254 search results for "pca"

Using R and r.mapcalc (GRASS) to Estimate Mean Topographic Curvature

August 3, 2010
By
Using R and r.mapcalc (GRASS) to Estimate Mean Topographic Curvature

Recently I was re-reading a paper on predictive soil mapping (Park et al, 2001), and considered testing one of their proposed terrain attributes in GRASS. The attribute, originally described by Blaszczynski (1997), is the distance-weighted mean differe...

Read more »

Tutorial: Principal Components Analysis (PCA) in R

May 20, 2010
By

Found this tutorial by Emily Mankin on how to do principal components analysis (PCA) using R. Has a nice example with R code and several good references. The example starts by doing the PCA manually, then uses R's built in prcomp() function to do the s...

Read more »

Compcache on Ubuntu on Amazon EC2

May 4, 2010
By
Compcache on Ubuntu on Amazon EC2

The following fully-automatic Bash script downloads, compiles, and initializes compcache version 0.6.2 on Ubuntu Karmic Koala (9.10). This script creates two swaps with a maximum of 4GB uncompressed size each. Two swaps are used to take advantage of 2 CPUs (or CPU cores in a multicore CPU). Compcache is a fascinating memory compression system. The

Read more »

stone flakes IV

June 29, 2014
By
stone flakes IV

In this post I want to try something new, a causal graphical model. The aim here is just as much to get myself a feel what these things do as to understand how the stone flakes data fit together. DataData are stone flakes data which I analyzed previous...

Read more »

Multivariate Data Analysis and Visualization Through Network Mapping

June 27, 2014
By
Multivariate Data Analysis and  Visualization Through Network Mapping

Recently I had the pleasure of speaking about one of my favorite topics, Network Mapping. This is a continuation of a general theme I’ve previously discussed and involves the merger of statistical and multivariate data analysis results with a network. Over the past year I’ve been working on two major tools, DeviumWeb and MetaMapR, which

Read more »

Tailoring univariate probability distributions

June 26, 2014
By
Tailoring univariate probability distributions

This post shows how to build a custom univariate distribution in R from scratch, so that you end up with the essential functions: a probability density function, cumulative distribution function, quantile function and random number generator. In the beginning all you need is an equation of the probability density function, … Continue reading →

Read more »

Bedtools tutorial from 2013 CSHL course

June 24, 2014
By
Bedtools tutorial from 2013 CSHL course

A couple of months ago I posted about how to visualize exome coverage with bedtools and R. But if you're looking to get a basic handle on genome arithmetic, take a look at Aaron Quinlan's bedtools tutorials from the 2013 CSHL course. The tutorial uses ...

Read more »

stone flakes

June 6, 2014
By
stone flakes

I browsed through UC Irvine Machine Learning Repository! the other day and noticed a nice data set regarding stone flakes produced by our ancestors, the prehistoric men. To quote the dataset owners:'The data set concerns the earliest history ...

Read more »

Using Repeated Measures to Remove Artifacts from Longitudinal Data

June 4, 2014
By
Using Repeated Measures to Remove Artifacts from Longitudinal Data

Recently I was tasked with evaluating and most importantly removing analytical variance form a longitudinal metabolomic analysis carried out over a few years and including >2,5000 measurements for >5,000 patients. Even using state-of-the-art analytical instruments and techniques long term biological studies are plagued with unwanted trends which are unrelated to the original experimental design and stem from analytical

Read more »

SMART Hackathon: Day 2: Writing Packages in RStudio

May 6, 2014
By
SMART Hackathon: Day 2: Writing Packages in RStudio

So day 2 of the #JHUSMARTHack was last week, but I figured this would be a good time to discuss what was accomplished. I created some packages that are somewhat specialized and aren't fully finished yet, so I'll hold off. What I really want to discuss though is why I like using RStudio for making

Read more »