Displaying 20 results from an estimated 800 matches similar to: "Sperman Correlation with rcorr (Hmisc)"
2008 Sep 02
2
cluster a distance(analogue)-object using agnes(cluster)
I try to perform a clustering using an existing dissimilarity matrix that I
calculated using distance (analogue)
I tried two different things. One of them worked and one not and I don`t
understand why.
Here the code:
not working example
library(cluster)
library(analogue)
iris2<-as.data.frame(iris)
str(iris2)
'data.frame': 150 obs. of 5 variables:
$ Sepal.Length: num 5.1 4.9 4.7
2008 Jun 18
2
randomForest outlier
I try to use ?randomForest to find variables that are the most important to
divide my dataset (continuous, categorical variables) in two given groups.
But when I plot the outliers:
plot(outlier(FemMalSex_NAavoid88.rf33, cls=FemMalSex_NAavoid88$Sex),
type="h",col=c("red","green")[as.numeric(FemMalSex_NAavoid88$Sex)])
it seems to me that all my values appear as
2008 Aug 06
1
Correlation dichotomous factor, continous (numerical) and ordered factor
Hello R-User!
I appologise in advance if this should also go into statistics but I am
presently puzzled.
I have a data.frame (about 300 rows and about 80 variables) and my variables
are dichotomous factors, continuous (numerical) and ordered factors.
I would like to calculate the linear correlation between every pair of my
variables, because I would like to perform a logistic regression (glm())
2008 Aug 13
2
Tiny help for tiny function
I just started to write tiny functions and therefore I appologise in advance
if I am asking stupid question.
I wrote a tiny function to give me back from the original matrix, a matrix
showing only the values smaller -0.8 and bigger 0.8.
y<-c(0.1,0.2,0.3,-0.8,-0.4,0.9)
x<-c(0.5,0.3,0.9,-0.9,-0.7,0.3)
XY<-rbind(x,y)
extract.values<-function (x)
{
if(x>=0.8|x<=-0.8)x
2011 May 22
1
How to calculate confidence interval of C statistic by rcorr.cens
Hi,
I'm trying to calculate 95% confidence interval of C statistic of
logistic regression model using rcorr.cens in rms package. I wrote a
brief function for this purpose as the followings;
CstatisticCI <- function(x) # x is object of rcorr.cens.
{
se <- x["S.D."]/sqrt(x["n"])
Low95 <- x["C Index"] - 1.96*se
Upper95 <- x["C
2011 Aug 19
1
Hmisc::rcorr on a 'data.frame'?
Dear all
?Hmisc::rcorr states that it takes as main argument "a numeric
matrix". But is it normal that it fails in such an ugly way on a data
frame? (See below.) If the function didn't attempt any conversion to a
matrix, I would have expected it to state that in the error message
that it didn't accept 'data.frame' objects in its input. Also, I
vaguely remember having used
2010 May 05
1
rcorr p-values for pearson's correlation coefficients
Hi! All,
To find co-expressed genes from a expression matrix of dimension (9275
X 569), I used rcorr function from library(Hmisc) to calculate pearson
correlation coefficient (PCC) and their corresponding p-values. From
the correlation matrix (9275 X 9275) and pvalue matrix (9275 X 9275)
obtained using rcorr function, I wanted to select those pairs whose
PCC's are above 0.8 cut-off and then
2002 Sep 05
1
rcorr in Hmisc
Dear list,
I get the following message when I use rcorr in library "Hmisc"
------------------------------------------------------
> rcorr(lskPox0t30, type=c("spearman"))
Error in "[<-.data.frame"(*tmp*, is.na(x), value = 1e+30) :
matrix subscripts not allowed in replacement
------------------------------------------------------
I do not understand
2012 Sep 12
1
digit precision in p value of rcorr
Hi all,
Sorry about posting a really novice question.
I was able to run rcorr after converting the list to a matrix by your help.
I'm though wondering if there is any way to find out an exact p value as
the output only gave me 0 for P value as shown below.
I've added options(digits=10), which doesn't seem to help at all. Any help
would be appreciated.
P
D Prime T
2011 Mar 01
1
which does the "S.D." returned by {Hmisc} rcorr.cens measure?
