Hi Arun It seems to be an error on the server side and not on the client.
The error on the server results in the client receiving a string giving the type of error on the server. And this doesn't work with read.table of course. So if one wants to query for thousands of point one really needs to do error catching using try () or tryCatching (). I shall check when I get close to my R. Actually, if the thousands of points is on regular grid ( 0.25 degree resolution) within a confined region then one could just query for that region instead of doing the loop. Eliza should know. Br. Frede Sendt fra Samsung mobil -------- Oprindelig meddelelse -------- Fra: arun Dato:12/04/2014 12.31 (GMT+01:00) Til: Frede Aakmann Tøgersen Cc: Eliza Botto ,"R. Help" Emne: Re: [R] calling in inverted commas HI, Thanks for the link. I should have used ?sprintf(). BTW, I am not able to reproduce your results. urlPattern <- "http://disc2.nascom.nasa.gov/daac-bin/Giovanni/tovas/Giovanni_cgi.pl?west=%s&north=%s&east=%s&south=%¶ms=0|3B42_V7&plot_type=Time+Plot&byr=1998&bmo=01&bdy=1&eyr=2007&emo=12&edy=31&begin_date=1998%%2F01%%2F01&end_date=2014%%2F01%%2F31&cbar=cdyn&cmin=&cmax=&yaxis=ydyn&ymin=&ymax=&yint=&ascres=0.25x0.25&global_cfg=tovas.global.cfg.pl&instance_id=TRMM_V7â_id=3B42_daily&action=ASCII+Output" ## ## some coordinates df2 <- data.frame(Longitude = c(68.25, 68.75, 69.25), Latitude = c(24.75, 25.25, 25.75)) fileDestination <- getwd() fileNames <- paste("precip", df2[,1], df2[,2], sep = "_") fileNames <- paste(fileNames, "txt", sep = ".") files <- file.path(fileDestination, fileNames) for (i in 1:nrow(df2)){ queryUrl <- sprintf(urlPattern, df2[i, 1], df2[i, 2], df2[i, 1], df2[i, 2]) download.file(queryUrl, files[i]) } precip <- read.table(files[1], skip = 4, header = TRUE, na.strings = "-9999.9", + sep = "", check.names = FALSE, stringsAsFactors = FALSE) Error in read.table(files[1], skip = 4, header = TRUE, na.strings = "-9999.9", : more columns than column names So, I checked the file "precip_68.25_24.75.txt" Giovanni Error Message Giovanni Error Message Page Error: instance configuration file is not found. Error: product configuration file is not found. Please send email to Help Desk: h...@daac.gs fc.nasa.gov sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-unknown-linux-gnu (64-bit) A.K. On Saturday, April 12, 2014 3:24 AM, Frede Aakmann Tøgersen <fr...@vestas.com> wrote: Hi Sigh I'm getting a headache seeing ugly formatted R code. Arun, your code is almost unreadable. Have a look at e.g. http://yihui.name/en/2010/04/formatr-farewell-to-ugly-r-code/ Now to the substantial. Why not use the sprintf() function for formatting the url instead of the more involved approach using several gsub and regular expressions that not many people (including myself) easily understand. ## here is a small example using sprintf(), see ?sprintf ## %s is format specifier for string exampleStr <- "west=%s&north=%s&east=%s&south=%s" sprintf(exampleStr, 1, 2, 3, 4) ## > [1] "west=1&north=2&east=3&south=4" ## since % is used in format specification then if a literal % is needed in the string as here ## where you have e.g. %2F01% then escape those % with a %, i.e. % becomes %% in