R cor有时返回NaN [英] R cor returns NaN sometimes
问题描述
我一直在处理一些数据，可在这里找到: Dropbox' csv文件(请使用它复制错误).
I've been working on some data, available here: Dropbox' csv file (please be kind to use it to replicate the error).
当我运行代码时:
t<-read.csv("120.csv")
x<-NULL
for (i in 1:100){
x<-c(x,cor(t$nitrate,t$sulfate,use="na.or.complete"))
}
sum(is.nan(x))
我得到最后一个表达式的随机值，通常在55到60之间.我希望cor给出重复的结果，所以我希望x是一个length = 100的向量，由相同的值组成.例如，请参阅两次独立运行的输出:
I get random values of the last expression, usually around 55 to 60. I expect cor to give repetible results, so I expect x to be a vector of length=100 made of identical values. See, for example, the output of two independent runs:
> x<-NULL; for (i in 1:100){x<-c(x,cor(t$nitrate,t$sulfate,use="na.or.complete"))}
> sum(is.nan(x))
[1] 62
> head(x,10)
[1] NaN NaN 0.2967441 NaN 0.2967441 NaN NaN NaN
[9] 0.2967441 NaN
> x<-NULL; for (i in 1:100){x<-c(x,cor(t$nitrate,t$sulfate,use="na.or.complete"))}
> sum(is.nan(x))
[1] 52
> head(x,10)
[1] 0.2967441 NaN NaN NaN NaN 0.2967441 0.2967441 NaN
[9] 0.2967441 0.2967441
>
我想知道我在这里做错什么了吗，还是一个[n] [未知]的错误.如果是这样的话，我很感谢有能力比我帮助我报告给CRAN更高的专家.
I wonder if I'm doing something wrong here, or if it's a[n] [un]known bug. If that's the case, I appreciate if somebody more profficient than I helps me reporting it to CRAN.
我读了一篇非常古老的文章(2001年)，其中cor.test表现出相同的行为(请参见
I read a very old (2001) post where the same behavior was exhibited by cor.test (see cor.test produces NaN sometimes.
感谢您的友好解释，因为我对R不满意.谢谢！
I appreciate your kind explanations, as I'm a nOOb to R. Thanks!
Per Ben的建议:
Per Ben's Suggestion:
> sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=Spanish_Colombia.1252 LC_CTYPE=Spanish_Colombia.1252 LC_MONETARY=Spanish_Colombia.1252 LC_NUMERIC=C
[5] LC_TIME=Spanish_Colombia.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] stringr_0.6.2 digest_0.6.4 RCurl_1.95-4.3 bitops_1.0-6 qpcR_1.4-0 Matrix_1.1-4 robustbase_0.91-1 rgl_0.95.1157
[9] minpack.lm_1.1-8 MASS_7.3-35 plyr_1.8.1 swirl_2.2.16 ggplot2_1.0.0 lattice_0.20-29
loaded via a namespace (and not attached):
[1] colorspace_1.2-4 DEoptimR_1.0-2 grid_3.1.1 gtable_0.1.2 httr_0.5 labeling_0.3 munsell_0.4.2 proto_0.3-10 Rcpp_0.11.3
[10] reshape2_1.4 scales_0.2.4 testthat_0.9.1 tools_3.1.1 yaml_2.1.13
find("cor")的结果:
Results of find("cor"):
> find("cor")
[1] "package:stats"
---------- ###第二次编辑### --------
---------- ### Second Edit ###--------
我重新启动了会话(我不太了解如何传递--vanilla参数.我正在使用Rstudio)，这是新的sessionInfo:
I restarted the session (I didn't quite find how to pass the --vanilla argument. I'm using Rstudio), and this is the new sessionInfo:
> sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=Spanish_Colombia.1252 LC_CTYPE=Spanish_Colombia.1252 LC_MONETARY=Spanish_Colombia.1252 LC_NUMERIC=C
[5] LC_TIME=Spanish_Colombia.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] tools_3.1.1
我在新会话中再次运行命令，仍然得到sum(is.nan(x))= 52:(
I run the commands again in the new session, and still get sum(is.nan(x))=52 :(
以防万一:
> cor
function (x, y = NULL, use = "everything", method = c("pearson",
"kendall", "spearman"))
{
na.method <- pmatch(use, c("all.obs", "complete.obs", "pairwise.complete.obs",
"everything", "na.or.complete"))
if (is.na(na.method))
stop("invalid 'use' argument")
method <- match.arg(method)
if (is.data.frame(y))
y <- as.matrix(y)
if (is.data.frame(x))
x <- as.matrix(x)
if (!is.matrix(x) && is.null(y))
stop("supply both 'x' and 'y' or a matrix-like 'x'")
if (!(is.numeric(x) || is.logical(x)))
stop("'x' must be numeric")
stopifnot(is.atomic(x))
if (!is.null(y)) {
if (!(is.numeric(y) || is.logical(y)))
