thr3ads.net - R help - [R] cenboxplot(): Reporting Limit Twice Correct Concentration [Sep 2012]

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Rich Shepard

2012-Sep-04 23:14 UTC

[R] cenboxplot(): Reporting Limit Twice Correct Concentration

I've gone over the data and do not see my error; the dput() output of the
data frame and the pdf output of cenboxplot() are attached.

   The command used:

cenboxplot(sb.t$quant, sb.t$ceneq1, range=1.5, main='Total Recoverable
Antimony', xlab='Pre-Mining Era', ylab='Concentration (log
mg/L)')

(on a single line in emacs).

   The RL on the plot is drawn at 0.01 rather than at 0.005 and I'd like to
learn why.

Rich
-------------- next part --------------
structure(list(site = structure(c(12L, 12L, 12L, 12L, 12L, 12L, 
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"NiDis", "NiTot", "PDis", "PTot",
    "PbDis", "PbTot", "SC", "SO4",
"SbDis", "SbTot", "SeDis",
    "SeTot", "SrDis", "SrTot", "TDS",
"TSS", "TlDis", "TlTot",
    "Vdis", "Vtot", "ZnDis", "ZnTot",
"oilgrease", "pH"), class = "factor"),
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    0.005, 0.007, 0.005, 0.005, 0.005, 0.005, 0.005, 0.005, 0.005, 
    0.005, 0.01, 0.005, 0.005, 0.005, 0.005, 0.005, 0.008, 0.005, 
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    0.005, 0.005, 0.005, 0.005, 0.005, 0.005, 0.005, 0.005, 0.005, 
    0.005, 0.005, 0.005, 0.008, 0.005, 0.005, 0.005, 0.006, 0.005, 
    0.006, 0.005, 0.005, 0.005, 0.01, 0.006, 0.007, 0.005, 0.005, 
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    0.005, 0.005, 0.005, 0.005, 0.006, 0.005, 0.008, 0.005, 0.005, 
    0.005, 0.005, 0.005, 0.005, 0.005), ceneq1 = c(TRUE, TRUE, 
    TRUE, TRUE, TRUE, FALSE, TRUE, FALSE, FALSE, TRUE, FALSE, 
    TRUE, FALSE, FALSE, TRUE, FALSE, FALSE, TRUE, TRUE, TRUE, 
    TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, 
    TRUE, TRUE, TRUE, FALSE, FALSE, FALSE, TRUE, TRUE, TRUE, 
    TRUE, FALSE, TRUE, TRUE, FALSE, FALSE, TRUE, FALSE, FALSE, 
    TRUE, FALSE, FALSE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, 
    TRUE, TRUE, FALSE, TRUE, TRUE, TRUE, TRUE, FALSE, FALSE, 
    FALSE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, 
    TRUE, FALSE, FALSE, TRUE, FALSE, FALSE, TRUE, TRUE, TRUE, 
    TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, FALSE, TRUE, TRUE, TRUE, 
    TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, 
    TRUE, TRUE, FALSE, TRUE, TRUE, FALSE, FALSE, FALSE, TRUE, 
    TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, 
    TRUE, TRUE, FALSE, FALSE, FALSE, TRUE, TRUE, TRUE, TRUE, 
    TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, FALSE, FALSE, 
    FALSE, FALSE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, 
    TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, FALSE, TRUE, 
    TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, 
    FALSE, FALSE, FALSE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, 
    TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, 
    FALSE, TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, FALSE, TRUE, 
    FALSE, TRUE, TRUE, TRUE, FALSE, FALSE, FALSE, FALSE, TRUE, 
    TRUE, TRUE, TRUE, FALSE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, 
    TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, TRUE, TRUE, TRUE, 
    TRUE, TRUE, FALSE, FALSE, FALSE, FALSE, TRUE, FALSE, FALSE, 
    FALSE, FALSE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, 
    FALSE, TRUE, TRUE, TRUE, TRUE, FALSE, TRUE, FALSE, TRUE, 
    TRUE, TRUE, TRUE, FALSE, TRUE, TRUE, TRUE, TRUE, FALSE, FALSE, 
    FALSE, TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, FALSE, TRUE, 
    TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, 
    TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, 
    TRUE, TRUE, TRUE, TRUE, FALSE, TRUE, TRUE, TRUE, TRUE, TRUE, 
    FALSE, TRUE, TRUE, FALSE, TRUE, FALSE, FALSE, TRUE, TRUE, 
    TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, 
    TRUE, TRUE, FALSE, FALSE, TRUE, TRUE, TRUE, FALSE, FALSE, 
    TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, TRUE, TRUE, TRUE, 
    TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, 
    FALSE, TRUE, TRUE, TRUE, TRUE, FALSE, FALSE, FALSE, FALSE, 
    TRUE, TRUE, FALSE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, 
    TRUE, TRUE, FALSE, TRUE, TRUE, TRUE, TRUE, FALSE, TRUE, FALSE, 
    FALSE, TRUE, TRUE, FALSE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, 
    TRUE, TRUE, FALSE, TRUE, TRUE, TRUE, TRUE, FALSE, TRUE, TRUE, 
    TRUE, TRUE, FALSE, FALSE, FALSE, TRUE, TRUE, TRUE, TRUE, 
    FALSE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, 
    TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, TRUE, TRUE, FALSE, TRUE, 
    FALSE, FALSE, FALSE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, 
    TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, 
    TRUE, TRUE, TRUE, FALSE, TRUE, FALSE, TRUE, TRUE, TRUE, FALSE, 
    FALSE, FALSE, TRUE, TRUE, TRUE, FALSE, TRUE, TRUE, FALSE, 
    TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, FALSE, TRUE, 
    TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, FALSE, TRUE, FALSE, 
    FALSE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, FALSE, 
    TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, TRUE, FALSE, TRUE, TRUE, 
    TRUE, FALSE, FALSE, FALSE, TRUE, TRUE, TRUE, TRUE, TRUE, 
    TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, TRUE, 
    TRUE, TRUE, TRUE, TRUE, FALSE, FALSE, TRUE, TRUE, TRUE, TRUE, 
    TRUE, FALSE, FALSE, FALSE, TRUE, TRUE, TRUE, TRUE, TRUE, 
    TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, 
    TRUE, TRUE, FALSE, TRUE, FALSE, TRUE, TRUE, TRUE, TRUE, TRUE, 
    TRUE, TRUE), floor = c(0, 0, 0, 0, 0, 0.007, 0, 0.009, 0.006, 
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    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.009, 0, 0, 0.008, 0, 0, 
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    0, 0, 0, 0, 0, 0.007, 0.006, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
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"era", "param",
"quant", "ceneq1", "floor", "ceiling"),
row.names = c(10064L,
10100L, 10136L, 10172L, 10208L, 10244L, 10280L, 10313L, 10347L, 
10383L, 10419L, 10455L, 10491L, 10527L, 10563L, 10616L, 10657L, 
10693L, 10729L, 10765L, 10801L, 10837L, 10873L, 10909L, 10945L, 
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64576L), class = "data.frame")
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Nordlund, Dan (DSHS/RDA)

