Trycatch in for loop- continue to next r dataRetrieval










1














I have a list containing the following site id numbers:
sitelist <- c("02074500", "02077200", "208111310", "02081500", "02082950")



I want to use the dataRetrieval package to collect additional information about these sites and save it into individual .csv files. Site number "208111310" does not exist, so it returns an error and stops the code.



I want the code to ignore site numbers that do not return data and continue to the next number in sitelist.
I've tried trycatch in several ways but can't get the correct syntax. Here is my for loop without trycatch.



for (i in sitelist)
test_gage <- readNWISdv(siteNumbers = i,
parameterCd = pCode)

df = test_gage
df = subset(df, select= c(site_no, Date, X_00060_00003))
names(df)[3] <- c("flow in m3/s")
df$Year <- as.character(year(df$Date))

write.csv(df, paste0("./gage_flow/",i,".csv"), row.names = F)
rm(list=setdiff(ls(),c("sitelist", "pCode")))










share|improve this question




























    1














    I have a list containing the following site id numbers:
    sitelist <- c("02074500", "02077200", "208111310", "02081500", "02082950")



    I want to use the dataRetrieval package to collect additional information about these sites and save it into individual .csv files. Site number "208111310" does not exist, so it returns an error and stops the code.



    I want the code to ignore site numbers that do not return data and continue to the next number in sitelist.
    I've tried trycatch in several ways but can't get the correct syntax. Here is my for loop without trycatch.



    for (i in sitelist)
    test_gage <- readNWISdv(siteNumbers = i,
    parameterCd = pCode)

    df = test_gage
    df = subset(df, select= c(site_no, Date, X_00060_00003))
    names(df)[3] <- c("flow in m3/s")
    df$Year <- as.character(year(df$Date))

    write.csv(df, paste0("./gage_flow/",i,".csv"), row.names = F)
    rm(list=setdiff(ls(),c("sitelist", "pCode")))










    share|improve this question


























      1












      1








      1







      I have a list containing the following site id numbers:
      sitelist <- c("02074500", "02077200", "208111310", "02081500", "02082950")



      I want to use the dataRetrieval package to collect additional information about these sites and save it into individual .csv files. Site number "208111310" does not exist, so it returns an error and stops the code.



      I want the code to ignore site numbers that do not return data and continue to the next number in sitelist.
      I've tried trycatch in several ways but can't get the correct syntax. Here is my for loop without trycatch.



      for (i in sitelist)
      test_gage <- readNWISdv(siteNumbers = i,
      parameterCd = pCode)

      df = test_gage
      df = subset(df, select= c(site_no, Date, X_00060_00003))
      names(df)[3] <- c("flow in m3/s")
      df$Year <- as.character(year(df$Date))

      write.csv(df, paste0("./gage_flow/",i,".csv"), row.names = F)
      rm(list=setdiff(ls(),c("sitelist", "pCode")))










      share|improve this question















      I have a list containing the following site id numbers:
      sitelist <- c("02074500", "02077200", "208111310", "02081500", "02082950")



      I want to use the dataRetrieval package to collect additional information about these sites and save it into individual .csv files. Site number "208111310" does not exist, so it returns an error and stops the code.



      I want the code to ignore site numbers that do not return data and continue to the next number in sitelist.
      I've tried trycatch in several ways but can't get the correct syntax. Here is my for loop without trycatch.



      for (i in sitelist)
      test_gage <- readNWISdv(siteNumbers = i,
      parameterCd = pCode)

      df = test_gage
      df = subset(df, select= c(site_no, Date, X_00060_00003))
      names(df)[3] <- c("flow in m3/s")
      df$Year <- as.character(year(df$Date))

      write.csv(df, paste0("./gage_flow/",i,".csv"), row.names = F)
      rm(list=setdiff(ls(),c("sitelist", "pCode")))







      r try-catch






      share|improve this question















      share|improve this question













      share|improve this question




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      edited Nov 13 '18 at 3:37









      prosoitos

      935219




      935219










      asked Nov 13 '18 at 2:35









      HeyBales

      84




      84






















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          You can use the variable error in the function trycatch to specify what happened when an error occurs and store the return value using operator <<-.



