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

2012-09-05 Thread Rich Shepard 

On Wed, 5 Sep 2012, Nordlund, Dan (DSHS/RDA) wrote:


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   sampdateera param quant ceneq1 floor ceiling
34169 MW-5 1995-01-10 Pre-mining SbTot  0.01   TRUE 00.01


Dan,

  Thanks for seeing what I missed evary time I went though the data. I knew
it had to be some mis-classified observation but after three times through I
thought that I had corrected all the misfits and didn't see that one. New
eyeballs are invaluable after one's looked at data or code a long time.

Very much appreciated,

Rich

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

2012-09-04 Thread Rich Shepard 

  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.

Richstructure(list(site = structure(c(12L, 12L, 12L, 12L, 12L, 12L, 
12L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 
12L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 16L, 16L, 17L, 
17L, 22L, 22L, 22L, 22L, 22L, 22L, 22L, 22L, 22L, 22L, 22L, 22L, 
22L, 22L, 22L, 22L, 22L, 22L, 22L, 22L, 22L, 22L, 22L, 22L, 22L, 
22L, 22L, 22L, 22L, 22L, 22L, 22L, 31L, 31L, 31L, 31L, 31L, 31L, 
31L, 31L, 31L, 31L, 31L, 31L, 31L, 31L, 31L, 31L, 31L, 31L, 31L, 
31L, 31L, 31L, 31L, 31L, 31L, 31L, 31L, 31L, 31L, 31L, 31L, 31L, 
32L, 32L, 32L, 32L, 32L, 32L, 32L, 32L, 32L, 32L, 32L, 32L, 32L, 
32L, 32L, 32L, 32L, 32L, 32L, 32L, 32L, 32L, 32L, 32L, 32L, 32L, 
32L, 32L, 32L, 32L, 33L, 33L, 33L, 33L, 33L, 33L, 33L, 33L, 33L, 
33L, 33L, 33L, 33L, 33L, 33L, 33L, 33L, 33L, 33L, 33L, 33L, 33L, 
33L, 33L, 33L, 33L, 33L, 33L, 33L, 33L, 33L, 33L, 35L, 35L, 35L, 
35L, 35L, 35L, 35L, 35L, 35L, 35L, 35L, 35L, 35L, 35L, 35L, 35L, 
35L, 35L, 35L, 35L, 35L, 35L, 35L, 35L, 35L, 35L, 35L, 35L, 35L, 
35L, 35L, 35L, 36L, 36L, 36L, 36L, 36L, 36L, 36L, 36L, 36L, 36L, 
36L, 36L, 36L, 36L, 36L, 36L, 36L, 36L, 36L, 36L, 36L, 36L, 36L, 
36L, 36L, 36L, 36L, 36L, 36L, 36L, 36L, 37L, 37L, 37L, 37L, 37L, 
37L, 37L, 37L, 37L, 37L, 37L, 37L, 37L, 37L, 37L, 37L, 37L, 37L, 
37L, 37L, 37L, 37L, 37L, 37L, 37L, 37L, 37L, 37L, 37L, 37L, 37L, 
37L, 47L, 47L, 47L, 47L, 47L, 47L, 47L, 47L, 47L, 47L, 47L, 47L, 
47L, 47L, 47L, 47L, 47L, 47L, 47L, 47L, 47L, 47L, 47L, 47L, 47L, 
47L, 47L, 47L, 47L, 47L, 48L, 48L, 48L, 48L, 48L, 48L, 48L, 48L, 
48L, 48L, 48L, 48L, 48L, 48L, 48L, 48L, 48L, 49L, 49L, 49L, 49L, 
49L, 49L, 49L, 49L, 49L, 49L, 49L, 49L, 49L, 49L, 49L, 49L, 49L, 
49L, 49L, 49L, 49L, 50L, 50L, 50L, 50L, 50L, 50L, 50L, 50L, 50L, 
50L, 50L, 50L, 50L, 50L, 50L, 50L, 50L, 50L, 50L, 50L, 50L, 50L, 
50L, 50L, 50L, 50L, 50L, 51L, 51L, 51L, 51L, 51L, 51L, 51L, 51L, 
51L, 51L, 51L, 51L, 51L, 51L, 51L, 51L, 51L, 51L, 51L, 51L, 51L, 
51L, 51L, 51L, 52L, 52L, 52L, 52L, 52L, 52L, 52L, 52L, 52L, 52L, 
52L, 52L, 52L, 52L, 52L, 52L, 52L, 52L, 52L, 52L, 52L, 57L, 57L, 
57L, 57L, 57L, 57L, 57L, 57L, 57L, 57L, 57L, 57L, 57L, 57L, 57L, 
57L, 57L, 57L, 57L, 57L, 57L, 57L, 57L, 57L, 57L, 57L, 57L, 57L, 
