R help - Jun 2015 - Formatting YYYY-MM after reading text file [RESOLVED]

Data file 'example.dat' has this format:

stream,sampdate,param,quant
B,1992-03,Cl,4
B,1992-03,SO4,33
B,1992-03,pH,8.43
B,1992-04,Cl,4
B,1992-04,SO4,32
B,1992-04,pH,8.46
B,1992-05,Cl,4
B,1992-05,SO4,31
B,1992-05,pH,8.43

   It's read into R with
allchem <- read.table('example.dat', stringsAsFactors=F, header=T,
sep=',')

and yields this structure:

str(allchem)
'data.frame':	2226 obs. of  4 variables:
  $ stream  : chr  "B" "B" "B" "B" ...
  $ sampdate: chr  "1992-03" "1992-03" "1992-03"
"1992-04" ...
  $ param   : chr  "Cl" "SO4" "pH" "Cl"
...
  $ quant   : num  4 33 8.43 4 32 8.46 4 31 8.43 6 ...

   Because the date field contains year and month but no day, as.Date() does
not work. ?as.Date displays the help file for yearmon in package 'zoo.'
Reading this lead me to try:

allchem$sampdate <- as.yearmon(format(%Y-%m))allchem$sampdate

which produces the error, Error: unexpected SPECIAL in "allchem$sampdate
<-
as.yearmon(format(%Y-%".

   I do not see the proper syntax to change the sampdate char string to
year-month dates. Advice appreciated.

Rich

On Fri, 26 Jun 2015, Rich Shepard wrote:
> allchem$sampdate <- as.yearmon(format(%Y-%m))allchem$sampdate
   Reading the yearmon help page again led me to try
 	allchem$sampdate <- as.yearmon(allchem$sampdate)
which produces the following structure:

'data.frame':	2226 obs. of  4 variables:
  $ stream  : chr  "B" "B" "B" "B" ...
  $ sampdate:Class 'yearmon'  num [1:2226] 1992 1992 1992 1992 1992 ...
  $ param   : chr  "Cl" "SO4" "pH" "Cl"
...
  $ quant   : num  4 33 8.43 4 32 8.46 4 31 8.43 6 ...

which appears to do what's needed:

allchem
      stream sampdate param    quant
1         B Mar 1992    Cl    4.000
2         B Mar 1992   SO4   33.000
3         B Mar 1992    pH    8.430
4         B Apr 1992    Cl    4.000
5         B Apr 1992   SO4   32.000
6         B Apr 1992    pH    8.460
7         B May 1992    Cl    4.000
8         B May 1992   SO4   31.000
9         B May 1992    pH    8.430
10        B Jun 1992    Cl    6.000

   Not having before worked with dates like this I'll soon see what happens
as the analyses proceed.

Rich

as.yearmon(allchem$sampdate)

worked for me.

David

On 26 June 2015 at 19:44, Rich Shepard <rshepard at appl-ecosys.com>
wrote:
>   Data file 'example.dat' has this format:
>
> stream,sampdate,param,quant
> B,1992-03,Cl,4
> B,1992-03,SO4,33
> B,1992-03,pH,8.43
> B,1992-04,Cl,4
> B,1992-04,SO4,32
> B,1992-04,pH,8.46
> B,1992-05,Cl,4
> B,1992-05,SO4,31
> B,1992-05,pH,8.43
>
>   It's read into R with
> allchem <- read.table('example.dat', stringsAsFactors=F,
header=T, sep=',')
>
> and yields this structure:
>
> str(allchem)
> 'data.frame':   2226 obs. of  4 variables:
>  $ stream  : chr  "B" "B" "B" "B"
...
>  $ sampdate: chr  "1992-03" "1992-03"
"1992-03" "1992-04" ...
>  $ param   : chr  "Cl" "SO4" "pH"
"Cl" ...
>  $ quant   : num  4 33 8.43 4 32 8.46 4 31 8.43 6 ...
>
>   Because the date field contains year and month but no day, as.Date() does
> not work. ?as.Date displays the help file for yearmon in package
'zoo.'
> Reading this lead me to try:
>
> allchem$sampdate <- as.yearmon(format(%Y-%m))allchem$sampdate
>
> which produces the error, Error: unexpected SPECIAL in
"allchem$sampdate <-
> as.yearmon(format(%Y-%".
>
>   I do not see the proper syntax to change the sampdate char string to
> year-month dates. Advice appreciated.
>
> Rich
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> 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.

I would have just assigned them all to the first day of the month, using
  as.Date( paste0(allchem$sampdate,'-01') )
(or maybe the middle of the month represented by the 15th)
and then had a variable that was of the Date class in the base R (with
which I am familiar, no small consideration).


Depending on what needs to be done with them -- plotting with a date axis?
-- calculating elapsed time between sampling events? -- I suppose one or
the other of 'yearmon' or 'Date' might be more convenient.

-Don

-- 
Don MacQueen

Lawrence Livermore National Laboratory
7000 East Ave., L-627
Livermore, CA 94550
925-423-1062





On 6/26/15, 12:04 PM, "R-help on behalf of Rich Shepard"
<r-help-bounces at r-project.org on behalf of rshepard at appl-ecosys.com>
wrote:
>On Fri, 26 Jun 2015, Rich Shepard wrote:
>
>> allchem$sampdate <- as.yearmon(format(%Y-%m))allchem$sampdate
>
>   Reading the yearmon help page again led me to try
> 	allchem$sampdate <- as.yearmon(allchem$sampdate)
>which produces the following structure:
>
>'data.frame':	2226 obs. of  4 variables:
>  $ stream  : chr  "B" "B" "B" "B"
...
>  $ sampdate:Class 'yearmon'  num [1:2226] 1992 1992 1992 1992 1992
...
>  $ param   : chr  "Cl" "SO4" "pH"
"Cl" ...
>  $ quant   : num  4 33 8.43 4 32 8.46 4 31 8.43 6 ...
>
>which appears to do what's needed:
>
>allchem
>      stream sampdate param    quant
>1         B Mar 1992    Cl    4.000
>2         B Mar 1992   SO4   33.000
>3         B Mar 1992    pH    8.430
>4         B Apr 1992    Cl    4.000
>5         B Apr 1992   SO4   32.000
>6         B Apr 1992    pH    8.460
>7         B May 1992    Cl    4.000
>8         B May 1992   SO4   31.000
>9         B May 1992    pH    8.430
>10        B Jun 1992    Cl    6.000
>
>   Not having before worked with dates like this I'll soon see what
>happens
>as the analyses proceed.
>
>Rich
>
>______________________________________________
>R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
>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.