Hi Dana > -----Original Message----- > From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] > On Behalf Of Dana77 > Sent: Wednesday, December 03, 2008 3:24 PM > To: r-help@r-project.org > Subject: [R] Help with reading code > > > I would like to give out the equation for calculating the maximum > likelihood. > Below is the code, but I still have problems with it. After I read the > code, I found there are two cases for "w(weights)". If "w" is not zero, > then the equation is given as "val <- 0.5 * (sum(log(w)) - N * (log(2 * > pi) > + 1 - log(N) + > log(sum(w * res^2))))". However, if "w" is zero, then I do not > know > what equation it should be since it does not make any sense for "log0". > Hope > someone can help me to figure this out. Thanks! > > > > > function (object, REML = FALSE, ...) > { > res <- object$residuals > p <- object$rank > N <- length(res) > if (is.null(w <- object$weights)) { > w <- rep.int(1, N) > } > else { > excl <- w == 0 #####I can not understand the following lines after this.
The command above sets a variable to "exclude" with. Any observation with weight equal to zero will get excluded. excl will have value TRUE for all observations with weight 0. > if (any(excl)) { ### If there are any observations to exclude > res <- res[!excl] ### then keep the ones with weight not zero > N <- length(res) > w <- w[!excl] } so the above chunk keeps only the residuals and weights for the observations with non-zero weights > } > N0 <- N > if (REML) > N <- N - p > val <- 0.5 * (sum(log(w)) - N * (log(2 * pi) + 1 - log(N) + > log(sum(w * res^2)))) so now there are no more observations with w == 0 in the above equation > if (REML) > val <- val - sum(log(abs(diag(object$qr$qr)[1:p]))) > attr(val, "nall") <- N0 > attr(val, "nobs") <- N > attr(val, "df") <- p + 1 > class(val) <- "logLik" > val > } > > > Best, > > Dana > -- > View this message in context: http://www.nabble.com/Help-with-reading- > code-tp20823979p20823979.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. Steven McKinney Statistician Molecular Oncology and Breast Cancer Program British Columbia Cancer Research Centre email: [EMAIL PROTECTED] tel: 604-675-8000 x7561 BCCRC Molecular Oncology 675 West 10th Ave, Floor 4 Vancouver B.C. V5Z 1L3 Canada ______________________________________________ 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.