[R-sig-Geo] Request for help about running a loop and reading .NC files

[Bhaskar Mitra]

Hello Everyone,

I have written a loop which reads hundreds of .nc files
and extract information from each .nc file and
exports that corresponding information as a csv file.

The loop works fine until it encounters a .nc file which it cannot read
and the loop stops. I would appreciate if anyone can suggest how can I
modify
the loop, whereby the loop will continue to run by bypassing those
particular
files which it cannot read.

In the end I was also hoping to modify the loop such that it
will generate a report which will inform me which
files were not read by the loop.  The codes are given below

Thanks,
Bhaskar Mitra
NAU

#_------------------------------------------------------------------


library(ncdf4)
library(reshape2)
library(dplyr)
library(stringr)


setwd("directory path")

Output <- "directory path"

flist <- list.files(path ="NCFiles/", pattern = "^.*\\.(nc|NC|Nc|Nc)$")

for (i in 1: length(flist))
{

  nc <- nc_open(paste0("NCFiles/",flist[i]))
  mean1 <- ncvar_get(nc,attributes(nc$dim)$names[3])
  nc_close(nc)

  mean_chl_df <- melt(mean1)
  trial.table.df <-as.data.frame(mean_chl_df)

write.csv(trial.table.df,paste0(Output,"/",tools::file_path_sans_ext(flist[i]),".csv"))

}

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