[R] back transforming output from negative binomial
Dear all, I used the glm.nb with the default values from the MASS package to run a negative binomial regression. Here is a simple example: set.seed(123) y - c( rep(0, 30), rpois(70, lambda=2) ) smoke - factor( sample( c(NO, YES), 100, replace=T ) ) height - c( rnorm(30, mean=100, sd=20), rnorm(70, mean=150, sd=20) ) fit - glm.nb( y ~ smoke + height ) coef(summary(fit)) Estimate Std. Errorz value Pr(|z|) (Intercept) -2.34907191 0.537610710 -4.3694664 1.245505e-05 smokeYES-0.03479730 0.197627539 -0.1760751 8.602349e-01 height 0.01942373 0.003527538 5.5063142 3.664243e-08 The question now is how do I report the results, say, for height? Do I simply take the anti logs. i.e. 1.019613 = exp(0.019423) ? I have seen one paper where they report using anti log base 10 instead of natural base but they use STATA though. Please kindly advise. Thank you. Regards, Adai __ R-help@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.
Re: [R] back transforming output from negative binomial
Adaikalavan Ramasamy a.ramasamy at imperial.ac.uk writes: Dear all, I used the glm.nb with the default values from the MASS package to run a negative binomial regression. Here is a simple example: [snip -- thanks for the example!] The question now is how do I report the results, say, for height? Do I simply take the anti logs. i.e. 1.019613 = exp(0.019423) ? I have seen one paper where they report using anti log base 10 instead of natural base but they use STATA though. Yes, exactly. If you look at ?glm.nb you will see that it uses a log link function, and therefore you should exponentiate (anti-log) to back-transform. Natural, not base-10 logs, are used. Don't forget that back-transforming standard errors by themselves is meaningless, you have to back-transform lower and upper confidence limits ... Ben Bolker __ R-help@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.
Re: [R] back transforming output from negative binomial
Adaikalavan Ramasamy wrote: Ben, fantastic. Thank you for confirming it. One more question. What do you call the back transformed variable? In my domain, people use something called the ratio of mean but I am not sure if it is the same. I am not what the ratio is between. It depends. For the intercept, the back-transformed parameter is essentially the geometric mean of the baseline group (assuming you're using treatment contrasts). For factors, the back-transf parameters are the ratios between the means of observations at one factor level and the mean at the baseline level. For continuous covariates, it's the proportional increase per unit of increase in the covariate. Regards, Adai Ben Bolker wrote: Adaikalavan Ramasamy a.ramasamy at imperial.ac.uk writes: Dear all, I used the glm.nb with the default values from the MASS package to run a negative binomial regression. Here is a simple example: [snip -- thanks for the example!] The question now is how do I report the results, say, for height? Do I simply take the anti logs. i.e. 1.019613 = exp(0.019423) ? I have seen one paper where they report using anti log base 10 instead of natural base but they use STATA though. Yes, exactly. If you look at ?glm.nb you will see that it uses a log link function, and therefore you should exponentiate (anti-log) to back-transform. Natural, not base-10 logs, are used. Don't forget that back-transforming standard errors by themselves is meaningless, you have to back-transform lower and upper confidence limits ... Ben Bolker __ R-help@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. __ R-help@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.
