similar to: survplot function

Dear list, does anyone know of a R-package that has implemented the increasingly popular inclusion of the number of patients at risk below Kaplan-Meier curves like in http://bloodjournal.hematologylibrary.org/content/vol116/issue19/images/large/zh89991058760001.jpeg any hint (or negative answer) is much appreciated. Thanks Thorsten -- Thorsten Raff 2nd Medical Department, University

Dear R-helpers, this is just a notice to inform everyone that the current versions of XML and odfWeave don't seem to be playing nice with each other. Since it took me quite some time to figure that out, I thought that I let you know. In my case it helped to install an older version of XML but your mileage of course may vary. Best regards Thorsten -- Thorsten Raff 2nd Medical

Hello I have the problem that I want to transform a dataframe as generated by diagnosis <- rep(diagnosis[1:3], 3) marker <- gl(3,3) values <- rnorm(9) dataframe <- cbind(diagnosis, marker, values) dataframe <- dataframe[c(1:5, 7:9), ] into a matrix where levels(diagnosis) is indicating the rows of the matrix, levels(marker) the columns and values are the actual content of the

Dear R-helpers, I am trying to plot a Bland-Altman-Plot using the BA.plot function from the package MethComp. While there is a function to transform the values for analysis as shown in the snippet below, I would like to have logarithmic axes for display as well. The usual log = 'xy' does not work because of the properties of the y-asxis (positive and negative values). I am sure that

Hello, I am looking for a package implementing unconditional tests for comparing two binomials (Barnard's test or derivatives). As I am looking for rare genotypes within my groups, my number of subjects in one of the cells of the 2x2 table is often 2-4 resulting in a too conservative result by Fisher's exact test due to the discrete sample space of the test statistic. As I want to use

Dear R users, I know one way to see the code for a hidden function, say function_x, is using default.function_x (e.g. summary.default). But how can I see the code for imported packages that have no namespace (in this case Design)? Many Thanks Eleni

Hi I am a new fan of R after getting mad with the graphical functional in SPSS. I have been able to create a nice looking Kaplan Meyer graph using Survplot function. However I have difficulties in turning the y axis to percent instead of the default 0-1 scale. Further I have tried the function yaxt="n" without any results. Any help in this matter will be appreciated. The code is

Hello, I apologize for the post as I am certainly overlooking a simple solution to my difficulties with getting a legend to print on a survplot from the rms package. I am plotting the following: survplot(survest(fita), n.risk=T, conf='none', cex.n.risk=.85, dots=T, col='gray10', lty=2) survplot(survest(fit), n.risk=F, conf='none', add=T) survplot(survest(fitb), n.risk=F,

Dear R-help How can one get survplot() to place the number at risk just below the survival curve as opposed to the default which is just above the x-axis? I tried the code bellow but the result is not satisfactory as some numbers are repeated several times at different y coordinates and the position of the n.risk numbers corresponds to the x-axis tick marks not the survival curve time of

Hi, I have a Cox PH model that's large for my server, 120K rows, ~300 factors with 3 levels each, so about 1000 columns. The 300 factors all pass a preliminary test of association with the outcome. Solving this with cph from Design takes about 3 hours. I have created the fit with x=T, y=T to save the model data. I want to validate the PH assumption by calling survplot(fit, gender=NA,

Dear all, I am trying to plot KM curves with confidence bands with function survplot under package rms. However, the following codes do not seem to work. The KM curves are produced, but the confidence bands are not there. Any insights? Thanks in advance. library(rms) ########data generation############ n <- 1000 set.seed(731) age <- 50 + 12*rnorm(n) label(age) <- "Age"

Dear useRs, I was asked to produce a survival curve like this: http://www.palug.net/Members/jabba/immaginetta.png/view with the cardinality of the riskset at the bottom. I do not like doing it, because it doesn't add any valuable information and because it doesn't discriminate between died and censored. Nevertheless, is there someone able to tell me how to do it? Currently the only

Hi, in Design package, a plot of survival probability vs. a covariate can be generated by survplot() on a cph object using the folliowing code: n <- 1000 set.seed(731) age <- 50 + 12*rnorm(n) label(age) <- "Age" sex <- factor(sample(c('male','female'), n, TRUE)) cens <- 15*runif(n) h <- .02*exp(.04*(age-50)+.8*(sex=='Female')) dt <-

Dear All, I know this may be a trivial question. In the past I have used glm to make logistic regressions on data. The output creates an object with the results of the logistic regression. This object can then be used to make predictions. Great. I have a different problem. I need to make predictions from a logistic regression taken from a paper. Thus I need to (by hand) enter the reported odds

Hello R-experts, I have a simple question: how do I aggregate data using the median function with na.rm = TRUE, i.e. aggregate(x, list(x$y, x$z), FUN = '????') I have tried 'median(x, na.rm = TRUE)' but that doesn't help. Any suggestions are very much appreciated, Thorsten

Dear users, I can access an database oracle database using sql developer. This was done by importing an xml file that contains the login details - username, password and specifies that it uses the KERBEROS_AUTHENTICATION. I'm trying to connect R - so that it can access this database - do sql queries and convert the resulting tables into dataframes. I am a novice in SQL and database access

deaR user, I found an unexpected behaviour of the rms::survplot.survfit function, that is giving me inverted labels for the patient-at-risk rows. The problem is that, for some reason, the survival::summary.survfit function changes the order of two of the suvfit object's strata when called (on my dataset) with the times= option (is this another unexpected behaviour?). survplot takes the

Dear R users, Please can you help me with a relatively straightforward problem that I am struggling with? I am simply trying to plot a baseline survivor and hazard function for a simple data set of lung cancer survival where `futime' is follow up time in months and status is 1=dead and 0=alive. Using the survival package: lung.wbs <- survreg( Surv(futime, status)~ 1, data=lung,

Hello, I write to know how can I modify the x axis : when I plot a survival object, R plots a graph with x values = 0, 10, 20, 30 while I want a graph with values 0, 6, 12, 18, 24 in the x axis. How can I do this? In R 2.1.1 version there was "time.inc" in survplot, but in version R 2.2.0 there isn't it! I am sorry for my english and I hope that you understand my problem. Thank you

R-ers! Referees demand that the line in the KM-curve should be changed to dotted at the point where standarerror is <= 10 %. I don't think it's a good habit but I urgently need to implement such a thing in R with survfit, survplot or another program. They also want numbers at risk below the curve Some help, please.... Fredrik ######################## Fredrik Lundgren