[R] difficulties with read.table applied to files from URL

[David Winsemius]

On Aug 5, 2010, at 2:48 PM, Archana Dayalu wrote:

> Hello,
> I am using read.table to read files directly from a public ftp site.  
> I have
> a general list of files that may or may not exist in the ftp  
> directory, but
> my hope was that R would read the file if it existed and ignored it  
> if it
> didn't exist and move on to the next one. However, when R arrives at  
> a file
> that does not exist I get the error message "Error in file(file,  
> "rt") :
> cannot open the connection" This makes sense, but I was wondering if  
> there
> was any way I could circumvent this error message and have R instead  
> give me
> a warning message without terminating my entire loop.

Yes.

?try


> Ideally, I would get a
> warning message saying the connection does not exist, and then have  
> R skip
> to the next file.
> My code is copied below.
>

Something like these modifications .... untested:

> hourly.years <- c(2000:2008)
> hourly.species <- c('ch4','co2','co')
> station.names <-
> c 
> ('alt482n00 
> ','chm449n00 
> ','egb444n01 
> ','etl454n00','fsd449n00','llb454n01','wsa443n00','cdl453n00')
> for (kk in hourly.years) {
>    for (i in hourly.species) {
>        for (nn in station.names) {
>            file1 <- paste('ftp://gaw.kishou.go.jp/pub/data/current/
> ',i,'/hourly/y',kk,'/',nn,'.ec.as.cn.',i,'.nl.hr',kk,'.anc',sep='')
> #ancillary data
>            file2 <- paste('ftp://gaw.kishou.go.jp/pub/data/current/
> ',i,'/hourly/y',kk,'/',nn,'.ec.as.cn.',i,'.nl.hr',kk,'.dat',sep='')
> #concentration data
>            dumm.anc <-  
> try( read.table(file1,skip=32,header=F,as.is=T) )
if (class(dumm.anc) == "try-error" {} else {
>            colnames(dumm.anc) <- c('DATE','TIME','WD','WS','RH','AT')
>            r.obj.anc <- paste(substr(nn,1,3),i,kk,'anc.cont',sep='.')
>            assign(r.obj.anc,dumm.anc)
                                              }
>            dumm.dat <-  
> try( read.table(file2,skip=32,header=F,as.is=T) )
if (class(dumm.dat) == "try-error" {} else {  #will skip over  
following commands if "try-error-ed"
>            colnames(dumm.dat) <-
> c('DATE','TIME','DATE','TIME','CH4','ND','SD','F','CS','REM')
>             r.obj.dat <- paste(substr(nn,1,3),i,kk,'dat.cont',sep='.')
>             assign(r.obj.dat,dumm.dat)
                   }

#  --------------presumably these do not depend on the read- 
tries---------
>            status<-paste(i,nn,kk,'----EC HOURLY/CONTINUOUS DAT/ANC  
> read
> complete',sep=' ')
>            print(status,quote=F)
>            }
>        }
>    }
>

-- 

David Winsemius, MD
West Hartford, CT