[R] NADA Package: Referencing Data Frame Columns

[Rich Shepard]

   The sample data sets that come with the NADA package are limited to one or
two variables and a censored measurement indicator column. I try to mimic
examples using my data but keep missing the target.

   My water chemistry data is available in two formats: long (as seen in a
database table) and wide (as seen in a spreadsheet). The two structures are:

str(chem)
'data.frame':	65349 obs. of  8 variables:
  $ site    : Factor w/ 64 levels "D-1","D-2","D-3",..: 1 1 1 1 1 1 1 ...
  $ sampdate: Date, format: "2007-12-12" "2007-12-12" ...
  $ era     : Factor w/ 2 levels "Post","Pre": 1 1 1 1 1 1 1 1 1 1 ...
  $ param   : Factor w/ 64 levels "AgDis","AgTot",..: 2 4 5 7 11 15 25 ...
  $ quant   : num  1.30e-04 1.06e-01 2.31e+02 1.13e-02 5.00e-03 ...
  $ ceneq1  : logi  TRUE FALSE FALSE FALSE TRUE FALSE ...
  $ floor   : num  0 0.106 231 0.0113 0 100 0 1.43 0 0.0239 ...
  $ ceiling : num  1.30e-04 1.06e-01 2.31e+02 1.13e-02 5.00e-03 2.39e-02 ...

and

str(chem.cast)
'data.frame':	56938 obs. of  70 variables:
  $ site     : Factor w/ 64 levels "D-1","D-2","D-3",..: 1 1 1 1 1 ...
  $ sampdate : Date, format: "2007-12-12" "2007-12-12" ...
  $ era      : Factor w/ 2 levels "Post","Pre": 1 1 1 1 1 1 1 1 1 1 ...
  $ ceneq1   : logi  TRUE FALSE FALSE FALSE TRUE FALSE ...
  $ floor    : num  0 0.106 231 0.0113 0 100 0 1.43 0 0.0239 ...
  $ ceiling  : num  1.30e-04 1.06e-01 2.31e+02 1.13e-02 5.00e-03 ...
  $ AgDis    : num  NA NA NA NA NA NA NA NA NA NA ...
  $ AgTot    : num  0.00013 NA NA NA NA NA NA NA NA NA ...
  $ AlDis    : num  NA NA NA NA NA NA NA NA NA NA ...
  $ AlTot    : num  NA 0.106 NA NA NA NA NA NA NA NA ...
  $ Alk      : num  NA NA 231 NA NA NA NA NA NA NA ...
  $ AsDis    : num  NA NA NA NA NA NA NA NA NA NA ...
   and so on.

   I do not know if the latter is appropriate; that is, that the ceneq1,
floor, and ceiling values are available for each site, sampdate, and
chemical.

   Is the appropriate way to use the NADA methods for analyses and plotting
to subset each chemical separately from the 'chem' data frame? Or, is there
a syntax other than, for example,

cenboxplot(chem&Vdis, chem$ceneq1, chem$era)
Error in cenros(obs[group == i], cen[group == i]) :
   error in evaluating the argument 'obs' in selecting a method for function
'ros': Error: object 'Vdis' not found

   I get the same error when trying to use the 'chem.cast' data frame.

Rich