stop("'y' must be numeric")
stopifnot(is.atomic(y))
}
Rank <- function(u) {
if (length(u) == 0L)
u
else if (is.matrix(u)) {
if (nrow(u) > 1L)
apply(u, 2L, rank, na.last = "keep")
else row(u)
}
else rank(u, na.last = "keep")
}
if (method == "pearson")
.Call(C_cor, x, y, na.method, FALSE)
else if (na.method %in% c(2L, 5L)) {
if (is.null(y)) {
.Call(C_cor, Rank(na.omit(x)), NULL, na.method, method ==
"kendall")
}
else {
nas <- attr(na.omit(cbind(x, y)), "na.action")
dropNA <- function(x, nas) {
if (length(nas)) {
if (is.matrix(x))
x[-nas, , drop = FALSE]
else x[-nas]
}
else x
}
.Call(C_cor, Rank(dropNA(x, nas)), Rank(dropNA(y,
nas)), na.method, method == "kendall")
}
}
else if (na.method != 3L) {
x <- Rank(x)
if (!is.null(y))
y <- Rank(y)
.Call(C_cor, x, y, na.method, method == "kendall")
}
else {
if (is.null(y)) {
ncy <- ncx <- ncol(x)
if (ncx == 0)
stop("'x' is empty")
r <- matrix(0, nrow = ncx, ncol = ncy)
for (i in seq_len(ncx)) {
for (j in seq_len(i)) {
x2 <- x[, i]
y2 <- x[, j]
ok <- complete.cases(x2, y2)
x2 <- rank(x2[ok])
y2 <- rank(y2[ok])
r[i, j] <- if (any(ok))
.Call(C_cor, x2, y2, 1L, method == "kendall")
else NA
}
}
r <- r + t(r) - diag(diag(r))
rownames(r) <- colnames(x)
colnames(r) <- colnames(x)
r
}
else {
if (length(x) == 0L || length(y) == 0L)
stop("both 'x' and 'y' must be non-empty")
matrix_result <- is.matrix(x) || is.matrix(y)
if (!is.matrix(x))
x <- matrix(x, ncol = 1L)
if (!is.matrix(y))
y <- matrix(y, ncol = 1L)
ncx <- ncol(x)
ncy <- ncol(y)
r <- matrix(0, nrow = ncx, ncol = ncy)
for (i in seq_len(ncx)) {
for (j in seq_len(ncy)) {
x2 <- x[, i]
y2 <- y[, j]
ok <- complete.cases(x2, y2)
x2 <- rank(x2[ok])
y2 <- rank(y2[ok])
r[i, j] <- if (any(ok))
.Call(C_cor, x2, y2, 1L, method == "kendall")
else NA
}
}
rownames(r) <- colnames(x)
colnames(r) <- colnames(y)
if (matrix_result)
r
else drop(r)
}
}
}
<bytecode: 0x0000000008ce0158>
<environment: namespace:stats>
再次感谢.
推荐答案
像我一样困惑的是，我开始玩弄cor的use=参数上的各种选项.我发现如果使用cor(t$nitrate,t$sulfate,use="pairwise.complete.obs")，我可以得到一致的结果:
Puzzled as I was, I started playing around with the various options on the use= argument of cor. I found that I can have consistent results if I use cor(t$nitrate,t$sulfate,use="pairwise.complete.obs"):
> x<-NULL; for (i in 1:100){x<-c(x,cor(t$nitrate,t$sulfate,use="pairwise.complete.obs"))};x
[1] 0.2967441 0.2967441 0.2967441 0.2967441 0.2967441 0.2967441 0.2967441 0.2967441 0.2967441 0.2967441 0.2967441
[12] 0.2967441 0.2967441 0.2967441 0.2967441 0.2967441 0.2967441 0.2967441 0.2967441 0.2967441 0.2967441 0.2967441
[23] 0.2967441 0.2967441 0.2967441 0.2967441 0.2967441 0.2967441 0.2967441 0.2967441 0.2967441 0.2967441 0.2967441
[34] 0.2967441 0.2967441 0.2967441 0.2967441 0.2967441 0.2967441 0.2967441 0.2967441 0.2967441 0.2967441 0.2967441
[45] 0.2967441 0.2967441 0.2967441 0.2967441 0.2967441 0.2967441 0.2967441 0.2967441 0.2967441 0.2967441 0.2967441
[56] 0.2967441 0.2967441 0.2967441 0.2967441 0.2967441 0.2967441 0.2967441 0.2967441 0.2967441 0.2967441 0.2967441
[67] 0.2967441 0.2967441 0.2967441 0.2967441 0.2967441 0.2967441 0.2967441 0.2967441 0.2967441 0.2967441 0.2967441
[78] 0.2967441 0.2967441 0.2967441 0.2967441 0.2967441 0.2967441 0.2967441 0.2967441 0.2967441 0.2967441 0.2967441
[89] 0.2967441 0.2967441 0.2967441 0.2967441 0.2967441 0.2967441 0.2967441 0.2967441 0.2967441 0.2967441 0.2967441
[100] 0.2967441
我仍然不明白为什么其他用户传递的use其他选项不会引起怪异的行为.
I still don't get why other options of use passed by other users didn't cause the weird behavior.
这篇关于R cor有时返回NaN的文章就介绍到这了，希望我们推荐的答案对大家有所帮助，也希望大家多多支持IT屋！
