CLASS-L Archives

November 2009

CLASS-L@LISTS.SUNYSB.EDU

Options: Use Monospaced Font
Show HTML Part by Default
Show All Mail Headers

Message: [<< First] [< Prev] [Next >] [Last >>]
Topic: [<< First] [< Prev] [Next >] [Last >>]
Author: [<< First] [< Prev] [Next >] [Last >>]

Print Reply
Subject:
From:
"Ahmed N. Albatineh" <[log in to unmask]>
Reply To:
Classification, clustering, and phylogeny estimation
Date:
Tue, 10 Nov 2009 07:12:28 -0800
Content-Type:
multipart/alternative
Parts/Attachments:
text/plain (10 kB) , text/html (15 kB)
Hello Bill;
If you want to look at any index of similarity you can not ignore the concept of correction for chance agreement as these indices measure agreement between two clusterings or partitions of the data. Hubert and Arabie (1985) and Morey and Agresti (1984) offered correction for Rand index for chance agreement. The reason for that is correction for chance agreement improves the performance of the index, in the sense that when there is no clustering structure it gives a value close to zero and a value of unity for identical partitions. In a paper I wrote in 2006 (find below the citation) I proved that Kulczinski's index is identical to McConnaughy (1964) index once corrected for chance agreement hence the choice of the index becomes irrelevant, see also other interesting results in the paper. In no software you will find the Kulczynski's index calculated with correction for chance agreement. Of course you can find it in the R software in the package "simba".
 If you like I am willing to send you a piece of R code that calculates the corrected Kulczynski's index for chance agreement.

see the paper in the Journal of Classifcation Volume 23 issue 1 (2006) by Albatineh et al.

my only two cents

Ahmed Albatineh, PhD

Assistant Professor of Biostatistics
Department of Epidemiology and Biostatistics

Florida International University

University Park Campus

11200 SW 8th Street

Miami, Florida 33199

--- On Mon, 11/9/09, Richard Wright <[log in to unmask]> wrote:

From: Richard Wright <[log in to unmask]>
Subject: Re: Kulczynski's quantitative symmetric measure
To: [log in to unmask]
Date: Monday, November 9, 2009, 7:10 PM

The second of these coefficients is also available in the freely distributable package PAST.

Richard


----- Original Message ---------------

Subject: Re: Kulczynski's quantitative symmetric measure
   From: "F. James Rohlf" <[log in to unmask]>
   Date: Mon, 9 Nov 2009 12:22:06 -0500
     To: [log in to unmask]

