Re: [R] how to add a vertical line for each panel in a lattice dotplot with log scale?

Fri, 08 Jun 2012 06:24:17 -0700 


On Jun 8, 2012, at 3:52 AM, maxbre wrote:


thanks david,
yes, you are right PART of the confusion is because of what you mentioned (sorry for that) but going back to my own data this is JUST PART of the 
problem…

...see my reproducible example

teq<-structure(list(site = structure(c(4L, 2L, 2L, 4L, 2L, 4L, 4L,
3L, 1L, 3L, 1L, 1L, 3L, 4L, 5L, 4L, 3L, 1L, 3L, 1L, 4L, 4L, 2L,
4L, 4L, 2L, 1L, 3L, 4L, 4L, 2L, 4L, 4L, 2L, 4L, 4L, 2L, 4L, 4L,
2L, 4L, 2L, 4L, 2L, 4L, 2L, 4L, 2L, 2L, 2L, 2L, 4L), .Label = c("A",
"B", "C", "D", "E"), class = "factor"), lower_b_i = c(0.302,
0.956, 0.72, 1.21, 0.887, 0.728, 1.294, 20.493, 0.902, 0.031,
0.468, 2.318, 4.795, 89.581, 4.59, 3.366, 32.786, 5.506, 61.038,
1.485, 42.25, 31.279, 21.375, 96.62, 36.099, 30.173, 0.532, 1.005,
0.697, 6.248, 2.121, 0.576, 0.335, 0.442, 22.704, 18.244, 16.53,
626.664, 42.714, 59.87, 9.983, 110.158, 4.763, 3.363, 2.608,
2.41, 23.904, 73.281, 3618.353, 109.663, 21.797, 3.39), date_sampl_time_recs 
= structure(c(11L,
10L, 9L, 8L, 12L, 12L, 13L, 7L, 6L, 14L, 14L, 4L, 3L, 5L, 2L,
1L, 18L, 19L, 24L, 23L, 17L, 15L, 16L, 20L, 21L, 22L, 26L, 25L,
29L, 28L, 27L, 32L, 31L, 30L, 34L, 33L, 33L, 35L, 36L, 37L, 38L,
39L, 40L, 41L, 42L, 43L, 46L, 47L, 48L, 49L, 45L, 44L), .Label =
c("2008-07-15, 2 h, 16/17",
"2008-07-16, 2 h, 14/17", "2008-12-03, 4 h, 13/17", "2008-12-03, 4 h,
15/17",
"2009-01-29, 24 h, 0/17", "2009-03-17, 24 h, 14/17", "2009-03-17, 24 h, 
8/17",
"2009-04-17, 135 h, 13/17", "2009-04-20, 96 h, 14/17", "2009-04-21, 24 h, 
13/17",
"2009-04-21, 24 h, 14/17", "2009-07-17, 168 h, 13/17", "2009-07-21, 24 h, 
12/17",
"2009-08-18, 24 h, 16/17", "2009-10-27, 168 h, 3/17", "2009-10-27, 168 h, 
5/17",
"2009-11-01, 24 h, 4/17", "2009-12-15, 24 h, 6/17", "2009-12-15, 24 h,
9/17",
"2010-01-05, 12 h, 3/17", "2010-01-15, 168 h, 3/17", "2010-01-15, 168 h, 
5/17",
"2010-01-19, 24 h, 12/17", "2010-01-19, 24 h, 2/17", "2010-03-30, 24 h, 
13/17",
"2010-03-30, 24 h, 14/17", "2010-04-22, 168 h, 11/17", "2010-04-22, 168 h, 
9/17",
"2010-04-22, 24 h, 14/17", "2010-07-22, 168 h, 14/17", "2010-07-22, 168 h, 
15/17",
"2010-07-22, 24 h, 15/17", "2010-10-26, 168 h, 7/17", "2010-10-26, 24 h, 
8/17",
"2011-01-05, 12 h, 0/17", "2011-01-11, 168 h, 0/17", "2011-01-19, 168 h, 
0/17",
"2011-03-15, 168 h, 2/17", "2011-03-23, 168 h, 0/17", "2011-05-10, 168 h, 
5/17",
"2011-05-18, 168 h, 7/17", "2011-07-05, 168 h, 7/17", "2011-07-13, 168 h, 
7/17",
"2011-09-13, 168 h, 6/17", "2011-09-21, 168 h, 1/17", "2011-11-08, 168 h, 
0/17",
"2011-11-16, 168 h, 0/17", "2012-01-05, 12 h, 1/17", "2012-01-09, 12 h, 
2/17"
), class = "factor")), .Names = c("site", "lower_b_i",
"date_sampl_time_recs"
), class = "data.frame", row.names = c(NA, -52L))

...and my code

dotplot(date_sampl_time_recs ~ lower_b_i | site, data=teq,
       scales=list(x=list(log=TRUE)),
       xscale.components = xscale.components.logpower,
       layout=c(5,1),
       panel = function(x,y,...) {
         panel.grid(h=53, v=-1, lty="dotted", col="gray")
         panel.dotplot(x,y,...)
         medians <- median(x)
         panel.abline(v=medians, col.line="red", lty="dotted")
         means<-mean(x)
         panel.abline(v=means, col.line="blue", lty="dotted")
       }
       )

attach(teq)

#check median values
tapply(lower_b_i,site,median)

> tapply(lower_b_i,site,median)
      A       B       C       D       E
 1.1935 18.9525 12.6440  6.2480  4.5900
> #check mean values
> tapply(lower_b_i,site,mean)
        A         B         C         D         E
  1.86850 254.50619  20.02467  46.32865   4.59000


#check mean values

> #check mean values
> tapply(lower_b_i,site,mean)
        A         B         C         D         E
  1.86850 254.50619  20.02467  46.32865   4.59000

tapply(lower_b_i,site,mean)

detach(teq)
...and now the question is why the plotting of means (but not medians) is 
wrong (check against results of tapply)?



This is the context that you failed to include:
Part of the confusion may be that you have reversed the colors for mean and median in two different examples. The other confusion may be that mean(log(.)) != log(mean(.))
I do not see reference to which of those sources of confusion you believe you have adequately addressed. I suspect you may have only read the first sentence. 

with(teq, tapply(lower_b_i,site,function(x) exp(mean(log(x) )) )  )
        A         B         C         D         E
 1.273034 12.084054  4.277616  7.151560  4.590000



--

David Winsemius, MD
West Hartford, CT

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