On Sep 15, 2013, at 2:15 AM, Lutfor Rahman wrote: > Thanks for that. Still I am a bit confused. Please advice me. > Now, I have got minimal adequate model keeping all the those significant > predictors in the model which is shown below: > Coefficients: > Estimate Std. Error z value Pr(>|z|) > (Intercept) 5.846747 0.987461 5.921 3.2e-09 *** > orgmatter -0.886985 0.235347 -3.769 0.000164 *** > baresoil -0.935106 0.293838 -3.182 0.001461 ** > orgmatter:moistcont 0.009452 0.002759 3.426 0.000612 *** > baresoil:moistcont 0.025640 0.009698 2.644 0.008194 ** > wood10:grass10 0.007433 0.003187 2.333 0.019667 * > grass10:rdnet10 0.004822 0.001563 3.085 0.002036 ** > wood10:rdnet10 -0.045485 0.016890 -2.693 0.007081 ** > > But when I do anova test of this minimal adequate model, only > baresoil:moistcont, grass10:rdnet, wood10:rdnet10 were found significant. > > Df Deviance Resid. Df Resid. Dev Pr(>Chi) > NULL 17 36.167 > orgmatter 1 2.4260 16 33.741 0.119334 > baresoil 1 1.0871 15 32.654 0.297104 > orgmatter:moistcont 1 2.5611 14 30.093 0.109526 > baresoil:moistcont 1 8.2976 13 21.795 0.003970 ** > wood10:grass10 1 0.0184 12 21.777 0.892042 > grass10:rdnet10 1 5.4520 11 16.325 0.019546 * > wood10:rdnet10 1 8.1565 10 8.168 0.004291 ** > > So, when I report the outcome of this model, should I show summary > significance values or anova significance value (chi-square).
I don't think you should report anything. You need a consultation. Rhelp is established to offer technical advice about running R code. >From the Posting Guide: "Questions about statistics: The R mailing lists are primarily intended for questions and discussion about the R software. However, questions about statistical methodology are sometimes posted. If the question is well-asked and of interest to someone on the list, it may elicit an informative up-to-date answer. See also the Usenet groups sci.stat.consult (applied statistics and consulting) and sci.stat.math (mathematical stat and probability). Basic statistics and classroom homework: R-help is not intended for these." -- David. > > Regards > Lutfor > > > > > > On Fri, Sep 13, 2013 at 7:42 PM, David Winsemius <dwinsem...@comcast.net> > wrote: > > On Sep 13, 2013, at 9:38 AM, Lutfor Rahman wrote: > > Dear forum members, > > Please help me understanding significance value when GLM done in r. > > After doing minimal adequate model, I have found a number of independent > values which are significant. But doing their anova significant values are > different. Please find my result following. Which significant values should > I use. > > > glm(formula = richness ~ moistcont + orgmatter + baresoil + grass10 + > wood10 + rdnet10 + moistcont:orgmatter + moistcont:baresoil + > grass10:wood10 + grass10:rdnet10 + wood10:rdnet10, family = poisson, > data = data) > > Deviance Residuals: > Min 1Q Median 3Q Max > -1.19112 -0.33682 0.09813 0.32808 0.70509 > > Coefficients: > Estimate Std. Error z value Pr(>|z|) > (Intercept) 11.384447 4.014170 2.836 0.00457 ** > moistcont -0.095813 0.084995 -1.127 0.25962 > orgmatter -1.810116 0.613688 -2.950 0.00318 ** > baresoil -1.636707 0.559129 -2.927 0.00342 ** > grass10 -0.018979 0.065647 -0.289 0.77250 > wood10 0.150683 0.128386 1.174 0.24053 > rdnet10 -0.011448 0.068090 -0.168 0.86648 > moistcont:orgmatter 0.025698 0.011521 2.231 0.02571 * > moistcont:baresoil 0.044110 0.015799 2.792 0.00524 ** > grass10:wood10 0.010740 0.006498 1.653 0.09838 . > grass10:rdnet10 0.011013 0.004412 2.496 0.01255 * > wood10:rdnet10 -0.088297 0.027120 -3.256 0.00113 ** > > The only p-value I would have expected to be the same would have been the > last one in the avova output: > > Df Deviance Resid. Df Resid. Dev Pr(>Chi) > ..... > > wood10:rdnet10 1 10.7812 6 3.928 0.001025 ** > > And that particular p-value is not far off from the 0.00113 value reported in > the model summary. The other p-values are not of the same sort. The p-values > above are basically reporting the "significance" of removing single > predictors or interactions from the full model. The anova reported below is > perfoming sequential addition of terms to a NULL model as well as doing a > different test: LR tests instead of Wald statistics. > > -- > David. > > > --- > Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 > > (Dispersion parameter for poisson family taken to be 1) > > Null deviance: 36.1673 on 17 degrees of freedom > Residual deviance: 3.9276 on 6 degrees of freedom > AIC: 97.893 > > Number of Fisher Scoring iterations: 4 > > anova(data1, test="Chisq") > Analysis of Deviance Table > > Model: poisson, link: log > > Response: richness > > Terms added sequentially (first to last) > > > Df Deviance Resid. Df Resid. Dev Pr(>Chi) > NULL 17 36.167 > moistcont 1 8.6322 16 27.535 0.003303 ** > orgmatter 1 2.1244 15 25.411 0.144966 > baresoil 1 0.0029 14 25.408 0.956986 > grass10 1 1.5251 13 23.883 0.216842 > wood10 1 3.6952 12 20.187 0.054570 . > rdnet10 1 0.0001 11 20.187 0.990564 > moistcont:orgmatter 1 2.0482 10 18.139 0.152381 > moistcont:baresoil 1 2.8730 9 15.266 0.090076 . > grass10:wood10 1 0.1431 8 15.123 0.705247 > grass10:rdnet10 1 0.4141 7 14.709 0.519883 > wood10:rdnet10 1 10.7812 6 3.928 0.001025 ** > --- > Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 > > [[alternative HTML version deleted]] > > ______________________________________________ > 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. > > David Winsemius, MD > Alameda, CA, USA > > David Winsemius Alameda, CA, USA ______________________________________________ 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.
