lincoln
2012-May-07 17:05 UTC
[R] Can't find the error in a Binomial GLM I am doing, please help
Hi all, I can't find the error in the binomial GLM I have done. I want to use that because there are more than one explanatory variables (all categorical) and a binary response variable. This is how my data set looks like:> str(data)'data.frame': 1004 obs. of 5 variables: $ site : int 0 0 0 0 0 0 0 0 0 0 ... $ sex : Factor w/ 2 levels "0","1": NA NA NA NA 1 NA NA NA NA NA ... $ age : Factor w/ 2 levels "0","1": 1 1 1 1 1 1 1 1 1 1 ... $ cohort: Factor w/ 11 levels "1996","2000",..: 11 11 11 11 11 11 11 11 11 11 ... $ birth : Factor w/ 3 levels "5","6","7": 3 3 2 2 2 2 2 2 2 2 ... I know that, particularly for one level of variable "cohort" (2004 value), it should be a strong effect of variable "cohort" on variable "site" so I do a Chi square test that confirms the null hypothesis there is a difference in sites on the way "cohort" is distributed:> (chisq.test(data$site,data$cohort))Pearson's Chi-squared test data: data$site and data$cohort X-squared = 82.6016, df = 10, *p-value = 1.549e-13* Mensajes de aviso perdidos In chisq.test(data$site, data$cohort) : Chi-squared approximation may be incorrect After that, I have tried to use a binomial GLM with all the explanatory variables but I couldn't find any significance of any variable, neither cohort, and for this reason I tried to use only cohort as predictor and I get this:> BinomialGlm <- glm(site ~ cohort, data=data,binomial) > summary(BinomialGlm)Call: glm(formula = site ~ cohort, family = binomial, data = data) Deviance Residuals: Min 1Q Median 3Q Max -1.9239 -0.9365 -0.9365 1.3584 1.6651 Coefficients: Estimate Std. Error z value Pr(>|z|) (Intercept) -12.57 324.74 -0.039 0.969 cohort2000 11.47 324.75 0.035 0.972 cohort2001 13.82 324.74 0.043 0.966 cohort2002 12.97 324.74 0.040 0.968 cohort2003 13.66 324.74 0.042 0.966 *cohort2004 14.25 324.74 0.044 0.965* cohort2006 12.21 324.74 0.038 0.970 cohort2007 11.81 324.74 0.036 0.971 cohort2008 12.41 324.74 0.038 0.970 cohort2009 12.15 324.74 0.037 0.970 cohort2010 11.97 324.74 0.037 0.971 (Dispersion parameter for binomial family taken to be 1) Null deviance: 1369.3 on 1003 degrees of freedom Residual deviance: 1283.7 on 993 degrees of freedom AIC: 1305.7 Number of Fisher Scoring iterations: 11 I tired to use simple GLM (gaussian family) and I get results that are more logicals:> GaussGlm <- glm(site ~ cohort, data=data) > summary(GaussGlm)Call: glm(formula = site ~ cohort, data = data) Deviance Residuals: Min 1Q Median 3Q Max -0.8429 -0.3550 -0.3550 0.6025 0.7500 Coefficients: Estimate Std. Error t value Pr(>|t|) (Intercept) 5.740e-14 4.762e-01 0.000 1.0000 cohort2000 2.500e-01 5.324e-01 0.470 0.6388 cohort2001 7.778e-01 5.020e-01 1.549 0.1216 cohort2002 6.000e-01 4.880e-01 1.230 0.2192 cohort2003 7.500e-01 4.861e-01 1.543 0.1231 *cohort2004 8.429e-01 4.796e-01 1.757 0.0792 .* cohort2006 4.118e-01 4.832e-01 0.852 0.3943 cohort2007 3.204e-01 4.785e-01 0.670 0.5033 cohort2008 4.600e-01 4.786e-01 0.961 0.3367 cohort2009 3.975e-01 4.772e-01 0.833 0.4051 cohort2010 3.550e-01 4.768e-01 0.745 0.4567 --- Signif. codes: 0 ?***? 0.001 ?**? 0.01 ?*? 0.05 ?.? 0.1 ? ? 1 (Dispersion parameter for gaussian family taken to be 0.2267955) Null deviance: 245.40 on 1003 degrees of freedom Residual deviance: 225.21 on 993 degrees of freedom AIC: 1372.5 Number of Fisher Scoring iterations: 2 What is going on? Any suggestion/commentary? -- View this message in context: http://r.789695.n4.nabble.com/Can-t-find-the-error-in-a-Binomial-GLM-I-am-doing-please-help-tp4615340.html Sent from the R help mailing list archive at Nabble.com.
