search for: rcorr

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 Index"] + 1....

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 &...

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...

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...

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 analy...

...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 the distance. I found the function rcorr.cens (outx=true) of the Hmisc package which should do it. What I don't understand is how to define the input vectors x, y with my vegetation dataset. The other thing how I can use the output of rcorr.cens for a distance measure in the cluster analysis (e.g. in vegan or amap). Any help would be...

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 ---------------------------------...

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 fo...

...d the two csv files to you? I'd really > appreciate your help. > > Thanking you > ? > > ------------------------- > FROM: ruipbarradas at sapo.pt <ruipbarradas at sapo.pt> > SENT: Wednesday, September 20, 2017 5:21:04 PM > TO: Chaitanya Ganne > SUBJECT: Re: rcorr error in R stat > > Hello, > > Maybe I'm completely off, but read.csv returns data.frames, which > are lists with a dim attribute. > Instead of as.vector try unlist(x) and unlist(y). > > Note that if 'df' is a data.frame, class(as.vector(df)) returns "data...

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 observed factors? I.e. x = predicted class and S = observed class? Or is there a better way to obtain this? I used the maximum individual probability for each observation to determine the predicted cla...

...ally >> appreciate your help. >> >> Thanking you >> ? >> >> ------------------------- >> FROM: ruipbarradas at sapo.pt <ruipbarradas at sapo.pt> >> SENT: Wednesday, September 20, 2017 5:21:04 PM >> TO: Chaitanya Ganne >> SUBJECT: Re: rcorr error in R stat >> >> Hello, >> >> Maybe I'm completely off, but read.csv returns data.frames, which >> are lists with a dim attribute. >> Instead of as.vector try unlist(x) and unlist(y). >> >> Note that if 'df' is a data.frame, class(as....

Hello, I'd like to test a significance of two variables in their correlation using rcorr, which gave me an error of format incompatibility. Below are the lines that I typed in the R window and let me know if anyone knows how to resolve this. Var=read.csv("03apr10ab_corr_matrix_in_overlaps.csv",header=F) colnames(Var)=c("D Prime","T statistics")...

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 probabilities and "s" a vector containing the observed response variable? Or does anybody know an alternative? Any help would be greatly appreciated, T...

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 significan...

Hello R-User! I have a data.frame with 82 variables (columns) and 290 rows. The variables are set to classes factor, ordered factor and numeric. I used the following code Matrix.My.data<-as.matrix(Df.My.Data[2:82]) Matrix.My.data.rcorr<-rcorr(Matrix.My.data, type="spearman") and got the following message: Fehler in storage.mode(x) <- if (.R.) "double" else "single" : (list) Objekt kann nicht nach 'double' umgewandelt werden Error Fehler in storage.mode(x) <- if (.R.) "doub...

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...

...ml --latex --example' 'Rcmd INSTALL': now doing 'eval ... do_install': * Installing *source* package 'Hmisc' ... ** libs ++ mkdir -p /home/dupontct/Hmisc.Rcheck/Hmisc/libs ++ test -f src/Makefile ++ cd src +++ ls cidxcn.f cidxcp.f hoeffd.f jacklins.f largrec.f ranksort.c rcorr.f string_box.c wclosest.f '*.cc' '*.cpp' '*.f90' '*.f95' ++ srcs='cidxcn.f cidxcp.f hoeffd.f jacklins.f largrec.f ranksort.c rcorr.f string_box.c wclosest.f' +++ cd /usr/lib/R/bin/exec +++ ls ++ archs=R ++ R_ARCH_keep= ++ test -n 'cidxcn.f cidxcp.f hoeffd...

...I generated a square correlation matrix for the dat dataframe below; > dat<-data.frame(g1=c(1,0,0,1,1,1,0,0,0), > g2=c(0,1,0,1,0,1,1,0,0), > g3=c(1,1,0,0,0,1,0,0,0), > g4=c(0,1,0,1,1,1,1,1,0)) > library("Hmisc") > dat.rcorr = rcorr(as.matrix(dat)) > dat.r <-round(dat.rcorr$r,2) > > however, I want to modify this correlation calculation; > my dat has more than 1000 rows and 22 columns; > in each column, less than 10% values are 1, most of them are 0; > so I want to remove a row with value of zero...

Hi R users, I generated a square correlation matrix for the dat dataframe below; dat<-data.frame(g1=c(1,0,0,1,1,1,0,0,0), g2=c(0,1,0,1,0,1,1,0,0), g3=c(1,1,0,0,0,1,0,0,0), g4=c(0,1,0,1,1,1,1,1,0)) library("Hmisc") dat.rcorr = rcorr(as.matrix(dat)) dat.r <-round(dat.rcorr$r,2) however, I want to modify this correlation calculation; my dat has more than 1000 rows and 22 columns; in each column, less than 10% values are 1, most of them are 0; so I want to remove a row with value of zero in both columns when calculat...

...d.f -o hoeffd.o g77 -fno-common -g -O2 -c jacklins.f -o jacklins.o g77 -fno-common -g -O2 -c largrec.f -o largrec.o gcc-3.3 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/usr/local/include -fno-common -g -O2 -c ranksort.c -o ranksort.o g77 -fno-common -g -O2 -c rcorr.f -o rcorr.o g77 -fno-common -g -O2 -c wclosest.f -o wclosest.o gcc-3.3 -bundle -flat_namespace -undefined suppress -L/usr/local/lib -o Hmisc.so cidxcn.o cidxcp.o hoeffd.o jacklins.o largrec.o ranksort.o rcorr.o wclosest.o -L/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2 -lg2c -lSystem -lc...