Consider having readChangeoDb wrap fread() instead of read.table()

[Eric Mukherjee]

It would really speed this up; file i/o is the bottleneck for my thesis project right now!

Btw this package is really great, thanks for all your work

[Jason Vander Heiden]

Thanks! Good suggestion. I'll take a look at it soon, and make the change if dplyr and data.table agree to play nice (I don't anticipate a problem).

[Jason Vander Heiden]

Hi @emukherj,

I've changed the default behavior of readChangeoDb() to use data.table::fread() in the current (development) version of the package in the default branch. As fread() doesn't currently support compressed (gz, etc) files, it'll fall back on utils::read.table() if fread() can't open the file. Also, I had it return a data.frame instead of a data.table. I'll have to check everything later for data.table compatibility before switching over entirely.

Please let me know if you have any trouble.

[Eric Mukherjee]

I'd like to test this out; how do I download the development version?

[Jason Vander Heiden]

It's pretty straight forward. The only tricky part is that if you are using Windows then you must install the same version of Rtools as your R version.

To install from the current code, first install the build dependencies:

install.packages(c("devtools", "roxygen2", "testthat", 
                   "knitr", "rmarkdown"))

Then use the bitbucket installer from devtools:

library(devtools)
install_bitbucket("kleinstein/alakazam@default")

If you have any trouble with this I can provide more detailed instructions.

[Jason Vander Heiden]

Seems to be working. Reopen if troubles arise.