Courtney Coon
2011-Jul-26 17:46 UTC
[R] using subset command in glm and glm coefficients output
I am a graduate student who's just starting to use more advanced statistics and is completely new to R. ?I'm looking for whether parasite prevalence varies with region. ?I'd like to try using just a subset of the data defined by one these covariates, sex, looking at data only from adults, without using it as a covariate in the analyses. ?I tried using subset=sex=='A' in the following context: malaria1<-glm(Malaria ~ X2sppclass+place+place*X2sppclass, subset=sex=='A', na.action=na.omit, family=binomial(link="logit"")) with sex being the column name and 'A' standing for adult but R doesn't seem to like that. ?It says there is an unexpected '=' but that's how I found it coded in other R forums. Because I couldn't get the above code to work, I ended up running the following model: malaria2<-glm(Malaria ~ X2sppclass+place+place*X2sppclass, na.action=na.omit, family=binomial(link='logit')) but I don't understand the summary output for the coefficients: Coefficients: (2 not defined because of singularities) ? ? ? ? ? ? ? ? ? ? ?Estimate Std. Error z value Pr(>|z|) (Intercept) ? ? ? ? ? ?12.9786 ? 624.1941 ? 0.021 ? 0.9834 X2sppclassH ? ? ? ? ? -12.4375 ? 624.1941 ?-0.020 ? 0.9841 X2sppclassN ? ? ? ? ? -12.5512 ? 624.1940 ?-0.020 ? 0.9840 placeEast ? ? ? ? ? ? ? 1.3304 ? ? 0.5870 ? 2.266 ? 0.0234 * placeWest ? ? ? ? ? ? ? 1.5875 ? ? 0.5468 ? 2.903 ? 0.0037 ** X2sppclassH:placeEast ? 0.9532 ? ? 0.7325 ? 1.301 ? 0.1931 X2sppclassN:placeEast ? ? ? NA ? ? ? ? NA ? ? ?NA ? ? ? NA X2sppclassH:placeWest ? 0.2992 ? ? 0.7218 ? 0.414 ? 0.6785 X2sppclassN:placeWest ? ? ? NA ? ? ? ? NA ? ? ?NA ? ? ? NA issue 1: the error "2 not defined because of singularities" even though I know there are multiple individuals that are 'N' and from the East or West. issue 2: It never gives any output for placeCentral. ?Is this because I'm using a binomial function and one of my predictors (place) is not binomial? Thanks for any help. -- Courtney Coon PhD candidate Department of Integrative Biology University of South Florida 4202 E. Fowler Ave., SCA 110 Tampa, FL 33620-5200 813-974-0157