On Aug 7, 4:02 pm, Brad <[email protected]> wrote: > Hi, > > I just downloaded and installed v4.7 of Sage on Mac OS X 10.6.8. > > I really like the application and appreciate all of the hard work the > Sage team has done to produce this great software package.
Great! > Lately, I have been trying to learn R and rpy2 for statistical > analyses. Good. > Unfortunately, I have been experiencing some problems as I work > through the rpy2 documentation pages (http://rpy.sourceforge.net/rpy2/ > doc-2.0/html/introduction.html#getting-started) from within Sage. Yes, there aren't that many people using rpy2 with Sage - for instance, William Stein found something nasty about Numpy and rpy2 not that long ago, at least them not working together in Sage: http://flask.sagenb.org/home/pub/57/ (I assume this worksheet still exists?) > > For instance, this simple worksheet input, > > --------------------------------- > import rpy2.robjects as robjects > piplus2 = robjects.r('pi') + 2 > --------------------------------- sage: piplus2 = robjects.r('pi')+int(2) should work. The problem is that we don't have much casting to RPy; most of the work has gone into the R pexpect interface instead, working directly with R. I find RPy confusing, myself :) and work directly with R, though I do have to use r.eval("stuff") a lot for positional arguments, which don't always work well with it. > --------------------------------- > > I then switched to r mode on the worksheet and typed a set of R > commands given in the same rpy2 documentation: > > --------------------------------- > ctl <- c(4.17,5.58,5.18,6.11,4.50,4.61,5.17,4.53,5.33,5.14) > trt <- c(4.81,4.17,4.41,3.59,5.87,3.83,6.03,4.89,4.32,4.69) > group <- gl(2, 10, 20, labels = c("Ctl","Trt")) > weight <- c(ctl, trt) > anova(lm.D9 <- lm(weight ~ group)) > summary(lm.D90 <- lm(weight ~ group - 1))# omitting intercept > --------------------------------- Hmm, that surprises me. This should not be calling rpy2. I get Analysis of Variance Table Response: weight Df Sum Sq Mean Sq F value Pr(>F) group 1 0.6882 0.68820 1.4191 0.249 Residuals 18 8.7293 0.48496 Call: lm(formula = weight ~ group - 1) Residuals: Min 1Q Median 3Q Max -1.0710 -0.4938 0.0685 0.2462 1.3690 Coefficients: Estimate Std. Error t value Pr(>|t|) groupCtl 5.0320 0.2202 22.85 9.55e-15 *** groupTrt 4.6610 0.2202 21.16 3.62e-14 *** --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 Residual standard error: 0.6964 on 18 degrees of freedom Multiple R-squared: 0.9818, Adjusted R-squared: 0.9798 F-statistic: 485.1 on 2 and 18 DF, p-value: < 2.2e-16 My guess is that you still had some residue of weirdness left over from having imported rpy2. Try restarting the worksheet and NOT importing rpy2. Good luck! We really value contributions from R users. By the way, another open source project you may find interesting (though it wouldn't integrate with Python/Sage) is http://rstudio.org/. - kcrisman -- To post to this group, send email to [email protected] To unsubscribe from this group, send email to [email protected] For more options, visit this group at http://groups.google.com/group/sage-support URL: http://www.sagemath.org
