How to bypass errors in for loops in r? - r

Question

I created a for loop to merge several csv files in a directory together into one table. In some cases the files that are indicated in the loop have not been created. When the files do not exist the loop produces an error and no files are merged. I am trying to adjust the code so the loop inserts "NULL" or "error" in the parts of the matrix reserved for the files.
Here is the original code:
COMP_raw <- cbind(m, matrix(-9999, ncol = length(dirnames), nrow = 169))
setwd() #actual wd is removed for posting
for(i in length(dirnames)){
j<-dirnames[1] #Take the directory folder name
id<-gsub("_.*$","",dirnames[1]) #Take the numeric identifier of the indicator
fpath <- file.path(paste(j,"/",id,"_2016",".csv", sep = "")) #Merge the directory folder name and desired csv to a file path format
data<-read.csv(fpath,header = TRUE, as.is = TRUE)
last <- max(ncol(data))
COMP_raw[,(1+1)] <- data[,last]
colnames(COMP_raw)[(1+1)] <- names(data[last])
}
This above code works for every loop where the "fpath" actually exists in my directory. When the csv does not exist the following message occurs.
Error in file(file, "rt") : cannot open the connection
In addition: Warning message:
In file(file, "rt") :
cannot open file '2.1_PermitIndirectCosts/2.1_2016.csv': No such file or directory
I looked at a few other posts to see how to solve the issue and tried the following
COMP_raw <- cbind(m, matrix(-9999, ncol = length(dirnames), nrow = 169))
for(i in length(dirnames)){
j<-dirnames[1] #Take the directory folder name
id<-gsub("_.*$","",dirnames[1]) #Take the numeric identifier of the indicator
fpath <- file.path(paste(j,"/",id,"_2016",".csv", sep = "")) #Merge the directory folder name and desired csv to a file path format
possibleerror<- tryCatch(data<-read.csv(fpath,header = TRUE, as.is = TRUE),silent = TRUE),
error=function(e) e
)
if(!inherits(possibleerror,"error"))
{last <- max(ncol(data))
COMP_raw[,(1+3)] <- data[,last]
colnames(COMP_raw)[(1+3)] <- names(data[last])}
}
But that is still generating an error

Answer 1

What about using file.exists().
file.exists returns a logical vector indicating whether the files named by its argument exist.
COMP_raw <- cbind(m, matrix(-9999, ncol = length(dirnames), nrow = 169))
setwd() #actual wd is removed for posting
for(i in length(dirnames)){
j <- dirnames[1] #Take the directory folder name
id <- gsub("_.*$","",dirnames[1]) #Take the numeric identifier of the indicator
fpath <- file.path(paste(j,"/",id,"_2016",".csv", sep = "")) #Merge the directory folder name and desired csv to a file path format
#Checks if file exists if not, assign NULL
if(file.exists(fpath)){
data <- read.csv(fpath,header = TRUE, as.is = TRUE)
last <- max(ncol(data))
COMP_raw[,(1+1)] <- data[,last]
colnames(COMP_raw)[(1+1)] <- names(data[last])
} else{
colnames(COMP_raw)[(1+1)] <- NULL
}
}

Answer 2

Not specific to your example (I'm on a mobile) but it should help:
var <- try(some function)
if(is(var, "try-error")){
some other function
next;}
If try fails, it will assign the variable a value of "try-error" which you can handle accordingly. next will go to the next item in the loop.