similar to: By() with method = spearman

Hi. I am currently trying to run some Spearman correlations, and have encountered two issues. 1) When using cor.test() with a variable that includes ties, I get the "Cannot compute exact p-values with ties" error. I have read that this function now uses an asymptotic formula that allows for ties, so do not understand why I am getting this error. (I am running version 2.4.0.) I

I have two data matrices that I want to make the correlation between each column from data1 and each column from data 2 and also calculate the p-value Matrices dont have the same size and I tried such a script. > bg <- read.table (file.choose(), header=T, row.names) > bg > Otu00022 Otu00029 Otu00039 Otu00042 Otu00101 Otu00105 Otu00125 Otu00131 Otu00137 Otu00155 Otu00158 Otu00172

Hi, I am using R 1.8.1 on WinXP. I encounter a problem when trying to compute a Spearman correlation under certain conditions (at least I think there is a problem, but maybe this is the normal behavior). > X<-array(0,c(20,2)) > > X[,1]<-c(runif(10),rep(NA,10)) > X[,2]<-c(runif(10),rep(NA,10)) > > Y<-X[1:10,] > >

Dear all, Suppose my data frame is as follows: id price distance 1 2 4 1 3 5 ... 2 4 8 2 5 9 ... n 3 7 n 8 9 I would like to calculate the rank-order correlation between price and distance for each id. cor(price,distance,method = "spearman") calculate a correlation for all. Then I tried to use apply(data,list='id',cor(price , distance , method =

Dear R-helpers, I would like to do a Spearman rank order test, and used the cor() function with the method "spearman". It gives me a number (correlation coefficient?) , but how can I get the p-value? Thank you for the help in advance! Regards, Anne-Katrin -- [[alternative HTML version deleted]]

Hi all, I am trying to figure out the formula used by R's Spearman rho (using cor(method="spearman")) because I can't seem to get the same value as by calculating "by hand". Perhaps I'm using "cor" wrong, but I don't know where. Basically, I am running these commands: > y=read.table(file="tmp",header=TRUE,sep="\t") >

Hi all, Is there a convenient way to calculate Spearman correlation coefficients in R? Nick Nianqing Xiao, Ph.D NCI Center for Bioinformatics, NIH SAIC/Advanced Systems Group > 6116 EXECUTIVE BLVD 4026J > MSC 8335 > BETHESDA MD 20852 Phone: 301-451-6357 Fax: 301-480-4222 -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read

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): >

Hello R gurus, I want to calculate the Spearman rho between two ranked lists. I am getting results with cor.test that differ in comparison to my own spearman function: > my.spearman function(l1, l2) { if(length(l1) != length(l2)) stop("lists must have same length") r1 <- rank(l1) r2 <- rank(l2) dsq <- sapply(r1-r2,function(x) x^2) 1 - ((6 * sum(dsq))

Hi, A following function was kindly provided by GGally?s maintainer, Barret Schloerke. function(data, mapping, ...) { p <- ggplot(data = data, mapping = mapping) + geom_point(color = I("blue")) + geom_smooth(method = "lm", color = I("black"), ...) + theme_blank() + theme(panel.border=element_rect(fill=NA, linetype =

Hallo, does anybody know if there is an implementation of the Spearman rank correlation in R that gives a correct (or at least 'safe') p-value in the case of ties?? I have browsed the R-help archives but I found nothing. Thanks a lot in advance for any help, Antonino Casile

Hello, I would like to do a PCA with dudi.pca or PCA, but also with the use of Spearman or Kendall correlations Is it possible ? Otherwise, how can I do, according to you ? Thanking you in advance Eric Bourgade RTE France [[alternative HTML version deleted]]

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,

Full_Name: Vladimir Obolonkin Version: tested in 2.0 to 2.4.1 OS: linux, win, mac Submission from: (NULL) (202.14.96.194) {{ Subject shortened manually -- to pass anti-spam filters Original-subject: Incorrect matrix of spearman correlations working \ large (24000 by 425 and 78 by 425 data frames) in 64-bit Linux machines;\ the same code gives correct results in 32-bits Win and

Full_Name: David Simcha Version: 2.10 OS: Windows XP Home Submission from: (NULL) (173.3.208.5) > a <- c(1:10) > b <- c(1:10) > cor.test(a, b, method = "spearman", alternative = "greater", exact = TRUE) Spearman's rank correlation rho data: a and b S = 0, p-value < 2.2e-16 alternative hypothesis: true rho is greater than 0 sample estimates:

Hi, I'm currently trying to find/define a relationship between one dependent and several independant variables. The problem is that i cannot use the normal multiple regression/correlation in Spss because the data is not normal distributed. i calculated the spearman roh and Kendalls tau Correlation and also some partial correlations in R. Now i wanna find out the the multiple correlation

Hi, I am not really familiar with Correlation foundations, although I read a lot. So maybe if someone kindly help me to interpret the following results. I had the following R commands: correlation <-cor( vector_CitationProximity , vector_Impact, method = "spearman", use="na.or.complete") cor_test<-cor.test(vector_CitationProximity, vector_Impact,

In the ouput below, what is the "S" statistic (S = 96) that is used for Spearman? I don't have easy access to the books cited on the help page. Other texts and web sources that I have found use t or z as a test for Spearman, perhaps inappropriately. Can anyone tell me how S is computed or refer to a web resource? I see from the code for that: q <- as.integer((n^3 - n) * (1

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

Hello, Does anyone know if the cor function, when method = "spearman", returns a correlation coefficient corrected for any ties in the ranks of the data? I have data with quite a few ties and am thinking that I should use a calculation of the coefficient corrected for ties, but before I try and code this calculation myself, I thought I should check whether or not cor() automatically