2012-Sep-05 01:07 UTC

head link

[R] cenboxplot(): Reporting Limit Twice Correct Concentration

> -----Original Message-----
> From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-
> project.org] On Behalf Of Rich Shepard
> Sent: Tuesday, September 04, 2012 4:15 PM
> To: r-help at r-project.org
> Subject: [R] cenboxplot(): Reporting Limit Twice Correct Concentration
> 
>    I've gone over the data and do not see my error; the dput() output
> of the
> data frame and the pdf output of cenboxplot() are attached.
> 
>    The command used:
> 
> cenboxplot(sb.t$quant, sb.t$ceneq1, range=1.5, main='Total Recoverable
> Antimony', xlab='Pre-Mining Era', ylab='Concentration (log
mg/L)')
> 
> (on a single line in emacs).
> 
>    The RL on the plot is drawn at 0.01 rather than at 0.005 and I'd
> like to
> learn why.
> 
> Rich
Rich,

The line is drawn at the maximum censored value.  
>max(sb.t$quant[sb.t$ceneq1==TRUE])[1] 0.01

The line is drawn at 0.01 because there is a censored record where quant=0.01,
i.e.
>sb.t[which(sb.t$quant==0.01 & sb.t$ceneq1==TRUE),]      site   sampdate        era param quant ceneq1 floor ceiling
34169 MW-5 1995-01-10 Pre-mining SbTot  0.01   TRUE     0    0.01



Hope this is helpful,

Dan

Daniel J. Nordlund
Washington State Department of Social and Health Services
Planning, Performance, and Accountability
Research and Data Analysis Division
Olympia, WA 98504-5204

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