CODEWITHSUNDEEP
r
helen.h
helen.h

Reputation: 1023

r pre-specify parts of file path

I currently have individual scripts for each species in my analysis, I'd like to try and get it into one script where I can specify at the beginning which species/year of data etc. I am analysing. I'd like to know if it is possible to instead set at the beginning of the script certain objects and then have more generic code to read in the files. for example;

existing code

ABR <- read.csv("Y:/Pelagic Work/FIN Data/2015/HOM/Abroad.csv",sep=",",skip = 2,header=T)
SCO <- read.csv("Y:/Pelagic Work/FIN Data/2015/HOM/Scotland.csv",sep=",",skip = 2,header=T)

I'd like something like;

Year <- 2015 
Species <- HOM

ABR <- read.csv("Y:/Pelagic Work/FIN Data/Year/Species/Abroad.csv",sep=",",skip = 2,header=T)
SCO <- read.csv("Y:/Pelagic Work/FIN Data/Year/Species/Scotland.csv",sep=",",skip = 2,header=T)

Upvotes: 1

Views: 67

Answers (3)

Tim Biegeleisen
Tim Biegeleisen

Reputation: 522762

I defined a helper function getFileName() which does the heavy lifting of building the path of the file you want to read.

getFileName <- function(root, year, species, file) {
    return (paste(root, year, species, file, sep="/"))
}

root <- "Y:/Pelagic Work/FIN Data"
year <- "2015"
species <- "HOM"
file <- "Abroad.csv"

fileName <- getFileName(root, year, species, file, sep="/")

ABR <- read.csv(fileName,sep=",",skip = 2,header=T)

Upvotes: 2

mnel
mnel

Reputation: 115505

file.path is the function for which you are looking

root <- "Y:/Pelagic Work/FIN Data"
year <- "2015"
species <- "HOM"

file <- "Abroad.csv"
ABR <- file.path(root, year, species, file)

From the docs "Faster than paste(...)" and works with the appropriate filepath separator for the system

Upvotes: 2

m0nhawk
m0nhawk

Reputation: 24280

You can use sprintf for this:

Year <- 2015
Species <- HOM

abroad.path <- sprintf("Y:/Pelagic Work/FIN Data/%s/%s/Abroad.csv", Year, Species)
scotland.path <- sprintf("Y:/Pelagic Work/FIN Data/%s/%s/Scotland.csv", Year, Species)

ABR <- read.csv(abroad.path, sep=",", skip=2, header=T)
SCO <- read.csv(scotland.path, sep=",", skip=2, header=T)

Upvotes: 2

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