From: Charles C. Berry <cberry_at_tajo.ucsd.edu>

Date: Sat, 26 Jun 2010 14:09:09 -0700

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. Received on Sat 26 Jun 2010 - 21:13:27 GMT

Date: Sat, 26 Jun 2010 14:09:09 -0700

On Sat, 26 Jun 2010, Bryan Hanson wrote:

> Thanks Chuck, I understand much better what is going on with your example.

*> But I'm still uncertain why the b2$t array does not have the dimensions of R
**> x no. of strata.
*

Because the test statistic returned by mm() is a scalar. It has nothing to do with the use or number of strata.

Look at what the first case in example( boot ) is doing:

*> ncol(boot(grav1, diff.means, R=999, stype="f")$t)
*

[1] 2

*> ncol(boot(grav1, diff.means, R=999, stype="f",strata=grav1[,1])$t)
*

[1] 2

*> diff.means(grav1,1:nrow(grav1))
*

[1] -4.100549 14.722902

*>
*

Chuck

*>
*

> Any further insight would be appreciated. Bryan

*> *************
**> Bryan Hanson
**> Acting Chair
**> Professor of Chemistry & Biochemistry
**> DePauw University, Greencastle IN USA
**>
**>
**>
**> On 6/26/10 12:43 PM, "Charles C. Berry" <cberry_at_tajo.ucsd.edu> wrote:
**>
**>> On Sat, 26 Jun 2010, Bryan Hanson wrote:
**>>
**>>> Hello All. I must be missing the really obvious here:
**>>>
**>>> mm <- function(d, i) median(d[i])
**>>> b1 <- boot(gravity$g, mm, R = 1000)
**>>> b1
**>>> b2 <- boot(gravity$g, mm, R = 1000, strata = gravity$series)
**>>> b2
**>>>
**>>> Both b1 and b2 seem to have done (almost) the same thing, but it looks like
**>>> the strata argument in b2 has been ignored. However, str(b1) vs str(b2)
**>>> does show that the strata have been noted correctly. But b2$t is a 1000 x 1
**>>> array, not a 1000 x 8 array (gravity$series is a factor with 8 levels).
**>>>
**>>> There is a more complex example in ?boot using the same data set that gives
**>>> a result that seems to make sense (2 levels in the factor, so $t has 2
**>>> columns).
**>>>
**>>> I either misunderstand the expected behavior or I've missed some punctuation
**>>> or syntax detail.
**>>
**>> Your punctuation and syntax is OK.
**>>
**>> Note:
**>>
**>>> SISWR <- function(x) sample(x,length(x),repl=TRUE)
**>>> # no strata
**>>> var(replicate(1000,median(SISWR(gravity$g))))
**>> [1] 0.4588338
**>>> # now stratify on series
**>>> gsplit <- split(gravity$g,gravity$series)
**>>> var(replicate(1000,median(unlist(lapply(gsplit,SISWR)))))
**>> [1] 0.3882272
**>>>
**>>> sqrt(.45) # this agrees with b1
**>> [1] 0.6708204
**>>> sqrt(.39) # this agrees with b2
**>> [1] 0.6244998
**>>>
**>>
**>> The effect of stratification depends on the relative amount of variation
**>> within vs between strata. This suggests there is not a lot:
**>>
**>>> aov(g~series,gravity)
**>> Call:
**>> aov(formula = g ~ series, data = gravity)
**>>
**>> Terms:
**>> series Residuals
**>> Sum of Squares 2818.624 8239.376
**>> Deg. of Freedom 7 73
**>>
**>> Residual standard error: 10.62394
**>> Estimated effects may be unbalanced
**>>>
**>>
**>>
**>> HTH,
**>>
**>> Chuck
**>>
**>>>
**>>> TIA, Bryan
**>>>
**>>> *************
**>>> Bryan Hanson
**>>> Acting Chair
**>>> Professor of Chemistry & Biochemistry
**>>> DePauw University, Greencastle IN USA
**>>>
**>>>> sessionInfo()
**>>> R version 2.11.0 (2010-04-22)
**>>> x86_64-apple-darwin9.8.0
**>>>
**>>> locale:
**>>> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
**>>>
**>>> attached base packages:
**>>> [1] datasets tools grid graphics grDevices utils stats
**>>> [8] methods base
**>>>
**>>> other attached packages:
**>>> [1] boot_1.2-42 brew_1.0-3 faraway_1.0.4
**>>> [4] GGally_0.2 xtable_1.5-6 mvbutils_2.5.1
**>>> [7] ggplot2_0.8.7 digest_0.4.2 reshape_0.8.3
**>>> [10] proto_0.3-8 ChemoSpec_1.43 R.utils_1.4.0
**>>> [13] R.oo_1.7.2 R.methodsS3_1.2.0 rgl_0.91
**>>> [16] lattice_0.18-5 mvoutlier_1.4 plyr_0.1.9
**>>> [19] RColorBrewer_1.0-2 chemometrics_0.8 som_0.3-5
**>>> [22] robustbase_0.5-0-1 rpart_3.1-46 pls_2.1-0
**>>> [25] pcaPP_1.8-1 mvtnorm_0.9-9 nnet_7.3-1
**>>> [28] mclust_3.4.4 MASS_7.3-5 lars_0.9-7
**>>> [31] e1071_1.5-23 class_7.3-2
**>>>
**>>> ______________________________________________
**>>> 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.
**>>>
**>>
**>> Charles C. Berry (858) 534-2098
**>> Dept of Family/Preventive
**>> Medicine
**>> E mailto:cberry_at_tajo.ucsd.edu UC San Diego
**>> http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego 92093-0901
**>>
**>>
**>
**> ______________________________________________
**> 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.
**>
*

Charles C. Berry (858) 534-2098 Dept of Family/Preventive Medicine E mailto:cberry_at_tajo.ucsd.edu UC San Diegohttp://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego 92093-0901

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