On Dec 20, 2007 3:04 PM, Simon Beaumont <[EMAIL PROTECTED]> wrote: > > Is there some secret handshake I should use or did I ask a difficult > question?
Give us money :-) Just kidding! A lot of Sage developers -- like me -- are on vacation for the holidays right now. > On Dec 18, 10:26 pm, Simon Beaumont <[EMAIL PROTECTED]> wrote: > > Just installed 2.9 - how do I use the newly integrated R from sage? > > documentation seems to be behind on this ;-) Yep, there's no documentation at all included with Sage on how to use R from Sage or even that R is included in Sage. To use R in a way that integrates nicely with Sage, check out this webpage: http://rpy.sourceforge.net/ Here is a notebook session that illustrates doing some things with the R <--> Sage interface: {{{id=16| from rpy import * r.t_test(range(10)) /// {'null.value': {'mean': 0.0}, 'data.name': '0:9', 'method': 'One Sample t-test', 'p.value': 0.0011200178871001592, 'statistic': {'t': 4.7000967108038418}, 'estimate': {'mean of x': 4.5}, 'conf.int': [2.3341494103318317, 6.6658505896681683], 'parameter': {'df': 9.0}, 'alternative': 'two.sided'} }}} {{{id=17| from rpy import * v = [1,2,5, 10] v = [int(z) for z in v] # rpy doesn't play well with Sage types yet!!! r.t_test(v) /// {'null.value': {'mean': 0.0}, 'data.name': 'c(1L, 2L, 5L, 10L)', 'method': 'One Sample t-test', 'p.value': 0.11231741583919484, 'statistic': {'t': 2.2269224668742709}, 'estimate': {'mean of x': 4.5}, 'conf.int': [-1.930851808629775, 10.930851808629777], 'parameter': {'df': 3.0}, 'alternative': 'two.sided'} }}} {{{id=18| from rpy import * v = [random.random() for _ in range(10^4)] r.mean(v) /// 0.50381458009226054 }}} {{{id=19| r.median(v) /// 0.50252807909097674 }}} {{{id=21| r.sd(v) /// 0.2889341870587569 }}} {{{id=22| }}} This last may or may not work for you. For me it popped up a window with a plot in it. {{{id=15| from rpy import * degrees = 4 grid = r.seq(0, 10, length=100) values = [r.dchisq(x, degrees) for x in grid] r.par(ann=0) r.plot(grid, values, type='lines') /// Warning message: In plot.xy(xy, type, ...) : plot type 'lines' will be truncated to first character }}} We haven't quite stabilized how we will do plotting with R and the Sage notebook yet. Here's another big example: {{{id=14| %python faithful_dat = get_remote_file('http://rpy.sourceforge.net/faithful.dat') from rpy import * faithful_data = {"eruption_duration":[], "waiting_time":[]} f = open(faithful_dat,'r') for row in f.readlines()[1:]: # skip the column header line splitrow = row[:-1].split(" ") faithful_data["eruption_duration"].append(float(splitrow[0])) faithful_data["waiting_time"].append(int(splitrow[1])) f.close() ed = faithful_data["eruption_duration"] edsummary = r.summary(ed) print "Summary of Old Faithful eruption duration data" for k in edsummary.keys(): print k + ": %.3f" % edsummary[k] print print "Stem-and-leaf plot of Old Faithful eruption duration data" print r.stem(ed) r.png('faithful_histogram.png',width=733,height=550) r.hist(ed,r.seq(1.6, 5.2, 0.2), prob=1,col="lightgreen", main="Old Faithful eruptions",xlab="Eruption duration (seconds)") r.lines(r.density(ed,bw=0.1),col="orange") r.rug(ed) r.dev_off() long_ed = filter(lambda x: x > 3, ed) r.library('ctest') print "Shapiro-Wilks normality test of Old Faithful eruptions longer than 3 seconds" sw = r.shapiro_test(long_ed) print "W = %.4f" % sw['statistic']['W'] print "p-value = %.5f" % sw['p.value'] print print "One-sample Kolmogorov-Smirnov test of Old Faithful eruptions longer than 3 seconds" ks = r.ks_test(long_ed,"pnorm", mean=r.mean(long_ed), sd=r.sqrt(r.var(long_ed))) print "D = %.4f" % ks['statistic']['D'] print "p-value = %.4f" % ks['p.value'] print "Alternative hypothesis: %s" % ks['alternative'] print /// Attempting to load remote file: http://rpy.sourceforge.net/faithful.dat Loading: [print "\x01r\x01e49" .] Summary of Old Faithful eruption duration data Min.: 1.600 1st Qu.: 2.163 3rd Qu.: 4.454 Median: 4.000 Max.: 5.100 Mean: 3.488 Stem-and-leaf plot of Old Faithful eruption duration data The decimal point is 1 digit(s) to the left of the | 16 | 070355555588 18 | 000022233333335577777777888822335777888 20 | 00002223378800035778 22 | 0002335578023578 24 | 00228 26 | 23 28 | 080 30 | 7 32 | 2337 34 | 250077 36 | 0000823577 38 | 2333335582225577 40 | 0000003357788888002233555577778 42 | 03335555778800233333555577778 44 | 02222335557780000000023333357778888 46 | 0000233357700000023578 48 | 00000022335800333 50 | 0370 None Warning message: package 'ctest' has been merged into 'stats' Shapiro-Wilks normality test of Old Faithful eruptions longer than 3 seconds W = 0.9793 p-value = 0.01052 One-sample Kolmogorov-Smirnov test of Old Faithful eruptions longer than 3 seconds Warning message: In function (x, y, ..., alternative = c("two.sided", "less", "greater"), : cannot compute correct p-values with ties D = 0.0661 p-value = 0.4284 Alternative hypothesis: two-sided }}} > > > > Whilst I'm here a vote of thanks! I have been playing with sage for > > about a week now - (almost non-stop) - and I am very impressed... This Awesome! > > is my modeling environment of choice from herein... after all it > > subsumes everything else of note and presents the coolest web based > > front end... brilliant work - just at the right time for me. > > > > Can't wait for the fully distributed notebook. What do you mean by the "fully distributed notebook"? -- William --~--~---------~--~----~------------~-------~--~----~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://sage.scipy.org/sage/ and http://modular.math.washington.edu/sage/ -~----------~----~----~----~------~----~------~--~---
