[R] svyhist
Muhuri, Pradip (SAMHSA/CBHSQ)
Pradip.Muhuri at samhsa.hhs.gov
Tue Oct 9 05:40:06 CEST 2012
Thomas,
Sorry about my repeat typo in the line () function, which caused the distortion of the line that did not match in the earlier graph. The revised code gives me the graphs that look lot better (please see the attachment). Thank you for catching that mistake and also for providing clarification regarding the kernel density estimator.
Pradip Muhuri
________________________________________
From: Thomas Lumley [tlumley at uw.edu]
Sent: Monday, October 08, 2012 8:40 PM
To: Muhuri, Pradip (SAMHSA/CBHSQ)
Cc: Anthony Damico; R help
Subject: Re: [R] svyhist
The line isn't a theoretical distribution, it's a kernel density
estimator and so should match your histogram.
It looks as though you use exactly the same call
lines (svysmooth(~dthage, bandwidth=5,subset(nhis, xspd2=='No SPD')), lwd=2)
for each plot, which gives a smooth curve estimating the age at death
for people with No SPD.
To get, eg, age at interview for the SPD group use something like:
lines (svysmooth(~age_p, bandwidth=5,subset(nhis, xspd2=='SPD')), lwd=2)
-thomas
On Sun, Oct 7, 2012 at 2:19 PM, Muhuri, Pradip (SAMHSA/CBHSQ)
<Pradip.Muhuri at samhsa.hhs.gov> wrote:
> Hi Anthony,
>
> The ylim () has been added to the code (please see below), and I got 4 plots that have the same y -dimension.
>
> Each plot displays 2 distributions - one as histogram from the data and another one as line (i.e., idealized theoretical normal distribution?).
>
> My question is, "Is there way to change the distribution in the line () function and try other theoretical distribution to approximate the observed distribution?"
>
>
> Thanks,
>
> Pradip Muhuri
>
>
> ########################################
>
> MyBreaks <- c(18,35,45,55,65,75,85,95)
>
> png("svyhist_no_spd_age_at_inteview.png")
> options( survey.lonely.psu = "adjust" )
> svyhist (~age_p,
> subset (nhis, xspd2=='No SPD'), breaks=MyBreaks,
> ylim = c(0,0.035),
> main= " ",
> col="grey80", xlab="Age at Interview among those Who had no SPD"
> )
>
> lines (svysmooth(~dthage, bandwidth=5,subset(nhis, xspd2=='No SPD')), lwd=2)
>
> dev.off ()
>
> ________________________________________
> From: Anthony Damico [ajdamico at gmail.com]
> Sent: Saturday, October 06, 2012 6:56 AM
> To: Muhuri, Pradip (SAMHSA/CBHSQ)
> Cc: David Winsemius; R help
> Subject: Re: [R] svyhist
>
> ?ylim says "numeric vectors of length 2" - so just the beginning and end.
>
> ?svyhist doesn't specifically mention the ylim parameter, meaning you should look for a "..." in the arguments list and click through to the page for ?hist
>
> ?hist has an example that shows the ylim parameter only containing the beginning and end values.
>
> try using
>
> ylim = c( 0 , 0.030 )
>
> if you're looking to set the tick marks, look at ?axis ;)
>
>
> On Fri, Oct 5, 2012 at 11:18 PM, Muhuri, Pradip (SAMHSA/CBHSQ) <Pradip.Muhuri at samhsa.hhs.gov<mailto:Pradip.Muhuri at samhsa.hhs.gov>> wrote:
> Dear Anthony and David,
>
> Sorry- the earlier-sent plots were mislabeled, which I have corrected and attached. But, the y-lim issue is yet to be resolved.
>
> Thanks,
>
> Pradip Muhuri
>
>
> ________________________________________
> From: Anthony Damico [ajdamico at gmail.com<mailto: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><mailto: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><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>><mailto: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><mailto: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><mailto: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.
>
>
>
> ______________________________________________
> 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.
>
--
Thomas Lumley
Professor of Biostatistics
University of Auckland
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