[R] svyhist
Muhuri, Pradip (SAMHSA/CBHSQ)
Pradip.Muhuri at samhsa.hhs.gov
Sat Oct 6 04:55:27 CEST 2012
Dear Anthony and David,
Thank you so much for your comments and suggestions!
The sample data set I had embedded in the earlier-sent R script was intended to be used for the reproducible example.
Now I have used Anthony's revised code on the the entire analytic file. The code has worked fine. Thanks, again.
Attached are the 2 .png files.
The only problem I see is that the y-lim in these 2 plots is not exactly the same. I have tried this: ylim = c(0,0.005, 0.010, 0.015, 0.020, 0.025, 0.030), which
did not work. Any thoughts?
Pradip Muhuri
####################################### Revised Code #######################
setwd ("E:/RDATA")
options(width = 120)
library (survey)
library (KernSmooth)
library (Hmisc)
load("tor.rdata")
#contents (tor)
# Grouping variable (xspd) to be factor
tor <- within(tor, {
xspd2 <- factor(xspd2,levels=c (1,2),
labels=c('SPD', 'No SPD'), ordered=TRUE)
}
)
# object with survey design variables and data
nhis <- svydesign (id=~psu,strat=~stratum, weights=~wt8, data=tor, nest=TRUE)
MyBreaks <- c(18,35,45,55,65,75,85,95)
png("svyhist_no_spd_age_at_death.png")
options( survey.lonely.psu = "adjust" )
svyhist (~dthage,
subset (nhis, mortstat==1 & xspd2=='No SPD'), breaks=MyBreaks,
main= " ",
col="grey80", xlab="Age at Death among those Who had SPD"
)
lines (svysmooth(~dthage, bandwidth=5,subset(nhis, xspd2=='No SPD')), lwd=2)
dev.off ()
png("svyhist_spd_age_at_death.png")
options( survey.lonely.psu = "adjust" )
svyhist (~dthage,
subset (nhis, mortstat==1 & xspd2=='SPD'), breaks=MyBreaks,
#ylim = c(0,0.005, 0.010, 0.015, 0.020, 0.025, 0.030),
main= " ",
col="grey80",
xlab="Age at Death among those Who had no SPD Distribution"
)
lines (svysmooth(~dthage, bandwidth=5,subset(nhis, xspd2=='No SPD')), lwd=2)
dev.off ()
##########################################################################################
________________________________________
From: Anthony Damico [ajdamico at gmail.com]
Sent: Friday, October 05, 2012 7:29 PM
To: David Winsemius
Cc: Muhuri, Pradip (SAMHSA/CBHSQ); R help
Subject: Re: [R] svyhist
this worked for me -- and doesn't require removing the PSUs from the design :)
options( survey.lonely.psu = "adjust" )
svyhist (~dthage,
subset (nhis, xspd2=='No SPD'), breaks=MyBreaks, main= " ",
col="grey80",
xlab="Age at Death Distribution"
)
lines (svysmooth(~dthage, bandwidth=5,subset(nhis, xspd2=='No SPD')), lwd=2)
Dr. Lumley has written quite a bit about single-PSU strata here: http://faculty.washington.edu/tlumley/survey/exmample-lonely.html
On Fri, Oct 5, 2012 at 7:16 PM, David Winsemius <dwinsemius at comcast.net<mailto:dwinsemius at comcast.net>> wrote:
On Oct 5, 2012, at 3:33 PM, Muhuri, Pradip (SAMHSA/CBHSQ) wrote:
> Hello,
>
> I was trying to draw histograms of age at death and got the following 2 error messages:
>
>
> 1) Error in tapply(1:NROW(x), list(factor(strata)), function(index) { :
>
> arguments must have same length
This is the top of the output of str applied to the data argument you offered to svyhist:
> str(subset (nhis, xspd2==2) )
List of 9
$ cluster :'data.frame': 0 obs. of 1 variable:
..$ psu: Factor w/ 47 levels "109.1","115.2",..:
..- attr(*, "terms")=Classes 'terms', 'formula' length 2 ~psu
.. .. ..- attr(*, "variables")= language list(psu)
.. .. ..- attr(*, "factors")= int [1, 1] 1
.. .. .. ..- attr(*, "dimnames")=List of 2
.. .. .. .. ..$ : chr "psu"
.. .. .. .. ..$ : chr "psu"
At least one problem seems pretty clear. No data. That can be corrected by wrapping as.numeric() around the factor on which you are subsetting in two places.
Another problem may arise when you restrict to one class only, namely there won't any "design" to work with. All the clusters .... there would be only one .... no longer have any multiplicity, and svyhist apparently isn't built to handle situation, at least with that design argument.
Error in onestrat(x[index, , drop = FALSE], clusters[index], nPSU[index][1], :
Stratum (2) has only one PSU at stage 1
Taking the 'stratum' argument out of the design() spec allows it to proceed, but I do not know if that is introducing invalidity in the analysis.
