[R] cox models
Hello, i'm a french student of medical oncology and i'm working on breast cancer. I have a variable with the histologic type of tumor wich is between 1 and 5. I use as.factor function to make some variable with level between 1 and 5. When i put it in the cox model i have only the level between 2 and 5. The level 1 doesn't appear. I think i have to change the number of level but i don't really know. Please can you help me? Class Levels: 1 2 3 4 5 coxph(formula = Surv(delai.etat, etat) ~ class, data = igr1) coef exp(coef) se(coef) z p class2 -0.093 0.9110.245 -0.38 7.0e-01 class3 -0.749 0.4730.286 -2.62 8.9e-03 class4 -0.600 0.5490.343 -1.75 8.0e-02 class5 -0.874 0.4170.197 -4.44 8.9e-06 Likelihood ratio test=24.9 on 4 df, p=5.28e-05 n=740 (1 observations deleted due to missing) Thanks for your help Bertrand __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] cox models
Dear Bertrand, There are only 4 degrees of freedom for a 5-level factor. By default, R creates contrasts for an unordered factor in a model formula using the function contr.treatment(), which, also by default, treats the first level of the factor (class, in your case) as the baseline or reference level. To see the contrasts, enter the command contrasts(igr1$class). A bit more information on contrasts is in Section 11.1.1 of the introductory manual that comes with R. I hope this helps, John John Fox Department of Sociology McMaster University Hamilton, Ontario Canada L8S 4M4 905-525-9140x23604 http://socserv.mcmaster.ca/jfox -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of bertrand Sent: Sunday, November 06, 2005 4:21 AM To: [EMAIL PROTECTED] Cc: r-help@stat.math.ethz.ch Subject: [R] cox models Hello, i'm a french student of medical oncology and i'm working on breast cancer. I have a variable with the histologic type of tumor wich is between 1 and 5. I use as.factor function to make some variable with level between 1 and 5. When i put it in the cox model i have only the level between 2 and 5. The level 1 doesn't appear. I think i have to change the number of level but i don't really know. Please can you help me? Class Levels: 1 2 3 4 5 coxph(formula = Surv(delai.etat, etat) ~ class, data = igr1) coef exp(coef) se(coef) z p class2 -0.093 0.9110.245 -0.38 7.0e-01 class3 -0.749 0.4730.286 -2.62 8.9e-03 class4 -0.600 0.5490.343 -1.75 8.0e-02 class5 -0.874 0.4170.197 -4.44 8.9e-06 Likelihood ratio test=24.9 on 4 df, p=5.28e-05 n=740 (1 observations deleted due to missing) Thanks for your help Bertrand __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] cox models
Level 1 is treated as the baseline. The coefficient for level 2 for example is for the hazard ratio between level 2 and level 1. Same thing for levels 3,4,5 in the output. HTH, On Sun, 6 Nov 2005, bertrand wrote: Hello, i'm a french student of medical oncology and i'm working on breast cancer. I have a variable with the histologic type of tumor wich is between 1 and 5. I use as.factor function to make some variable with level between 1 and 5. When i put it in the cox model i have only the level between 2 and 5. The level 1 doesn't appear. I think i have to change the number of level but i don't really know. Please can you help me? Class Levels: 1 2 3 4 5 coxph(formula = Surv(delai.etat, etat) ~ class, data = igr1) coef exp(coef) se(coef) z p class2 -0.093 0.9110.245 -0.38 7.0e-01 class3 -0.749 0.4730.286 -2.62 8.9e-03 class4 -0.600 0.5490.343 -1.75 8.0e-02 class5 -0.874 0.4170.197 -4.44 8.9e-06 Likelihood ratio test=24.9 on 4 df, p=5.28e-05 n=740 (1 observations deleted due to missing) Thanks for your help Bertrand __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html !DSPAM:436dcb0b22713230529779! __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
