Displaying 20 results from an estimated 7000 matches similar to: "how to see inbuilt function(cor.test) & how to get p-value from t-value(test of significance) ?"
2004 Mar 03
1
cor(..., method="spearman") or cor(..., method="kendall") (PR#6641)
Dear R maintainers,
R is great. Now that I have that out of the way, I believe I have
encountered a bug, or at least an inconsistency, in how Spearman and
Kendall rank correlations are handled. Specifically, cor() and
cor.test() do not produce the same answer when the data contain NAs.
cor() treats the NAs as data, while cor.test() eliminates them. The
option
use="complete.obs" has
2008 Nov 26
2
Very slow: using double apply and cor.test to compute correlation p.values for 2 matrices
My two matrices are roughly the sizes of m1 and m2. I tried using two apply and cor.test to compute the correlation p.values. More than an hour, and the codes are still running. Please help to make it more efficient.
m1 <- matrix(rnorm(100000), ncol=100)
m2 <- matrix(rnorm(10000000), ncol=100)
cor.pvalues <- apply(m1, 1, function(x) { apply(m2, 1, function(y) { cor.test(x,y)$p.value
2009 Mar 13
1
cor.test(x,y)
Hi,
I am not sure which kind of test is applied to the data if you use
cor.test(x, y) ?
Is it an unpaired t-Test?
Regards
--
View this message in context: http://www.nabble.com/cor.test%28x%2Cy%29-tp22492993p22492993.html
Sent from the R help mailing list archive at Nabble.com.
2008 Jan 02
2
strange behavior of cor() with pairwise.complete.obs
Hi all,
I'm not quite sure if this is a feature or a bug or if I just fail to understand
the documentation:
If I use cor() with pairwise.complete.obs and method=pearson, the result is a
scalar:
->cor(c(1,2,3),c(3,4,6),use="pairwise.complete.obs",method="pearson")
[1] 0.9819805
The documentation says that
" '"pairwise.complete.obs"' only
2011 May 16
2
about spearman and kendal correlation coefficient calculation in "cor"
Hi,
I have the following two measurements stored in mat:
> print(mat)
[,1] [,2]
[1,] -14.80976 -265.786
[2,] -14.92417 -54.724
[3,] -13.92087 -58.912
[4,] -9.11503 -115.580
[5,] -17.05970 -278.749
[6,] -25.23313 -219.513
[7,] -19.62465 -497.873
[8,] -13.92087 -659.486
[9,] -14.24629 -131.680
[10,] -20.81758 -604.961
[11,] -15.32194 -18.735
To calculate the ranking
2005 Feb 13
1
Bug in cor function (PR#7689)
I can't hardly accept the result of cor function with
pairwize.colplete.obs or complete.obs
insert print statements in cor function,
+ if (method != "pearson") {
+ Rank <- function(u) if (is.matrix(u))
+ apply(u, 2, rank, na.last = "keep")
+ else rank(u, na.last = "keep")
+ x <- Rank(x)
+
2003 Nov 07
2
Bug in cor.test - Spearman
Greetings.
There seems to be a problem with the P-value computation in the
cor.test with method="spearman". In R1.8.0 (MS Windows) I
seem to be getting intermittently nonsense P-values, but the rho's
are OK. I can get this reproducibly with the toy example attached
where the first use is OK and subsequent calls with the same data
give nonsense. (I have also seen the problem
2005 Oct 09
3
cor doesn't accept na.rm? (PR#8193)
Full_Name: Paul Bailey
Version: 2.1.1
OS: OS X 10.3
Submission from: (NULL) (68.252.250.144)
?cor
[tells me that it has a na.rm variable]
> cor(frame2[1,],frame2[2,],na.rm=T)
Error in cor(frame2[1, ], frame2[2, ], na.rm = T) :
unused argument(s) (na.rm ...)
hmm.
2004 Jul 09
1
cor.test p-value ties
R:
I got a warning message when running the cor.test function using both
Spearman and Kendall rank correlations saying that the p-value may be
incorrect due to ties in the data. My data has 35 obs and one series has
6 pairs of ties. Does anyone know if this would likely have a great
effect on the p-values calculated.. The values look good; tau = -0.68
with p-value = 8e-9 and rho = =0.84
2008 May 08
2
applying cor.test to a (m, n) matrix
Hi everybody,
I would like to apply cor.test to a matrix with m rows and n columns and get the results in a list of matrices , one matrix for p.val, one for the statistic, one for the correlation and 2 for upper and lower confidence intervals, something analog with cor() applied to a matrix.
I have done my own function to get a matrix of p.values and i suppose i can build similar functions for
2004 Aug 30
1
Wrong result with cor(x, y, method="spearman", use="complete.obs") with NA's???
Hallo!
Is there an error in cor to calculate Spearman
correlation with cor if there are NA's? cor.test gives
the correct result. At least there is a difference.