59L, 59L, 59L, 59L, 59L, 59L, 59L, 59L, 59L, 59L, 59L, 59L, 59L, 
59L, 59L, 59L, 59L, 59L, 59L, 59L, 59L, 59L, 59L, 59L, 59L, 59L, 
59L, 59L, 60L, 60L, 60L, 60L, 60L, 60L, 60L, 60L, 60L, 60L, 60L, 
60L, 60L, 60L, 60L, 60L, 60L, 60L, 60L, 60L, 60L, 60L, 60L, 60L, 
60L, 60L, 60L, 60L, 61L, 61L, 61L, 61L, 61L, 61L, 61L, 61L, 61L, 
61L, 61L, 61L, 61L, 61L, 61L, 61L, 61L, 61L, 61L, 61L, 62L, 62L, 
62L, 62L, 62L, 62L, 62L, 62L, 62L, 62L, 62L, 62L, 62L, 62L, 62L, 
62L, 62L, 62L, 62L, 62L, 62L, 62L, 62L, 62L, 62L, 62L, 62L, 62L, 
62L, 63L, 63L, 63L, 63L, 63L, 63L, 63L, 63L, 63L, 63L, 63L, 63L, 
63L, 63L, 63L, 63L, 63L, 63L, 63L, 63L, 63L, 63L, 63L, 63L, 63L, 
63L, 63L, 63L, 63L, 64L, 64L, 64L, 64L, 64L, 64L, 64L, 64L, 64L, 
64L, 64L, 64L, 64L, 64L), .Label = c(D-1, D-2, D-3, D-4, 
D-5, D-6, D-7, D-8, D-9, Effluent, GB-ES1, GW-2, 
Gold Bowl Sump, Influent, JJ-16, JJ-18, JJ-20, JJ-22, 
MC-1, MC-2, MC-3, MW-1, MW-10, MW-11, MW-12, MW-13, 
MW-14, MW-15, MW-16, MW-2R, MW-3, MW-4, MW-5, MW-6R, 
MW-7, MW-8, MW-9, Mine Domestic Well, P-10, P-5, 
P-6, P-8, P-9, RAS-001, SN-22, SW Zone Sump, SW-1, 
SW-10, SW-11, SW-12, SW-13, SW-14, SW-15, SW-16, 
SW-17, SW-18, SW-2, SW-3, SW-4, SW-5, SW-6, SW-7, 
SW-8, SW-9), class = factor), sampdate = structure(c(8421, 
8442, 8477, 8503, 8537, 8567, 8595, 8596, 8636, 8666, 8686, 8713, 
8741, 8782, 8810, 8833, 8861, 8889, 8924, 8957, 8988, 9022, 9049, 
9114, 9142, 9246, 9274, 9295, 9407, 8573, 8693, 8573, 8693, 8363, 
8390, 8421, 8442, 8476, 8505, 8532, 8567, 8604, 8638, 8665, 8686, 
8717, 8741, 8778, 8805, 8833, 8860, 8887, 8924, 8959, 8987, 9022, 
9050, 9113, 9141, 9169, 9205, 9244, 9274, 9296, 9408, 8364, 8391, 
8421, 8441, 8476, 8505, 8531, 8566, 8594, 8636, 8665, 8686, 8714, 
8741, 8777, 8805, 8832, 8861, , 8923, 8959, 8987, 9022, 9050, 
9112, 9141, 9168, 9205, 9244, 9274, 9293, 9408, 8367, 8392, 8420, 
8441, 8475, 8504, 8531, 8566, 8594, 8637, 8664, 8687, 8715, 8742, 
8777, 8806, 8832, 8861, , 8923, 8958, 8987, 9021, 9140, 9168, 
9204, 9246, 9274, 9295, 9406, 8364, 8392, 8421, 8441, 8476, 8504, 
8531, 8566, 8594, 8637, 8664, 8687, 8715, 8747, 8777, 8806, 8832, 
8861, , 8923, 8958, 8987, 9021, 9049, 9112, 9140, 9168, 9204, 
9246, 9274, 9296, 9406, 8364, 8397, 8419, 8441, 8474, 8505, 8531, 
8565, 8594, 8638, 8664, 8686, 8714, 8741, 8777, 8805, 8832, 8861, 
, 8923, 8959, 8987, 9022, 9050, 9112, 9141, 9168, 9204, 9246,

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

2012-09-04 Thread Nordlund, Dan (DSHS/RDA) 
 -Original Message-
 From: r-help-boun...@r-project.org [mailto:r-help-bounces@r-
 project.org] On Behalf Of Rich Shepard
 Sent: Tuesday, September 04, 2012 4:15 PM
 To: r-help@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   sampdateera param quant ceneq1 floor ceiling
34169 MW-5 1995-01-10 Pre-mining SbTot  0.01   TRUE 00.01



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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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.