the string ## I have done that in urlPattern: urlPattern <- "http://disc2.nascom.nasa.gov/daac-bin/Giovanni/tovas/Giovanni_cgi.pl?west=%s&north=%s&east=%s&south=%s¶ms=0|3B42_V7&plot_type=Time+Plot&byr=1998&bmo=01&bdy=1&eyr=2007&emo=12&edy=31&begin_date=1998%%2F01%%2F01&end_date=2014%%2F01%%2F31&cbar=cdyn&cmin=&cmax=&yaxis=ydyn&ymin=&ymax=&yint=&ascres=0.25x0.25&global_cfg=tovas.global.cfg.pl&instance_id=TRMM_V7â_id=3B42_daily&action=ASCII+Output" ## some coordinates df2 <- data.frame(Longitude = c(68.25, 68.75, 69.25), Latitude = c(24.75, 25.25, 25.75)) fileDestination <- c("C:/Temp") fileNames <- paste("precip", df2[,1], df2[,2], sep = "_") fileNames <- paste(fileNames, "txt", sep = ".") files <- file.path(fileDestination, fileNames) for (i in 1:nrow(df2)){ queryUrl <- sprintf(urlPattern, df2[i, 1], df2[i, 2], df2[i, 1], df2[i, 2]) download.file(queryUrl, files[i]) } ## import data in first file precip <- read.table(files[1], skip = 4, header = TRUE, na.strings = "-9999.9", sep = "", check.names = FALSE, stringsAsFactors = FALSE) head(precip) Here is another way using the url() function instead of download.file() ## Escaping the trouble with saving and reading files one can also do it this way ## having the dataframes in a named list precipList <- vector("list", nrow(df2)) names(precipList) <- fileNames for (i in 1:nrow(df2)){ queryUrl <- sprintf(urlPattern, df2[i, 1], df2[i, 2], df2[i, 1], df2[i, 2]) u <- url(queryUrl, open = "r") precipList[[i]] <- read.table(u, skip = 4, header = TRUE, na.strings = "-9999.9", sep = "", check.names = FALSE, stringsAsFactors = FALSE) close(u) } str(precipList) Have a nice day. Yours sincerely / Med venlig hilsen Frede Aakmann Tøgersen Specialist, M.Sc., Ph.D. Plant Performance & Modeling Technology & Service Solutions T +45 9730 5135 M +45 2547 6050 fr...@vestas.com http://www.vestas.com Company reg. name: Vestas Wind Systems A/S This e-mail is subject to our e-mail disclaimer statement. Please refer to www.vestas.com/legal/notice<http://www.vestas.com/legal/notice> If you have received this e-mail in error please contact the sender. > -----Original Message----- > From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] > On Behalf Of arun > Sent: 12. april 2014 07:16 > To: r-help@r-project.org > Subject: Re: [R] calling in inverted commas > > Hi, > I noticed some special characters after sending. > It should be: > toreplace <- gsub(".*\\.pl\\?(west\\=.*south=.*)\\¶ms.*","\\1",Url1) > end <- gsub(".*south=.*(\\¶ms.*)","\\1",Url1) > > > A.K. > > > On Saturday, April 12, 2014 1:06 AM, arun <smartpink...@yahoo.com> > wrote: > HI, > > Not sure if this helps: > df2 <- data.frame(Col1=c(68.25, 68.75, 69.25), Col2=c(24.75, 25.25, 25.75)) > > > Url1 <- "http://disc2.nascom.nasa.gov/daac- > bin/Giovanni/tovas/Giovanni_cgi.pl?west=68.25&north=24.75&east=68.25&s > outh=24.75¶ms=0%7C3B42_V7&plot_type=Time+Plot&byr=1998&bmo=01& > bdy=1&eyr=2007&emo=12&edy=31&begin_date=1998%2F01%2F01&end_da > te=2014%2F01%2F31&cbar=cdyn&cmin=&cmax=&yaxis=ydyn&ymin=&ymax > =&yint=&ascres=0.25x0.25&global_cfg=tovas.global.cfg.pl&instance_id=TRM > M_V7â_id=3B42_daily&action=ASCII+Output" > > > toreplace <- gsub(".*\\.pl\\?(west\\=.*south=.