search for: kidneys

Hi all, I'm new to R and have the following problem: I have a 2 factor design (a has 2 levels, b has 3 levels). I have an object kidney.aov which is an aov(y ~ a*b), and when I ask for model.tables(kidney.avo, se=T) I get the following message along with the table of effects: Design is unbalanced - use se.contrast() for se's but the design is NOT unbalanced... each fator level

Hi, I am trying to convert the following NLMIXED code to NLME, but am running into problems concerning 'Singularity in backsolve'. As I am new to R/S-Plus, I thought I may be missing something in the NLME code. NLMIXED *********** proc nlmixed data=kidney.kidney; parms delta=0.03 gamma=1.1 b1=-0.003 b2=-1.2 b3=0.09 b4=0.35 b5=-1.43 varu=0.5; eta=b1*age+b2*sex+b3*gn+b4*an+b5*pkn+u;

Dear all, in survival5, kidney data set, appears in help page: "survival5 does not reproduce the original analysis." What does it means? thanks in advance TCM -------------- next part -------------- An HTML attachment was scrubbed... URL: https://stat.ethz.ch/pipermail/r-help/attachments/20010927/e006b08d/attachment.html

...it's not,' she said. `I've gone very near with papa.' -----Original Message----- From: Guadalupe Simpson [mailto:hmeg@xtamkm.com] To: saul acton; minh fears; garry mcquilkin; patrick leavitt Sent: Sunday, July, 2004 1:33 AM Subject: good news - regenerating of the heart, liver, kidneys and other organs Tea over and the tray rem-oved, she again summoned us to the fire; we sat one on each side of her, and now a conversation followed between her and Helen, which it was indeed a privilege to be admitted to hear. I put her cool hand to my ho~t forehead; 'No, Die, not one whit.&...

...parameter list <code>par</code> should be as follows, for each possible value of <code>gorp</code>: <dl> <dt>melvin:</dt><dd>(Melvin Mingdinkler.) A vector with components <i>(beta,gamma,r)</i> which are respectively a load of dingos' kidneys, an elephant, and a duck. Note that <i>gamma</i> must be totally ridiculuous. </dd> <dt>clyde:</dt><dd>(Clyde, clyde, the cow's outside.) A vector with entries <i>(beta,gamma,r_0,r)</i> where <i>beta</i>, <i>gamma</i>, an...

hi, everyone: i have a question on the reshape function. i have the following dataset : gene tissue patient1 patient2 patient3............. _________________________________________________ gene1 breast 10 20 50 gene2 breast 20 40 60 gene3 breast 100 200 300 which i hope to convert to the following format: gene patientID

Dear R users - I have a list of patient identifiers and diagnoses from inpatient admissions. I would like to reorganize the list, presently in a long format to a wide format in reshape, but in the absence of a "time" element, I am uncertain how to do this - any help greatly appreciated. ID Dx A nausea A diabetes A kidney failure A heart attack A fever B fever B

...rvation. I have smoothed the measurements by b.splines in fda including a roughness penalty, and inspecting the mean curves for nephrectomized and sham animals indicate differences for several of the metabolites. Now the real idea is to use the NMR measurements to understand what goes on in the kidneys since we know the partial removal of kidney tissue will result in progressive damage in the kidneys - the nature of that is what we want to understand. We have a blood sample from the rats just prior to sacrifice, and the creatinine concentration there is a good proxy for "renal function&q...

Dear List, How do I extract the approximate Wald test for the frailty (in the following example 17.89 value)? What about the P-values, other Chisq, DF, se(coef) and se2? How can they be extracted? ######################################################> kfitm1 Call: coxph(formula = Surv(time, status) ~ age + sex + disease + frailty(id, dist = "gauss"), data = kidney)

Dear R-listers, I have a very strange problem. I made a package (under Windows and Linux). The package passed the R CMD Check without problem. Then, I installed the package and executed a function which calls to a 'dll' mod<-frailtyPenal(Surv(time,status)~sex+age+cluster(id), + n.knots=8,kappa1=10000,data=kidney) mod Call: frailtyPenal(formula = Surv(time, status)

Dear all, Does the frailty.object$history[[1]]$theta returns the Variance of random effect? Why is the value different? Here is an example with kidney data: > library(survival) > data(kidney) > frailty.object<-coxph(Surv(time, status)~ age + sex + disease + frailty(id), kidney) > frailty.object Call: coxph(formula = Surv(time, status) ~ age + sex + disease + frailty(id), data

Hi, I am doing an analysis to see if these is tissue specific effects on the gene expression data . Our data were collected from 6 different labs (batch effects). lab 1 has tissue type 1 and tissue type 2, lab 2 has tissue 3, 4,5,6. The other labs has one tissue type each. The 'sample' data is as below:

Dear R-users, I have noticed small discrepencies in the reported estimate of the variance of the frailty by the print method for survreg() and the 'theta' component included in the object fit: # Examples in R-2.6.2 for Windows library(survival) # version 2.34-1 (2008-03-31) # discrepancy fit1 <- survreg(Surv(time, status) ~ rx + frailty(litter), rats) fit1 fit1$history[[1]]$theta

I have data I'd like to plot using the formula interface to boxplot. I call boxplot like so: with(mydata, boxplot(count ~ geno * tissue)) I get a boxplot with x axis labels like "wt.kidney". I would like to change the '.' to a newline. Where is this separator configured? Thanks, -Ed

Hello Everyone, I am having problem in defining specific axis for plotting a vactor. vecAVG <- c(0.2, 0.4, 0.6, 0.2, 0.4) names(vecAVG)<-c("brain","heart","kidney","lung","blood") par(mar=c(12,4.1,4.1, 2.1))

Hi Dear R-users I have a database with 18000 observations and 20 variables. I am running cox regression on five variables and trying to use survfit to plot the survival based on a specific variable without success. Lets say I have the following coxph: >library(survival) >fit <- coxph(Surv(futime, fustat) ~ age + rx, data = ovarian) >fit what I am trying to do is plot a survival

Hello R users Would somebody know how to estimate survival from a frailty cox model, using the function survfit and the argument newdata ? (or from any other way that could provide individual expected survival with standard error); Is the problem related to how the random term is included in newdata ? kfitm1 <- coxph(Surv(time,status) ~ age + sex + disease + frailty(id,

Hello listers, Does anybody know how to add text to an xyplot without whipping out the existing curve? That's all. For instance, Lets say you generate a graph like this A <- data.frame(x = rnorm(100), y = rnorm(100)) xyplot(y ~ x, data = A) How would you add 'Hello world'? I tried 6.02E23 different partial solutions found on the web and failed. I just need one EXAMPLE that

mybp <- boxplot(count ~ geno * tissue, data = mydata, plot = FALSE) mybp$names <- gsub("\\.", "\n", mybp$names) bxp(mybp) See ?boxplot for details. Best, Ista On Thu, Sep 28, 2017 at 12:40 PM, Ed Siefker <ebs15242 at gmail.com> wrote: > I have data I'd like to plot using the formula interface to boxplot. > I call boxplot like so: > > with(mydata,

Dear friends. I wanted to reproduce a sheet of paper useful for plotting the reciprocal of some biochemical variable (creatinine) over time (Bleyer Am J Kidney Dis 34:576-578,1999). Time on X axis with units years and months. On Y axis, 1/creatinine, but with the original creatinine value indicated - to make it easier for people to use it. When using the graph, the linear decrease in 1/crea over