          for (i in sitelist) 
          test_gage <- NULL
          trycatch(error=function(message)
          test_gage <<- readNWISdv(siteNumbers = i,parameterCd = pCode)

          df = test_gage
          df = subset(df, select= c(site_no, Date, X_00060_00003))
          names(df)[3] <- c("flow in m3/s")
          df$Year <- as.character(year(df$Date)) write.csv(df, paste0("./gage_flow/",i,".csv"), row.names = F)
          rm(list=setdiff(ls(),c("sitelist", "pCode")))



          If you want to catch the warnings also just give a second argument to trycatch.



          trycatch(error=function(),warning=function())





          share|improve this answer




















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            1 Answer
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            1 Answer
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            active

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            1














            You can use the variable error in the function trycatch to specify what happened when an error occurs and store the return value using operator <<-.



            for (i in sitelist) 
            test_gage <- NULL
            trycatch(error=function(message)
            test_gage <<- readNWISdv(siteNumbers = i,parameterCd = pCode)

            df = test_gage
            df = subset(df, select= c(site_no, Date, X_00060_00003))
            names(df)[3] <- c("flow in m3/s")
            df$Year <- as.character(year(df$Date)) write.csv(df, paste0("./gage_flow/",i,".csv"), row.names = F)
            rm(list=setdiff(ls(),c("sitelist", "pCode")))



            If you want to catch the warnings also just give a second argument to trycatch.



            trycatch(error=function(),warning=function())





            share|improve this answer

























              1














              You can use the variable error in the function trycatch to specify what happened when an error occurs and store the return value using operator <<-.



              for (i in sitelist) 
              test_gage <- NULL
              trycatch(error=function(message)
              test_gage <<- readNWISdv(siteNumbers = i,parameterCd = pCode)

              df = test_gage
              df = subset(df, select= c(site_no, Date, X_00060_00003))
              names(df)[3] <- c("flow in m3/s")
              df$Year <- as.character(year(df$Date)) write.csv(df, paste0("./gage_flow/",i,".csv"), row.names = F)
              rm(list=setdiff(ls(),c("sitelist", "pCode")))



              If you want to catch the warnings also just give a second argument to trycatch.



              trycatch(error=function(),warning=function())





              share|improve this answer























                1












                1








                1






                You can use the variable error in the function trycatch to specify what happened when an error occurs and store the return value using operator <<-.



                for (i in sitelist) 
                test_gage <- NULL
                trycatch(error=function(message)
                test_gage <<- readNWISdv(siteNumbers = i,parameterCd = pCode)

                df = test_gage
                df = subset(df, select= c(site_no, Date, X_00060_00003))
                names(df)[3] <- c("flow in m3/s")
                df$Year <- as.character(year(df$Date)) write.csv(df, paste0("./gage_flow/",i,".csv"), row.names = F)
                rm(list=setdiff(ls(),c("sitelist", "pCode")))



                If you want to catch the warnings also just give a second argument to trycatch.



                trycatch(error=function(),warning=function())





                share|improve this answer












                You can use the variable error in the function trycatch to specify what happened when an error occurs and store the return value using operator <<-.



                for (i in sitelist) 
                test_gage <- NULL
                trycatch(error=function(message)
                test_gage <<- readNWISdv(siteNumbers = i,parameterCd = pCode)

                df = test_gage
                df = subset(df, select= c(site_no, Date, X_00060_00003))
                names(df)[3] <- c("flow in m3/s")
                df$Year <- as.character(year(df$Date)) write.csv(df, paste0("./gage_flow/",i,".csv"), row.names = F)
                rm(list=setdiff(ls(),c("sitelist", "pCode")))



                If you want to catch the warnings also just give a second argument to trycatch.



                trycatch(error=function(),warning=function())






                share|improve this answer












                share|improve this answer



                share|improve this answer










                answered Nov 13 '18 at 3:39









                Csd

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