*)\\¶ms.*","\\1",Url1) > begin <- gsub("(.*\\.pl\\?).*","\\1",Url1) > end <- gsub(".*south=.*(\\¶ms.*)","\\1",Url1) > > vec2 <- strsplit(toreplace,"&")[[1]] > > ##replace ".csv" with ".txt" and use write.table() if you need as text files. > > > lapply(seq_len(nrow(df2)),function(i) { val1 <- > as.vector(rep(unlist(df2[i,]),2));replaced <- > do.call(paste,list(lapply(seq_along(vec2),function(i) gsub("[- > +]?(\\d*[.])?\\d+",val1[i],vec2[i])),collapse="&")); UrlNew <- > paste0(begin,replaced,end); res <- > read.csv(UrlNew,header=TRUE,stringsAsFactors=FALSE,skip=4,sep="",check. > names=FALSE); > write.csv(res,file=paste0("file_",paste(val1[1:2],collapse="_"),".csv"),row.na > mes=FALSE,quote=FALSE)}) > > sapply(list.files(pattern="file_"),function(x) {x1 <- > read.csv(x,header=TRUE,stringsAsFactors=FALSE,check.names=FALSE); > dim(x1)[1]}) > #file_68.25_24.75.csv file_68.75_25.25.csv file_69.25_25.75.csv > > # 3652 3652 3652 > > ### reading the downloaded file > > lapply(list.files(pattern="file_"),function(x) {x1 <- > read.csv(x,header=TRUE,stringsAsFactors=FALSE,check.names=FALSE); > x1[5:7,]}) > > #[[1]] > > # Time(year:month:day) AccRain > > #5 1998:01:05 0.000 > > #6 1998:01:06 0.000 > #7 1998:01:07 0.984 > > # > > #[[2]] > > # Time(year:month:day) AccRain > #5 1998:01:05 0.0000 > #6 1998:01:06 0.0925 > #7 1998:01:07 0.2643 > # > #[[3]] > > # Time(year:month:day) AccRain > #5 1998:01:05 0.0000 > #6 1998:01:06 0.7043 > > #7 1998:01:07 0.5340 > > > > A.K. > > > On Friday, April 11, 2014 2:38 PM, eliza botto <eliza_bo...@hotmail.com> > wrote: > Dear useRs, > Here are three steps for downloading a file from a certain website in R. Here > you see that in "URL" command > (west=68.25&north=24.75&east=68.25&south=24.75) are actually the first > and second column values of 1st row of a matrix called df2 (300 rows and 2 > columns). more precisely, df2[1,][1]=68.25, df2[1,][2]=24.75. > Is there a way that I can make a loop so that remaining rows and columns get > inculcated in the link as such and then get saved at the desired mentioned > location in 300 different text files? > URL<-("http://disc2.nascom.nasa.gov/daac- > bin/Giovanni/tovas/Giovanni_cgi.pl?west=68.25&north=24.75&east=68.25&s > outh=24.75¶ms=0%7C3B42_V7&plot_type=Time+Plot&byr=1998&bmo=01& > bdy=1&eyr=2007&emo=12&edy=31&begin_date=1998%2F01%2F01&end_da > te=2014%2F01%2F31&cbar=cdyn&cmin=&cmax=&yaxis=ydyn&ymin=&ymax > =&yint=&ascres=0.25x0.25&global_cfg=tovas.global.cfg.pl&instance_id=TRM > M_V7â_id=3B42_daily&action=ASCII+Output") > > destfile <- "C:\\Users\\Eliza\\Desktop\\AA\\love.txt" > download.file(URL, destfile) > > Any suggestion? > Thankyou very much in advance, > Eliza > [[alternative HTML version deleted]] > > ______________________________________________ > R-help@r-project.org mailing list > 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. > > > ______________________________________________ > R-help@r-project.org mailing list > 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. 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______________________________________________ R-help@r-project.org mailing list 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.
