From: Bryan Hanson <hanson_at_depauw.edu>

Date: Sat, 26 Jun 2010 15:17:05 -0400

Bryan Hanson

Acting Chair

Professor of Chemistry & Biochemistry

DePauw University, Greencastle IN USA

>> 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.
*

>> SISWR <- function(x) sample(x,length(x),repl=TRUE)

*>> # no strata
*

*>> var(replicate(1000,median(SISWR(gravity$g))))
*

>> # now stratify on series

*>> gsplit <- split(gravity$g,gravity$series)
*

*>> var(replicate(1000,median(unlist(lapply(gsplit,SISWR)))))
*

*>>
*

>> sqrt(.45) # this agrees with b1

>> sqrt(.39) # this agrees with b2

*>>
*

>> aov(g~series,gravity)

*>>
*

*>>
*

>> TIA, Bryan

*>>
*

*>> *************
*

*>> Bryan Hanson
*

*>> Acting Chair
*

*>> Professor of Chemistry & Biochemistry
*

*>> DePauw University, Greencastle IN USA
*

*>>
*

>> 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.
*

*>>
*

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 - 19:23:28 GMT

Date: Sat, 26 Jun 2010 15:17:05 -0400

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.

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:

> > Your punctuation and syntax is OK. > > Note: >

>> SISWR <- function(x) sample(x,length(x),repl=TRUE)

> [1] 0.4588338

>> # now stratify on series

> [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

>>> sessionInfo()

>> R version 2.11.0 (2010-04-22)

> > 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. Received on Sat 26 Jun 2010 - 19:23:28 GMT

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