Tips & Tricks 4: Reading In Data Files

July 10, 2014
By

(This article was first published on geomorph, and kindly contributed to R-bloggers)

Today’s exercise is another nice and simple one, and allows you to get used to manipulating datasets in R.

Exercise 4 – How to read a file of coordinate data into R and make sure it is numeric.

Reading your data files into R  for analysis with geomorph or other packages can be challenging. Geomorph has several functions for common data file types of coordinate data (e.g. readland.tps(), readland.nts()).

But what if your data are not in this format?

One of the main issues people face is that using read.table() or read.delim(), numerical data can be coerced into a factor automatically. Below is a very simple solution to make sure your data are numerical:

mydata <- read.table(“data.txt”,header=TRUE,row.names=1,
stringsAsFactors = FALSE) 
# here we are reading in a tab-delimited text file from MorphoJ, but this can be an issue with data from any outside program. The stringsAsFactors = FALSE is VERY important here

is.numeric(mydata)
[1] FALSE # here R tells is the data are not numeric, even though we can see they are if we use View(mydata).

The solution is:
as.matrix(sapply(mydata[], as.numeric))

For example, say we know the shape coordinates are present in the file after two columns of non-shape coordinates (these could be centroid size, or a classifier), then:

shape <- as.matrix(sapply(mydata[,-(1:2)], as.numeric)) 
# here we say, use all columns except the first two.

is.numeric(shape)
[1] TRUE # now it’s numeric. Ready to go!

Simple! 

Emma

To leave a comment for the author, please follow the link and comment on their blog: geomorph.

R-bloggers.com offers daily e-mail updates about R news and tutorials on topics such as: Data science, Big Data, R jobs, visualization (ggplot2, Boxplots, maps, animation), programming (RStudio, Sweave, LaTeX, SQL, Eclipse, git, hadoop, Web Scraping) statistics (regression, PCA, time series, trading) and more...



If you got this far, why not subscribe for updates from the site? Choose your flavor: e-mail, twitter, RSS, or facebook...

Comments are closed.

Search R-bloggers


Sponsors

Never miss an update!
Subscribe to R-bloggers to receive
e-mails with the latest R posts.
(You will not see this message again.)

Click here to close (This popup will not appear again)