[R] Request for help about running a loop and reading .NC files
Bhaskar Mitra
bh@@k@r@ko|k@t@ @end|ng |rom gm@||@com
Tue Mar 24 00:16:42 CET 2020
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 or if any particular file has an error.
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 for your help,
Regards,
Bhaskar Mitra
#_------------------------------------------------------------------
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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