Hmisc/R/varclus.s

8            data=NULL, subset=NULL, na.action=na.retain, ...)
21       x <- list(formula=form, data=data, na.action=na.action, subset=subset)
43           isthere <- 1*(!is.na(x))
44           x[is.na(x)] <- 0
69   if(any(is.na(x)))
84                  method=method, na.action=nact),class="varclus")
91   if(length(x$na.action))
92     naprint(x$na.action)
134          (!is.expression(s) && (is.na(s) || s=='')))
177 na.retain <- function(mf) mf
182   ismiss <- function(x) if(is.character(x))x=='' else is.na(x)
184   na <- sapply(df, ismiss)*1
186   n <- nrow(na)
187   sim <- crossprod(na)/n
190   na.per.obs <- apply(na, 1, sum)
191   nc <- ncol(na)
192   mean.na <- rep(NA, nc)
193   names(mean.na) <- dimnames(na)[[2]]
196       y <- na[,i]==1
197       if(any(y)) mean.na[i] <- mean(na.per.obs[y]) - 1
201   res$na.per.obs <- na.per.obs
202   res$mean.na    <- mean.na
212   tab <- table(obj$na.per.obs)
213   na.per.var <- diag(obj$sim)
214   names(na.per.var) <- dimnames(obj$sim)[[2]]
215   mean.na <- obj$mean.na
218     dotchart(sort(na.per.var), xlab='Fraction of NAs',
227     dotchart(sort(mean.na),
241       plot(na.per.var, mean.na, xlab='Fraction of NAs for Single Variable',
247       s <- (1:length(na.per.var))[!is.na(mean.na)]
254           w <- s[s > i & abs(na.per.var[s]-na.per.var[i]) < eps &
255                  abs(mean.na[s]-mean.na[i]) < epsy]
259               text(na.per.var[i]+eps, mean.na[i],
260                    paste(names(na.per.var[c(i,w)]),collapse='\n'),adj=0)
262           else text(na.per.var[i]+eps, mean.na[i], names(na.per.var)[i], adj=0)
274   f <- table(x)/sum(!is.na(x))
297                         slim=range(pretty(c(0,max(s,na.rm=TRUE)))),