Dear R-help,
This is an example in the {Hmisc} manual under rcorr.cens function:
> set.seed(1)
> x <- round(rnorm(200))
> y <- rnorm(200)
> round(rcorr.cens(x, y, outx=F),4)
C Index Dxy S.D. n missing
uncensored Relevant Pairs Concordant Uncertain
0.4831 -0.0338 0.0462 200.0000
2008 Nov 11
1
how to export results of rcorr into excel
Hi,
I try to export the outputs of rcorr into excel. but I got error message,"cannot coerce class "rcorr" into a data.frame". Actually i just need export part of results of this analysis,e.g. p-values or stat-values.
Does anyone have sort of exprience before or you can help on how to export subset of results of analysis?
Many Thanks!
Xin
2009 Mar 09
1
rcorr.cens Goodman-Kruskal gamma
Dear r-helpers!
I want to classify my vegetation data with hierachical cluster analysis.
My Dataset consist of Abundance-Values (Braun-Blanquet ordinal scale; ranked) for each plant species and relev?.
I found a lot of r-packages dealing with cluster analysis, but none of them is able to calculate a distance measure for ranked data.
Podani recommends the use of Goodman and Kruskals' Gamma for
2011 Jun 21
0
relation between tdrocc AUC and c-statistic from rcorr.cens
I am using the rcorr.cens function from the Hmisc package and the time-dependent ROC curve obtained using tdrocc in the survcomp package.
I understand that the C statistic from rcorr.cens has to be subtracted from 1 if high values of the risk variable lower survival.
Given that I wonder what the connection is between that C statistic and the AUC from the tdrocc object. If they are substantially
2017 Sep 21
0
rcorr error in R stat
Hello,
Also, the other file, NPA.csv, is not in tabular form. Can you please
reformat it?
Rui Barradas
Citando ruipbarradas at sapo.pt:
> Hello,
>
> Please keep this on the list, always cc r-help.
> One of the files in your attachment is empty:
>
> y <- read.csv(file.choose("GT.csv"))
> Error in read.table(file = file, header = header, sep = sep, quote =
2017 Sep 21
2
rcorr error in R stat
Hello,
Please keep this on the list, always cc r-help.
One of the files in your attachment is empty:
y <- read.csv(file.choose("GT.csv"))
Error in read.table(file = file, header = header, sep = sep, quote = quote,? :
? no lines available in input
Rui Barradas
?
Citando Chaitanya Ganne <Chaitanya.Ganne at jefferson.edu>:
> Thank you so much for your input.
>
> I am
2007 Dec 19
1
using rcorr.cens for Goodman Kruskal gamma
Dear List,
I would like to calculate the Goodman-Kruskal gamma for the predicted
classes obtained from an ordinal regression model using lrm in the Design
package. I couldn't find a way to get gamma for predicted values in Design
so have found previous positings suggesting to use :
Rcorr.cens(x, S outx = TRUE) in the Hmisc package
My question is, will this work for predicted vs
2004 Jun 04
1
use of "rcorr.cens" with binary response?
Dear R-helpers,
I recently switched from SAS to R, in order to model the occurrence of
rare events through logistic regression.
Is there a package available in R to calculate the Goodman-Kruskal
Gamma?
After searching a bit I found a function "rcorr.cens" which should do
the job, but it is not clear to me how to define the input vectors? Is
"x" a vector with the fitted
2009 Jul 01
1
Rcorr
Hi,
I've just run an rcorr on some data in Spearman's mode and it's just
produced the following values;
[,1] [,2]
[1,] 1.00 -0.55
[2,] -0.55 1.00
n= 46
P
[,1] [,2]
[1,] 0
[2,] 0
I presume this means the p-value is lower than 0.00005, but is there any
way of increasing the number of significant figures used? How should I
interpret this value?
Cheers
Jim
2008 Jun 05
2
bartlett.test()
i'm trying to test the homogeneity of variance of 92 samples each one
contains 3 observations.
to use bartlett.test function i have created a (3,92) matrix (named xx):
>bartlett.test(xx)
this message appears:
>Erreur dans bartlett.test.default(xx) :
l'argument "g" est manquant, avec aucune valeur par d?faut
when i checked the help i have understood that in g i should
2008 Jun 30
1
ctree (party) plot meaning question
I tried to use ctree but am not sure about the meaning of the plot.
My.data.ct<-ctree(Resp~., data=My.data)
plot(My.data.ct)
My data.frame contains 88 explanatory variables (continous,ordered/unordered
multistate,count data) and one response with two groups.
In the plot are only two variables shown (2 internal nodes) and 3 final
nodes. Does it mean that only these two variables show a