Re: looking for a distance measure

[Art Kendall]

Perhaps you would want to look at your variables as having 2 values{0,1} and then as having 3 values {0,1,2}.  Maybe "not tried" could be treated as an actual value rather than a missing value since you know that it was not tried. wrt distance/similarity measures many can be found in SPSS see pp 1546 to 1556 in the  SPSS Statistics 17.0 Command Syntax Reference see pp 639-704 in the SPSS Statistics 17.0 Algorithms The TWOSTEP procedure in SPSS has Log-Likelihood Distance The log-likelihood distance measure can handle both continuous and categorical variables. It is a probability based distance. The distance between two clusters is related to the decrease in log-likelihood as they are combined into one cluster. In calculating log-likelihood, normal distributions for continuous variables and multinomial distributions for categorical variables are assumed. It is also assumed that the variables are independent of each other, and so are the cases. the algorithm for this measure can be found at pp 816 - 817 in the SPSS Statistics 17.0 Algorithms The same info can be found in documentation for earlier versions of SPSS but the page numbers would be different. I 'll send Bill PDFs of these pages and they can be found on the SPSS web page and on the CDs that comes with SPSS. Art Kendall Shannon, William wrote: A follow up based on some questions I got from members of the lsit. The data will be a list of distinct 0's and 1's and missing values. Suppose patient 1 received drug A with no effect and then drug B which was effective -- their data would be (0 1 Missing Missing). Patient 2 receives drugs C and D with no effect but A works, and B is never given -- their data would be (1 Missing 0 0). Etc. Assume the columns or entries of the vectors corresponding to drug A B C D where the entry is 0 if not effective, 1 if effective, and missing if not given. Assume also the order of drug given is random. It may be order and number of ineffective drugs given should be ignored and distance based on responding to the same drug or different drug. Thank you Bill Shannon, PhD Associate Prof. of Biostatistics in Medicine Washington University School of Medicine Director, Biostatistical Consulting Center 314-454-8356 ________________________________________ From: Shannon, William Sent: Wednesday, September 23, 2009 11:44 AM To: class l list (CLASS-L@LISTS.SUNYSB.EDU) Cc: Shannon, William; Farrokh Alemi Subject: looking for a distance measure Hi Everyone I may be working with a data set that has the following structure and will need to develop a distance measure. I have not had time to think carefully about it but am hoping someone might have already worked with data like this. Patients present to the doctor with a disease and it is unknown which of four drugs they will respond to (the goal of this project is to improve the ability to predict and be able to give the correct drug first). MD’s treat these patients empirically – give them drug A and see if they respond, if not give them drug B and see if they respond, etc. We assume a patient either responds or does not, and that there is no carry over or order of drug effect (i.e., if you respond to drug B it is irrelevant if you had already had drug A). I also assume there is no set order on which drugs are given first. The data for each patient will be a vector of 0’s for non response and a 1 for response, with the number of 0’s dependent on how many drugs were given empirically before a response occurred. How do we calculate a pair wise distance matrix between pairs of patients with this data? Thank you. Bill Shannon, PhD Associate Professor of Biostatistics in Medicine Washington University School of Medicine St. Louis, MO 314-454-8356 wshan...@wustl.edu<mailto:wshan...@wustl.edu> ---------------------------------------------- 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