Dear all, does anyone know how I can extract specific p-values for covariates from an aftreg object? After fitting a model with aftreg I can find all different variables by using str(), but there's no place where p-values are kept. The odd thing is that print() displays them correctly. EXAMPLE: > testdata start stop censor groupvar var1 var2 1 0 1 0 1 0.91663902 0.0847912 2 1 2 0 1 0.60470753 0.6487798 3 2 3 0 1 0.09599891 0.2195178 4 3 4 1 1 0.86384189 0.6667897 5 0 1 0 2 0.07747445 0.8782836 6 1 2 0 2 0.44608030 0.2218685 7 2 3 1 2 0.77317152 0.3813840 > fit1 <- aftreg(Surv(start, stop, censor)~var1, data=testdata) > fit1 Call: aftreg(formula = Surv(start, stop, censor) ~ var1, data = testdata) Covariate W.mean Coef Exp(Coef) se(Coef) Wald p var1 0.540 0.150 1.162 0.770 0.845 log(scale) 1.358 3.890 0.260 0.000 log(shape) 2.015 7.502 0.781 0.010 Events 2 Total time at risk 7 Max. log. likelihood -1.4026 LR test statistic 0.05 Degrees of freedom 1 Overall p-value 0.816436 WALD P IS DISPLAYED CORRECTLY. Any help is highly appreciated, I'm going nuts here ;) Thanks Philipp
2010/2/18 Philipp Rappold <philipp.rappold at gmail.com>:> Dear all, > > does anyone know how I can extract specific p-values for covariates from an > aftreg object? After fitting a model with aftreg I can find all different > variables by using str(), but there's no place where p-values are kept. The > odd thing is that print() displays them correctly. > > EXAMPLE: > >> testdata > ?start stop censor groupvar ? ? ? var1 ? ? ?var2 > 1 ? ? 0 ? ?1 ? ? ?0 ? ? ? ?1 0.91663902 0.0847912 > 2 ? ? 1 ? ?2 ? ? ?0 ? ? ? ?1 0.60470753 0.6487798 > 3 ? ? 2 ? ?3 ? ? ?0 ? ? ? ?1 0.09599891 0.2195178 > 4 ? ? 3 ? ?4 ? ? ?1 ? ? ? ?1 0.86384189 0.6667897 > 5 ? ? 0 ? ?1 ? ? ?0 ? ? ? ?2 0.07747445 0.8782836 > 6 ? ? 1 ? ?2 ? ? ?0 ? ? ? ?2 0.44608030 0.2218685 > 7 ? ? 2 ? ?3 ? ? ?1 ? ? ? ?2 0.77317152 0.3813840 > > >> fit1 <- aftreg(Surv(start, stop, censor)~var1, data=testdata) > > >> fit1 > Call: > aftreg(formula = Surv(start, stop, censor) ~ var1, data = testdata) > > Covariate ? ? ? ? ?W.mean ? ? ?Coef Exp(Coef) ?se(Coef) ? ?Wald p > var1 ? ? ? ? ? ? ? ?0.540 ? ? 0.150 ? ? 1.162 ? ? 0.770 ? ? 0.845 > > log(scale) ? ? ? ? ? ? ? ? ? ?1.358 ? ? 3.890 ? ? 0.260 ? ? 0.000 > log(shape) ? ? ? ? ? ? ? ? ? ?2.015 ? ? 7.502 ? ? 0.781 ? ? 0.010 > > Events ? ? ? ? ? ? ? ? ? ?2 > Total time at risk ? ? ? ? ? ? 7 > Max. log. likelihood ? ? ?-1.4026 > LR test statistic ? ? ? ? 0.05 > Degrees of freedom ? ? ? ?1 > Overall p-value ? ? ? ? ? 0.816436 > ? ? ? ?WALD P IS DISPLAYED CORRECTLY. > > > Any help is highly appreciated, I'm going nuts here ;)print.aftreg calculates the p-values like this: pchisq(x$coef^2 / diag(x$var), 1, lower.tail = FALSE) where x is the output from 'aftreg'. You could try the same. Thanks> Philipp > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. >-- G?ran Brostr?m
I don't seem to have the unnamed package loaded that has aftreg(), but in general you ought to be able to get what you want by looking not just at the aftreg-object but also at the print(aftreg)-object using str(). On Feb 18, 2010, at 11:07 AM, Philipp Rappold wrote:> Dear all, > > does anyone know how I can extract specific p-values for covariates > from an aftreg object? After fitting a model with aftreg I can find > all different variables by using str(), but there's no place where p- > values are kept. The odd thing is that print() displays them > correctly. > > EXAMPLE: > > > testdata > start stop censor groupvar var1 var2 > 1 0 1 0 1 0.91663902 0.0847912 > 2 1 2 0 1 0.60470753 0.6487798 > 3 2 3 0 1 0.09599891 0.2195178 > 4 3 4 1 1 0.86384189 0.6667897 > 5 0 1 0 2 0.07747445 0.8782836 > 6 1 2 0 2 0.44608030 0.2218685 > 7 2 3 1 2 0.77317152 0.3813840 > > > > fit1 <- aftreg(Surv(start, stop, censor)~var1, data=testdata) > > > > fit1 > Call: > aftreg(formula = Surv(start, stop, censor) ~ var1, data = testdata) > > Covariate W.mean Coef Exp(Coef) se(Coef) Wald p > var1 0.540 0.150 1.162 0.770 0.845 > > log(scale) 1.358 3.890 0.260 0.000 > log(shape) 2.015 7.502 0.781 0.010 > > Events 2 > Total time at risk 7 > Max. log. likelihood -1.4026 > LR test statistic 0.05 > Degrees of freedom 1 > Overall p-value 0.816436 > WALD P IS DISPLAYED CORRECTLY. > > > Any help is highly appreciated, I'm going nuts here ;) > > Thanks > Philipp-- David Winsemius, MD Heritage Laboratories West Hartford, CT