>See:
>
> Kulczynski, S. 1927. Die Pflanzenassoziationen der Pienienen.  Bull.
>Intern. Acad. Pol. Sci. Lett. Cl. Sci. Math. Nat., B (Sci. Nat.), 1927
>(Suppl. 2):57-203.
>
> 
>
>There are actually two coefficients. The first is the number of positive
>matches divided by the number of mismatches. The second is the average of
>the proportion of matches for the first object and the proportion of matches
>for the second object.
>
> 
>
>They are available in the NTSYSpc software.
>
> 
>
>Jim
>
> 
>
>----------------------
>
>F. James Rohlf, Distinguished Professor
>
>Dept. Ecology and Evolution, Stony Brook University, NY 11794-5245
>
> 
>
>From: Classification, clustering, and phylogeny estimation
>[mailto:[log in to unmask]] On Behalf Of Shannon, William
>Sent: Monday, November 09, 2009 11:42 AM
>To: [log in to unmask]
>Subject: Kulczynski's quantitative symmetric measure
>
> 
>
>Who has heard of Kulczynski's quantitative symmetric measure.  Not finding a
>lot yet in my online search.  It was suggested as a possible measure for
>some genetic data we are generating.
>
> 
>
> 
>
> 
>
>Thank you.
>
> 
>
>Bill Shannon, PhD
>
>Associate Professor of Biostatistics in Medicine
>
>Washington University School of Medicine
>
>St. Louis, MO
>
> 
>
>314-454-8356
>
>[log in to unmask]
>
> 
>
>---------------------------------------------- CLASS-L list. Instructions:
>http://www.classification-society.org/csna/lists.html#class-l 
>
>
>----------------------------------------------
>CLASS-L list.
>Instructions: http://www.classification-society.org/csna/lists.html#class-l
>
>--Boundary_(ID_xXsnq9qNo3EaNLAcmZMHSw)
>Content-type: text/html; charset=US-ASCII
>Content-transfer-encoding: 7BIT
>
><html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40">
>
><head>
><meta http-equiv=Content-Type content="text/html; charset=us-ascii">
><meta name=Generator content="Microsoft Word 12 (filtered medium)">
><style>
><!--
> /* Font Definitions */
> @font-face
>    {font-family:"Cambria Math";
>    panose-1:2 4 5 3 5 4 6 3 2 4;}
>@font-face
>    {font-family:Calibri;
>    panose-1:2 15 5 2 2 2 4 3 2 4;}
>@font-face
>    {font-family:Tahoma;
>    panose-1:2 11 6 4 3 5 4 4 2 4;}
> /* Style Definitions */
> p.MsoNormal, li.MsoNormal, div.MsoNormal
>    {margin:0in;
>    margin-bottom:.0001pt;
>    font-size:11.0pt;
>    font-family:"Calibri","sans-serif";}
>a:link, span.MsoHyperlink
>    {mso-style-priority:99;
>    color:blue;
>    text-decoration:underline;}
>a:visited, span.MsoHyperlinkFollowed
>    {mso-style-priority:99;
>    color:purple;
>    text-decoration:underline;}
>span.EmailStyle17
>    {mso-style-type:personal;
>    font-family:"Calibri","sans-serif";
>    color:windowtext;}
>span.apple-style-span
>    {mso-style-name:apple-style-span;}
>span.EmailStyle19
>    {mso-style-type:personal-reply;
>    font-family:"Calibri","sans-serif";
>    color:#1F497D;}
>.MsoChpDefault
>    {mso-style-type:export-only;
>    font-size:10.0pt;}
>@page Section1
>    {size:8.5in 11.0in;
>    margin:1.0in 1.0in 1.0in 1.0in;}
>div.Section1
>    {page:Section1;}
>-->
></style>
><!--[if gte mso 9]><xml>
> <o:shapedefaults v:ext="edit" spidmax="1026" />
></xml><![endif]--><!--[if gte mso 9]><xml>
> <o:shapelayout v:ext="edit">
>  <o:idmap v:ext="edit" data="1" />
> </o:shapelayout></xml><![endif]-->
></head>
>
><body lang=EN-US link=blue vlink=purple>
>
><div class=Section1>
>
><p class=MsoNormal style='mso-margin-top-alt:3.75pt;margin-right:6.75pt;
>margin-bottom:0in;margin-left:6.0pt;margin-bottom:.0001pt;text-autospace:none'><span
>style='color:#1F497D'>See:<o:p></o:p></span></p>
>
><p class=MsoNormal style='mso-margin-top-alt:3.75pt;margin-right:6.75pt;
>margin-bottom:0in;margin-left:6.0pt;margin-bottom:.0001pt;text-autospace:none'>&nbsp;Kulczynski,
>S. 1927. Die Pflanzenassoziationen der Pienienen.&nbsp; Bull. Intern. Acad.
>Pol. Sci. Lett. Cl. Sci. Math. Nat., B (Sci. Nat.), 1927 (Suppl. 2):57-203.<o:p></o:p></p>
>
><p class=MsoNormal><span style='color:#1F497D'><o:p>&nbsp;</o:p></span></p>
>
><p class=MsoNormal><span style='color:#1F497D'>There are actually two
>coefficients. The first is the number of positive matches divided by the number
