R for computational chemistry

Dasapta Erwin Irawan

April 12, 2016

intro

about me

my networks

my books

R history From Wikipedia

why R

R supports reproducibility

What’s R for?

Cran task view

Cran task view

Computational chemistry

definition Wikipedia/computational chemistry:

Computational chemistry is a branch of chemistry 
that uses computer simulation to assist in solving 
chemical problems. It uses methods of theoretical 
chemistry, incorporated into efficient computer 
programs, to calculate the structures and properties of 
molecules and solids.

from ACS

...Computational chemists' daily work influences 
our understanding of the way the world works, 
helps manufacturers design more productive and efficient 
processes, characterizes new compounds and materials, and 
helps other researchers extract useful knowledge from 
mountains of data.
... Many computational chemists develop and apply 
computer codes and algorithms, although practicing 
computational chemists can have rewarding careers 
without working on code development. 
Programming skills include compiling FORTRAN or C code, 
performing shell scripting with bash, Tcl/Tk, python, or perl, 
performing statistical analysis using *R* or SPSS, and 
working within a Windows, MacOS, or Linux environment...

built upon:

- math
- chemistry
- computer science (as tools)

you will do a lot of:

- clustering/classification
- correlation
- prediction
- simulation and modeling
- visualisation
R helps you to do part of those tasks

let’s dive in

R installation

R components

dataset formats

functions vs package

typical work flow

basic programming

reading data

object <- read.csv("datafile.csv")

running a function

object <- function(arguments)