--
David.
>
>
> 2) Error in findInterval(mm[, i], gx) : 'vec' contains NAs
>
> In addition: Warning messages:
>
> 1: In min(x) : no non-missing arguments to min; returning Inf
>
> 2: In max(x) : no non-missing arguments to max; returning -Inf
>
>
>
> I would appreciate if someone could help me resolve these issues.
>
>
>
> Below is reproducible example.
>
> Thanks,
>
> Pradip Muhuri
>
>
>
> setwd ("E:/RDATA")
> options(width = 120)
> library (survey)
> library (KernSmooth)
> xd1 <-
> "dthage ypll_75 xspd2 psu stratum wt8
> 56 19 2 2 33 1512.7287
> 86 0 2 2 129 1830.6400
> 81 0 2 1 67 536.1400
> 47 28 2 1 17 519.8350
> 71 4 1 1 225 254.4087
> 72 3 1 1 238 424.4787
> 75 0 2 2 115 407.0987
> 83 0 2 2 46 622.5137
> 79 -4 2 1 300 509.1212
> 78 -3 2 1 133 517.3325
> 71 4 2 2 328 1179.3063
> 64 11 2 1 2 301.5250
> 78 -3 2 1 62 253.9025
> 65 10 2 2 260 932.6575
> 75 0 2 1 247 145.5900
> 63 12 2 2 156 247.0650
> 71 4 2 1 146 829.4787
> 76 -1 2 2 234 432.5437
> 76 0 2 1 109 859.6888
> 68 7 2 1 228 1236.2975
> 64 11 2 2 167 347.5788
> 62 13 2 2 312 354.0500
> 77 0 2 2 275 882.1938
> 78 -3 2 1 28 481.5975
> 81 0 2 1 180 1285.5425
> 79 0 2 2 205 576.0000
> 70 5 2 1 173 128.3725
> 75 0 2 2 189 359.3863
> 78 0 2 1 332 512.8062
> 74 1 2 2 14 449.0800
> 77 0 2 1 242 283.0013
> 92 0 2 1 152 915.3200
> 69 6 2 2 217 672.7663
> 53 22 2 1 290 1430.8812
> 81 0 2 2 90 699.1075
> 67 8 2 2 316 607.6500
> 85 0 2 1 171 312.9850
> 93 0 2 2 119 936.1275
> 82 0 2 1 118 186.4450
> 71 4 2 2 329 729.1213
> 43 32 2 1 215 887.6313
> 74 1 2 1 180 569.9338
> 89 0 2 1 324 1054.0887
> 81 0 2 2 47 532.0987
> 70 5 2 1 53 450.8750
> 75 0 1 1 38 557.9750
> 56 19 2 1 17 512.6363
> 90 0 2 2 29 569.7888
> 70 5 2 1 251 554.2138
> 56 19 2 2 14 1114.1762"
> tor <- read.table (textConnection(xd1), header=TRUE, sep='', as.is<http://as.is>=TRUE)
>
>
> # Grouping variable (xspd) to be factor
> tor <- within(tor, {
> xspd2 <- factor(xspd2,levels=c (1,2),
> labels=c('SPD', 'No SPD'), ordered=TRUE)
> }
> )
> # object with survey design variables and data
> nhis <- svydesign (id=~psu,strat=~stratum, weights=~wt8, data=tor, nest=TRUE)
>
> MyBreaks <- c(18,35,45,55,65,75,85,95)
>
> png("svyhist_age_at_death.png")
>
> svyhist (~dthage,
> subset (nhis, xspd2==2), breaks=MyBreaks, main= " ",
> col="grey80",
> xlab="Age at Death Distribution"
> )
> lines (svysmooth(~dthage, bandwidth=5,subset(nhis, xspd2==2)), lwd=2)
>
> dev.off ()
>
>
>
>
>
>
> Pradip K. Muhuri
> Statistician
> Substance Abuse & Mental Health Services Administration
> The Center for Behavioral Health Statistics and Quality
> Division of Population Surveys
> 1 Choke Cherry Road, Room 2-1071
> Rockville, MD 20857
>
> Tel: 240-276-1070
> Fax: 240-276-1260
> e-mail: Pradip.Muhuri at samhsa.hhs.gov<mailto:Pradip.Muhuri at samhsa.hhs.gov><mailto:Pradip.Muhuri at samhsa.hhs.gov<mailto:Pradip.Muhuri at samhsa.hhs.gov>>
>
> The Center for Behavioral Health Statistics and Quality your feedback. Please click on the following link to complete a brief customer survey: http://cbhsqsurvey.samhsa.gov<http://cbhsqsurvey.samhsa.gov/>
>
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org<mailto: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.
David Winsemius, MD
Alameda, CA, USA
______________________________________________
R-help at r-project.org<mailto: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.
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