn.org/phpBB2/viewtopic.php?t=34), the “result will not have axes that in any way correspond to the SSH axes. SSH simply aims to get the maximum information in the selected number of axes.”

    Here is the dataset f.y.i. (the Unidentified variable was made extrinsic, and the columns were log transformed prior to analysis, Bray Curtis w/ default settings).

    http://tomandzoe.com/broadband/analyses/aquatic_inverts.xls

    And the project background:

    http://tomandzoe.com/phd.html

    Thanks,
    Tom (user id = rainman)

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