Bert Gunter
2012-May-07 17:39 UTC
[R] Can't find the error in a Binomial GLM I am doing, please help
1. As this is a statistical, rather than an R issue, you would do better posting on a statistical help site like stats.stackexchange.com (although some generous soul here may respond). 2. You would also probably do better consulting with a local statistical resource if available, as it is difficult to explain such issues remotely. Cheers, Bert On Mon, May 7, 2012 at 10:05 AM, lincoln <miseno77 at hotmail.com> wrote:> Hi all, > > I can't find the error in the binomial GLM I have done. I want to use that > because there are more than one explanatory variables (all categorical) and > a binary response variable. > This is how my data set looks like: >> str(data) > 'data.frame': ? 1004 obs. of ?5 variables: > ?$ site ?: int ?0 0 0 0 0 0 0 0 0 0 ... > ?$ sex ? : Factor w/ 2 levels "0","1": NA NA NA NA 1 NA NA NA NA NA ... > ?$ age ? : Factor w/ 2 levels "0","1": 1 1 1 1 1 1 1 1 1 1 ... > ?$ cohort: Factor w/ 11 levels "1996","2000",..: 11 11 11 11 11 11 11 11 11 > 11 ... > ?$ birth : Factor w/ 3 levels "5","6","7": 3 3 2 2 2 2 2 2 2 2 ... > > I know that, particularly for one level of variable "cohort" (2004 value), > it should be a strong effect of variable "cohort" on variable "site" so I do > a Chi square test that confirms the null hypothesis there is a difference in > sites on the way "cohort" is distributed: > >> (chisq.test(data$site,data$cohort)) > > ? ? ? ?Pearson's Chi-squared test > > data: ?data$site and data$cohort > X-squared = 82.6016, df = 10, *p-value = 1.549e-13* > > Mensajes de aviso perdidos > In chisq.test(data$site, data$cohort) : > ?Chi-squared approximation may be incorrect > > > > > After that, I have tried to use a binomial GLM with all the explanatory > variables but I couldn't find any significance of any variable, neither > cohort, and for this reason I tried to use only cohort as predictor and I > get this: > > >> BinomialGlm <- glm(site ~ ?cohort, data=data,binomial) >> summary(BinomialGlm) > > Call: > glm(formula = site ~ cohort, family = binomial, data = data) > > Deviance Residuals: > ? ?Min ? ? ? 1Q ? Median ? ? ? 3Q ? ? ?Max > -1.9239 ?-0.9365 ?-0.9365 ? 1.3584 ? 1.6651 > > Coefficients: > ? ? ? ? ? ?Estimate Std. Error z value Pr(>|z|) > (Intercept) ? -12.57 ? ? 324.74 ?-0.039 ? ?0.969 > cohort2000 ? ? 11.47 ? ? 324.75 ? 0.035 ? ?0.972 > cohort2001 ? ? 13.82 ? ? 324.74 ? 0.043 ? ?0.966 > cohort2002 ? ? 12.97 ? ? 324.74 ? 0.040 ? ?0.968 > cohort2003 ? ? 13.66 ? ? 324.74 ? 0.042 ? ?0.966 > *cohort2004 ? ? 14.25 ? ? 324.74 ? 0.044 ? ?0.965* > cohort2006 ? ? 12.21 ? ? 324.74 ? 0.038 ? ?0.970 > cohort2007 ? ? 11.81 ? ? 324.74 ? 0.036 ? ?0.971 > cohort2008 ? ? 12.41 ? ? 324.74 ? 0.038 ? ?0.970 > cohort2009 ? ? 12.15 ? ? 324.74 ? 0.037 ? ?0.970 > cohort2010 ? ? 11.97 ? ? 324.74 ? 0.037 ? ?0.971 > > (Dispersion parameter for binomial family taken to be 1) > > ? ?Null deviance: 1369.3 ?on 1003 ?degrees of freedom > Residual deviance: 1283.7 ?on ?993 ?degrees of freedom > AIC: 1305.7 > > Number of Fisher Scoring iterations: 11 > > > > > I tired to use simple GLM (gaussian family) and I get results that are more > logicals: > >> GaussGlm <- glm(site ~ ?cohort, data=data) >> summary(GaussGlm) > > Call: > glm(formula = site ~ cohort, data = data) > > Deviance Residuals: > ? ?Min ? ? ? 1Q ? Median ? ? ? 3Q ? ? ?Max > -0.8429 ?-0.3550 ?-0.3550 ? 0.6025 ? 0.7500 > > Coefficients: > ? ? ? ? ? ? Estimate Std. Error t value Pr(>|t|) > (Intercept) 5.740e-14 ?4.762e-01 ? 0.000 ? 1.0000 > cohort2000 ?2.500e-01 ?5.324e-01 ? 0.470 ? 0.6388 > cohort2001 ?7.778e-01 ?5.020e-01 ? 1.549 ? 0.1216 > cohort2002 ?6.000e-01 ?4.880e-01 ? 1.230 ? 0.2192 > cohort2003 ?7.500e-01 ?4.861e-01 ? 1.543 ? 0.1231 > *cohort2004 ?8.429e-01 ?4.796e-01 ? 1.757 ? 0.0792 .* > cohort2006 ?4.118e-01 ?4.832e-01 ? 0.852 ? 0.3943 > cohort2007 ?3.204e-01 ?4.785e-01 ? 0.670 ? 0.5033 > cohort2008 ?4.600e-01 ?4.786e-01 ? 0.961 ? 0.3367 > cohort2009 ?3.975e-01 ?4.772e-01 ? 0.833 ? 0.4051 > cohort2010 ?3.550e-01 ?4.768e-01 ? 0.745 ? 0.4567 > --- > Signif. codes: ?0 ?***? 0.001 ?**? 0.01 ?*? 0.05 ?.? 0.1 ? ? 1 > > (Dispersion parameter for gaussian family taken to be 0.2267955) > > ? ?Null deviance: 245.40 ?on 1003 ?degrees of freedom > Residual deviance: 225.21 ?on ?993 ?degrees of freedom > AIC: 1372.5 > > Number of Fisher Scoring iterations: 2 > > > > What is going on? Any suggestion/commentary? > > -- > View this message in context: http://r.789695.n4.nabble.com/Can-t-find-the-error-in-a-Binomial-GLM-I-am-doing-please-help-tp4615340.html > Sent from the R help mailing list archive at Nabble.com. > > ______________________________________________ > 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.-- Bert Gunter Genentech Nonclinical Biostatistics Internal Contact Info: Phone: 467-7374 Website: http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm