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...fito<-lrm(y~x) preo<-predict(fito) pre<-matrix(NA,nrow=100,ncol=200) for (i in 1:200) { sam<-sample(1:nrow(dat)) sam<-split(sam,1:10) for (j in 1:10) { fit<-lrm(y~x,data=dat[-sam[[j]],]) pre[sam[[j]],i]<-predict(fit,data=dat[sam[[j]],]) } } *Yao Zhu* *Department of Urology Fudan University Shanghai Cancer Center Shanghai, China* [[alternative HTML version deleted]]

After upgrading R to 2.9.2, I can't use the anova() fuction. It says "could not find function "Varcov" ". What's wrong with my computer? Help needed, thanks! Yao Zhu Department of Urology Fudan University Shanghai Cancer Center No. 270 Dongan Road, Shanghai, China [[alternative HTML version deleted]]

Dear R users: In Prof. Harrell's library rms, calibrate.rms plot the Bias-corrected Probability and Apparent Probability. The latter one can be retrieved from class calibrate.default. But how to retrieve the former one. BW *Yao Zhu* *Department of Urology Fudan University Shanghai Cancer Center Shanghai, China* [[alternative HTML version deleted]]

...t book. But I did not quite understand. I have two problems about the validation and calibration of prediction models: 1. Can someone explain the results outputted by the validate() function? How to get 95% of c-value of validate? 2. How to add 95% ci in the calibration plot? Yao Zhu Department of Urology Fudan University Shanghai Cancer Center [[alternative HTML version deleted]]

Dear R users: In stat, there is a "stpower" function for power analysis and sample-size determination in survival models. Is there a counterpart in R? Thanks Yao Zhu Department of Urology Fudan University Shanghai Cancer Center Shanghai, China [[alternative HTML version deleted]]

Dear R users: I want to externally validate a model with val.surv. Can I use only calculated survival (at 1 year) and actual survival? Or I needed the survival function and actual survival. Thanks *Yao Zhu* *Department of Urology Fudan University Shanghai Cancer Center Shanghai, China* [[alternative HTML version deleted]]

Dear R-users I want to generate a growth chart like this: http://php.med.unsw.edu.au/embryology/images/9/9a/WHO-XX_length_birth_to_2_years.png can you give some suggestions about the functions I should use? Thanks *Yao Zhu* *Department of Urology Fudan University Shanghai Cancer Center Shanghai, China* [[alternative HTML version deleted]]

...git `event' `predictors2' if set~=`j' quietly predict ptemp if set==`j' quietly replace `prediction2' = ptemp if set==`j' drop ptemp } I don't understand what's the difference between prediction1 and prediction2 3. Is my code right? Thanks ! Yao Zhu Department of Urology Fudan University Shanghai Cancer Center Shanghai, China [[alternative HTML version deleted]]

...expression was strongly correlated with B expression (chi-square) in this series. Prior reports by the same authors showed that B expression strongly correlated with survival (Log-rank). Please provide an explanation why then were the results not transitive. Thanks a lot. *Yao Zhu* *Department of Urology Fudan University Shanghai Cancer Center Shanghai, China* [[alternative HTML version deleted]]

...[[fit$dist]] : attempt to select less than one element Could some one explain for me? Error in survreg.distributions[[fit$dist]] : attempt to select less than one element Error in survreg.distributions[[fit$dist]] : attempt to select less than one element *Yao Zhu* *Department of Urology Fudan University Shanghai Cancer Center Shanghai, China* [[alternative HTML version deleted]]

...binomial",nfolds=5) plot(cvglmnet) cvglmnet$lambda.min which(cvglmnet$lambda==cvglmnet$lambda.min) glmn.fit2<-glmnet(x=factors,y=HRLNM,family="binomial",lambda=cvglmnet$lambda.min) coef(glmn.fit2) Thanks a lot btw: how to calculate the C.I. of coefs? *Yao Zhu* *Department of Urology Fudan University Shanghai Cancer Center Shanghai, China* [[alternative HTML version deleted]]

Dear Sir or Madam? I am a doctor of urology,and I am engaged in developing a nomogram of bladder cancer. May I ask for your help on below issue? I set up a dataset which include 317 cases. I got the Binary Logistic Regression model by SPSS.And then I try to reconstruct the model ?lrm(RECU~Complication+T.Num+T.Grade+Year+TS)? by R-Projec...

...seRs: I use pROC package to compute the bootstrap C.I. of AUC. The command was as follows: roc1<-roc(all$D,all$pre,ci=TRUE,boot.n=200) However, the result was: Area under the curve: 0.5903 95% CI: 0.479-0.7016 (DeLong) Why the C.I. was computed by the Delong Method? Yao Zhu Department of Urology Fudan University Shanghai Cancer Center Shanghai, China [[alternative HTML version deleted]]

...ollows: fit<-cph(pfsurv~log10(x1)+log10(x2),x=T,y=T,surv=T) after I run the nomogram function. I found "variable limits and transformations are such that an infinite axis value has resulted." How to add variable limits in the nomogram function? Thanks a lot *Yao Zhu* *Department of Urology Fudan University Shanghai Cancer Center Shanghai, China* [[alternative HTML version deleted]]

...t;http://jco.ascopubs.org/content/27/18/2931.long#ref-11> Could someone explain nonparametric logistic regression based on locally weighted scatterplot smoothing (lowess)? Or it is nonparametric regression based on locally weighted scatterplot smoothing (lowess) Thanks *Yao Zhu* *Department of Urology Fudan University Shanghai Cancer Center Shanghai, China* [[alternative HTML version deleted]]

Dear R users Function improveProb in the rms library calculate NRI and IDI for predictions of binary outcome. Do anyone extent its use in survival data? Many thanks. *Yao Zhu* *Department of Urology Fudan University Shanghai Cancer Center Shanghai, China* [[alternative HTML version deleted]]

...good. err:win32:do_relocations Forced to relocate system DLL (base > 2GB). This is not good. >>> ldapNameSpace = adsNameSpaces.getobject("", "LDAP:") >>> ldapCont = ldapNameSpace.OpenDSObject("LDAP://uhgexchange00/cn=MRRoach,cn=Corporate Office,ou=UHG,o=Urology Healthcare Group", "cn=myusername,dc=uhg", "mypassword", 0) >>> ldapCont.Getinfo() wine: Unhandled exception, starting debugger...

...e.. Zach - -------- Original Message -------- Subject: NDN: [Samba] Samba PDC With LDAP Backend, Failed to initialise SAM_ACCOUNT for us Date: Tue, 11 Jul 2006 12:54:51 -0500 From: Gateway To: zdennis <zdennis@mktec.com> Sorry. Your message could not be delivered to: samba,Arkansas Urology (The name was not found at the remote site. Check that the name has been entered correctly.) -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.1 (GNU/Linux) Comment: Using GnuPG with Thunderbird - http://enigmail.mozdev.org iD8DBQFEs/LHMyx0fW1d8G0RAumEAJ9qGddObh6z6ijY3Qc1ZKVwONz6dACeO5Hu KCYRXcczY...

Dear R users, I am a new R user and something stops me when I try to write a academic article. I want to make a nomogram to predict the risk of prostate cancer (PCa) using several factors which have been selected from the Logistic regression run under the SPSS. Always, a calibration plot is needed to validate the prediction accuracy of the nomogram. However, I tried many times and read a lot of

...seRs: I use pROC package to compute the bootstrap C.I. of AUC. The command was as follows: roc1<-roc(all$D,all$pre,ci=TRUE,boot.n=200) However, the result was: Area under the curve: 0.5903 95% CI: 0.479-0.7016 (DeLong) Why the C.I. was computed by the Delong Method? Yao Zhu Department of Urology Fudan University Shanghai Cancer Center Shanghai, China [[alternative HTML version deleted]] ------------------------------ Message: 31 Date: Wed, 13 Oct 2010 10:23:57 -0300 From: Henrique Dallazuanna <wwwhsd at gmail.com> To: dpender <d.pender at civil.gla.ac.uk> Cc: r-help at r-...