>of mismatches. The second is the average of the proportion of matches for the
>first object and the proportion of matches for the second object.<o:p></o:p></span></p>
>
><p class=MsoNormal><span style='color:#1F497D'><o:p>&nbsp;</o:p></span></p>
>
><p class=MsoNormal><span style='color:#1F497D'>They are available in the
>NTSYSpc software.<o:p></o:p></span></p>
>
><p class=MsoNormal><span style='color:#1F497D'><o:p>&nbsp;</o:p></span></p>
>
><p class=MsoNormal><span style='color:#1F497D'>Jim<o:p></o:p></span></p>
>
><p class=MsoNormal><span style='color:#1F497D'><o:p>&nbsp;</o:p></span></p>
>
><div>
>
><p class=MsoNormal><span style='color:#1F497D'>----------------------<o:p></o:p></span></p>
>
><p class=MsoNormal><span style='color:#1F497D'>F. James Rohlf, Distinguished
>Professor<o:p></o:p></span></p>
>
><p class=MsoNormal><span style='color:#1F497D'>Dept. Ecology and Evolution,
>Stony Brook University, NY 11794-5245<o:p></o:p></span></p>
>
></div>
>
><p class=MsoNormal><span style='color:#1F497D'><o:p>&nbsp;</o:p></span></p>
>
><div>
>
><div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in'>
>
><p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span
>style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> Classification,
>clustering, and phylogeny estimation [mailto:[log in to unmask]] <b>On
>Behalf Of </b>Shannon, William<br>
><b>Sent:</b> Monday, November 09, 2009 11:42 AM<br>
><b>To:</b> [log in to unmask]<br>
><b>Subject:</b> Kulczynski's quantitative symmetric measure<o:p></o:p></span></p>
>
></div>
>
></div>
>
><p class=MsoNormal><o:p>&nbsp;</o:p></p>
>
><p class=MsoNormal>Who has heard of <span class=apple-style-span><span
>style='font-size:10.5pt;font-family:"Arial","sans-serif"'>Kulczynski’s
>quantitative symmetric measure.&nbsp; Not finding a lot yet in my online
>search.&nbsp; It was suggested as a possible measure for some genetic data we
>are generating.<o:p></o:p></span></span></p>
>
><p class=MsoNormal><o:p>&nbsp;</o:p></p>
>
><p class=MsoNormal><o:p>&nbsp;</o:p></p>
>
><p class=MsoNormal><span style='font-family:"Arial","sans-serif";color:black'><o:p>&nbsp;</o:p></span></p>
>
><p class=MsoNormal><span style='font-family:"Arial","sans-serif";color:black'>Thank
>you.</span><span style='font-family:"Arial","sans-serif";color:#1F497D'><o:p></o:p></span></p>
>
><p class=MsoNormal><span style='font-family:"Arial","sans-serif";color:#1F497D'><o:p>&nbsp;</o:p></span></p>
>
><p class=MsoNormal><span style='font-family:"Arial","sans-serif";color:black'>Bill
>Shannon, PhD</span><span style='font-family:"Arial","sans-serif";color:#1F497D'><o:p></o:p></span></p>
>
><p class=MsoNormal><span style='font-family:"Arial","sans-serif"'>Associate Professor
>of Biostatistics in Medicine<o:p></o:p></span></p>
>
><p class=MsoNormal><span style='font-family:"Arial","sans-serif"'>Washington
>University School of Medicine<o:p></o:p></span></p>
>
><p class=MsoNormal><span style='font-family:"Arial","sans-serif"'>St. Louis, MO<o:p></o:p></span></p>
>
><p class=MsoNormal><span style='font-family:"Arial","sans-serif"'>&nbsp;<o:p></o:p></span></p>
>
><p class=MsoNormal><span style='font-family:"Arial","sans-serif"'>314-454-8356<o:p></o:p></span></p>
>
><p class=MsoNormal><span style='font-family:"Arial","sans-serif";color:#1F497D'><a
>href="mailto:[log in to unmask]">[log in to unmask]</a><o:p></o:p></span></p>
>
><p class=MsoNormal><o:p>&nbsp;</o:p></p>
>
><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman","serif"'>----------------------------------------------
>CLASS-L list. Instructions: http://www.classification-society.org/csna/lists.html#class-l
><o:p></o:p></span></p>
>
></div>
>
></body>
>
></html>
>----------------------------------------------
>CLASS-L list.
>Instructions: http://www.classification-society.org/csna/lists.html#class-l
>
>--Boundary_(ID_xXsnq9qNo3EaNLAcmZMHSw)--

----------------------------------------------
CLASS-L list.
Instructions: http://www.classification-society.org/csna/lists.html#class-l



      

----------------------------------------------
CLASS-L list.
Instructions: http://www.classification-society.org/csna/lists.html#class-l

ATOM RSS1 RSS2