Or am I doing something wrong???
Does anybody know something about this?
a<-c(2,4,3,NA)
b<-c(4,1,2,3)
cor(a, b, method="spearman", use="complete.obs")
# -0.9819805
cor.test(a, b,
2004 May 13
1
Bootstrapping kendall cor
Dear R-helpers,
I'm fighting with the following problem :
I want to do bootstrapping on a Kendall correlation with the following code
:
> cor.function <- function(data,i) cor(data[i, 1], data[i,
2],method="kendall")
> boot.ci <- boot.ci(boot.cor <- boot(cbind(x,y),cor.function,
R=1000),conf=c(0.95,0.99))
However, I've got problems because I've got ties
2008 Sep 10
3
making spearman correlation cor() call fail with log(0) as input
Hi,
How can I make the cor(x, y, method="spearman") call to produce an
error when the input to it (x, y) produces an error? Here is a simple
example:
> a <- c(0, 1, 2)
> b <- c(100, 2, 4)
## error:
> log(a)
[1] -Inf 0.0000000 0.6931472
## error, as expected:
> cor(log(a), log(b), method="pearson")
[1] NaN
## not an error any more (not expected):
>
2010 Jun 08
2
cor.test() -- how to get the value of a coefficient
Hi, all.
Yet another beginner to R : )
I wonder, how it's possible to get the value of a coefficient from the
object produced by cor.test() ?
> cor.test(a, b, method="spearman")
Spearman's rank correlation rho
data: a and b
S = 21554.28, p-value = 2.496e-11
alternative hypothesis: true rho is not equal to 0
sample estimates:
rho
0.6807955
Warning message:
In
2007 Sep 20
1
Bug with Cor(..., method='spearman") and by() (PR#9921)
I posted this on R help, and a few others responded indicating they too
were able to replicate the error as a function of missing data. I
believe this should not be the case and hence and reporting it here.
### Code provided on R-Help by Ivar Herfindal
# Simulate data
testdata <- cbind.data.frame(gr=3Drep(letters[1:4], each=3D5), =
aa=3Drnorm(20),
bb=3Drnorm(20))
# Introduce some missingness
2006 Sep 13
1
S in cor.test(..., method="spearman")
Dear HelpeRs,
I have some data:
"ice" <- structure(c(0.386, 0.374, 0.393, 0.425, 0.406, 0.344,
0.327, 0.288, 0.269, 0.256, 0.286, 0.298, 0.329, 0.318, 0.381,
0.381, 0.47, 0.443, 0.386, 0.342, 0.319, 0.307, 0.284, 0.326,
0.309, 0.359, 0.376, 0.416, 0.437, 0.548, 41, 56, 63, 68,
69, 65, 61, 47, 32, 24, 28, 26, 32, 40, 55, 63, 72, 72, 67,
60, 44, 40, 32, 27, 28, 33,
2010 Jun 09
1
bug? in stats::cor for use=complete.obs with NAs
Arrrrr,
I think I've found a bug in the behavior of the stats::cor function when
NAs are present, but in case I'm missing something, could you look over
this example and let me know what you think:
> a = c(1,3,NA,1,2)
> b = c(1,2,1,1,4)
> cor(a,b,method="spearman", use="complete.obs")
[1] 0.8164966
> cor(a,b,method="spearman",
2007 Aug 23
1
in cor.test, difference between exact=FALSE and exact=NULL
Pardon my ignorance, but is there a difference in cor.test between
exact=FALSE and exact=NULL when method=spearman?
Take for example:
x<-c(1,2,2,3,4,5)
y<-c(1,2,2,10,11,12)
cor.test(x,y, method="spearman", exact=NULL)
This gives an error message,
Warning message: Cannot compute exact p-values with ties in:
cor.test.default(x, y, method = "spearman", exact = NULL)
2008 Jun 19
3
how to extract object from stats test output (cor.test)?
Hello,
Is there a way to extract output objects from a stats test without viewing
the entire output? I am trying to do so in the following:
define a vector of length j
for( i in 1: length (vector)) {
vector[i] = cor.test (datavector1, datavector2[i], method=("spearman"))
}
I would like the reported Spearman's rho to be saved in a vector. I have
tried a few different ways of
2003 Oct 22
6
Something strange in cor.test in R-1.8.0 (PR#4718)
Full_Name: Ian Wilson
Version: R-1.8.0
OS: Windows (but own compilation)
Submission from: (NULL) (139.133.7.38)
the p-value is incorrect for cor.test using method "spearman" in R-1.8.0. This
was not the case in R-1.7.1.
Version R-1.8.0 on Windows
> cor.test(rnorm(50),rnorm(50),method="spearman")
Spearman's rank correlation rho
data: rnorm(50) and rnorm(50)
S