[R] Weighted pairwise LDA
Hello All, I am doing LDA, trying to build a model to identify type of bacteria. Unfortunately the training group sizes are very smalln=4 for each groupof which there are 10. I have noticed that LDA is highly influenced by outlying groups and 'pulls' the LDs towards them (as you would expect). I have looked around and found pair-wise weighted LDA. This is a rather clever way of 'normalising' the weight given to LD scores according to the euclidian distance between groups, thus giving better separation power to other groups to the minor loss of power for the outlying group. I am able to write a programme to do this for me, but my standard results (unweighted) are not as good as those from the R programme LDA. I know R does LDA in a slightly more sophisticated way than me.as I just using bog standard (Sw-1)Sb eigenvectors due to my general ignorance. I was wondering if anyone knew of an LDA package in R which features some sort of 'pair-wise' distance weighting. Thanks in advance, Ben -- View this message in context: http://r.789695.n4.nabble.com/Weighted-pairwise-LDA-tp4686145.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Actual code for LDA
Hi All, I've been trying to write my own code for LDA (linear discrim) so I can modify it to be weighted LDA since some of my groups are outliers. However, the code I write for standard LDA gives me slightly different results to those from R (slightly different LDAs.and not just scalar differences. Does R simply invert the pooled within groups scatter matrix e.g. solve(Sw) and multiply it by the between groups scatter Sb, then take the eigen vectors? This is the approach that I use, yet get slightly different results..does R by default use a slightly more robust inverse or estimate of Sw?? I've looked at the source code, and I find it very hard to follow. If anyone has any ideas that would be great!! Thanks, Ben -- View this message in context: http://r.789695.n4.nabble.com/Actual-code-for-LDA-tp4685194.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Optimum of lm
Hi All, I am trying to do some D o E. I would like to find the optima (maxima) of a 2 dimensional lm with quadratic terms. I'm sure there is a really simple solution but i can't find it. Also would there be any way to find some sort of confidence limits on these optima? Any help most appreciated! Cheers, Ben -- View this message in context: http://r.789695.n4.nabble.com/Optimum-of-lm-tp4670674.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Returning overall ms for CVlm
Hi All, when doing CVlm cross validation, I would just like to view the overall MS but i am having trouble getting just this value. I'm kina new to R. Any help really appreciates. Cheers, Ben -- View this message in context: http://r.789695.n4.nabble.com/Returning-overall-ms-for-CVlm-tp4664690.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Sequence analysis
Hiya, I am trying to look at the similarities between a number of sequences, for example i am trying to see how similar ababbbassdaa is to addffggssbbsbbs I was wondering is the some way for me to see how similar they are in terms of, for example, number of a's, number of b's, how often a and ab are consecutive, how often abab is together etc. Any advice would be really useful..any kind of shove in the right direction would be amazing! I've tried doing basic alignments but i think this is loosing quite a lot of information. Many thanks, Ben -- View this message in context: http://r.789695.n4.nabble.com/Sequence-analysis-tp4664693.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
