search for: kidney

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 combination has the same n I' d appreciat...

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; hazard=eta+log(delta)+log(gamma)+(gamma-1)*log(rtime); survivor=(-exp(eta))*delta*(rtime**gamma); ll=(event*hazard)+survivor; model rtime ~ general(ll); random u~normal(0,...

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/atta...

...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>, a...

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

...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 pneumonia B heart attack B nausea B cough C kidney failure C nausea C foot pain I want this to be ID nausea diabetes kidney_failure heart_attack fever pneumonia A 1 1 1...

Dear friends - We have 25 rats, 14 of these subjected to partial removal of kidney tissue, 11 to sham operation, and then followed for 6 weeks. So far we have data on 26 urine metabolites measured by NMR 7 times during the observation. I have smoothed the measurements by b.splines in fda including a roughness penalty, and inspecting the mean curves for nephrectomized and sham...

...lowing 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) coef se(coef) age 0.00489 0.0150 sex -1.69703 0.4609 diseaseGN 0.17980 0.5447 diseaseAN 0.39283 0.5447 diseasePKD -1.13630 0.8250 frailty(id, dist = "gauss...

...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) ~ sex + age + cluster(id), data = kidney, n.knots = 8, kappa1 = 10000) Shared Gamma Frailty model parameter estimates using a Penalized Likelihood on the hazard function coef exp(coef) se(coef) se(coef) HIH z p se...

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 = kidney) coef se(coef) se2 Ch...

...---------------- Sample.ID Gene tissue.type batch(lab) expression.level id1 gene1 liver batch1 0.67 id1 gene2 liver batch1 0.89 id2 gene1 kidney batch1 0.52 id2 gene2 kidney batch1 0.45 . . id10 gene1 brain batch4 0.56 id10 gene2 brain batch4 0.97 . . id1...

...iscrepancy fit1 <- survreg(Surv(time, status) ~ rx + frailty(litter), rats) fit1 fit1$history[[1]]$theta # OK fit2 <- survreg(Surv(time, status) ~ rx + frailty(litter, df = 13), rats) fit2 fit2$history[[1]]$theta # discrepancy fit3 <- survreg(Surv(time, status)~ age + sex + frailty(id), kidney) fit3 fit3$history[[1]]$theta # OK fit4 <- survreg(Surv(time, status)~ age + frailty(id), kidney) fit4 fit4$history[[1]]$theta Am I missing something? Thanks in advance for any pointers! Best, Dimitris ---- Dimitris Rizopoulos Biostatistical Centre School of Public Health Catholic Universit...

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)) plot(sort(vecAVG,decreasing=TRUE),type="p",pch=19,col="darkslateblue",axes=FALSE,ann=FALSE) g_range<-range(vecAVG) axis(1,at=0:l...

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

...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, dist='gauss'), kidney) survfit(kfitm1) #ok for mean expected survival Call: survfit.coxph(object = kfitm1) n events median 0.95LCL 0.95UCL 76 58 63 39 132 survfit(kfitm1, newdata=kidney[1,]) #return an error message Erreur dans x2 %*% coef : arguments inad?quats Thanks in Advance --...

...23 different partial solutions found on the web and failed. I just need one EXAMPLE that WORKS. Unfortunately, library(lattice) ?panel.text shows no examples. As you see, I bring you a formidable challenge. Thank you, Ivan Ivan Gregoretti, PhD National Institute of Diabetes and Digestive and Kidney Diseases National Institutes of Health 5 Memorial Dr, Building 5, Room 205. Bethesda, MD 20892. USA.

...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, 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 > > ______________________________________________ > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/list...

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 time will be useful for managing patients. Here is what I ca...