I have been relying upon methylKit, an R package for my RRBS data analysis. It is one the most highly cited R package for analysing bisulifite sequencing data. It is straight forward to install and it's vignette details all the major steps in the ... [Read more...]

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IntroductionSo I've been thinking a lot lately. Well, that's always true. I should say, I've been thinking a lot lately about the blog. When I started this blog I was very much into the whole quantified self thing, because it was new to me, I liked the... [Read more...]

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This post uses ggplot2 and rCharts to modify a grouped bar chart that appeared in an article that appeared online on October 19, 2014 in Wall Street Journal’s site. The article was titled “How to Sell a Liberal-Arts Education”. The code for the Rmarkdown file that generated this post can be ... [Read more...]

Many R scripts depend on CRAN packages, and most CRAN packages in turn depend on other CRAN packages. If you install an R package, you'll also be installing its dependencies to make it work, and possibly other packages as well to enable its full functionality. My colleague Andrie posted some ... [Read more...]

Big data is all the rage, but sometimes you don’t have big data. Sometimes you don’t even have average size data. Sometimes you only have eleven unique socks: Karl Broman is here putting forward a very interesting problem. Interesting, not only because it involves socks, but because it ... [Read more...]

Since the people at Alpha Architect were so kind as to feature my blog in a post, I figured I’d … Continue reading → [Read more...]

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The hts package for R allows for forecasting hierarchical and grouped time series data. The idea is to generate forecasts for all series at all levels of aggregation without imposing the aggregation constraints, and then to reconcile the forecasts so they satisfy the aggregation constraints. (An introduction to reconciling hierarchical ... [Read more...]

This post uses ggplot2 and rCharts to modify a grouped bar chart that appeared in an article that appeared online on October 19, 2014 in Wall Street Journal’s site. The article was titled “How to Sell a Liberal-Arts Education”. The code for the Rmarkdown file that generated this post can be ... [Read more...]

[This article was first published on Yet Another Blog in Statistical Computing » S+/R, and kindly contributed to R-bloggers]. (You can report issue about the content on this page here) Want to share your content on R-bloggers? click here if you have a blog, or here if you don't. pkgs <- c('sas7bdat', 'betareg', 'lmtest') lapply(pkgs, require, character.only = T) df1 <- read.sas7bdat("lgd.sas7bdat") df2 <- df1[which(df1$y < 1), ] xvar <- paste("x", 1:7, sep = '', collapse = " + ") fml1 <- as.formula(paste("y ~ ", xvar)) fml2 <- as.formula(paste("y ~ ", xvar, "|", xvar)) # FIT A BETA MODEL WITH THE FIXED PHI beta1 <- betareg(fml1, data = df2) summary(beta1) # Coefficients (mean model with logit link): # Estimate Std. Error z value Pr(>|z|) # (Intercept) -1.500242 0.329670 -4.551 5.35e-06 *** # x1 0.007516 0.026020 0.289 0.772680 # x2 0.429756 0.135899 3.162 0.001565 ** # x3 0.099202 0.022285 4.452 8.53e-06 *** # x4 2.465055 0.415657 5.931 3.02e-09 *** # x5 -0.003687 0.001070 -3.446 0.000568 *** # x6 0.007181 0.001821 3.943 8.06e-05 *** # x7 0.128796 0.186715 0.690 0.490319 # # Phi coefficients (precision model with identity link): # Estimate Std. Error z value Pr(>|z|) # (phi) 3.6868 0.1421 25.95 <2e-16 [...] [Read more...]

A new maintenance release of littler is available now. The main change are a few updates and extensions to the examples provided along with littler. Several of those continue to make use of the wonderful docopt package by Edwin de Jonge. Carl Boetti... [Read more...]

I am continuing with my trying all algorithms of Laplaces Demon. It is actually quite a bit more work than I expected but I do find that some of the things get clearer. Now that I am close to the end of calculating this second batch I learned that ther... [Read more...]

Last week, with @3wen, we were working a the revised version of our work on smoothing densities of spatial processes (with edge correction). Usually, once you have revised the paper, some references were added, others were droped. But you need to spend some time, to check that all references are ... [Read more...]

I have different sets of monthly data that I want to align and evaluate once a month. The different sources report the timestamp of the monthly data differently – one reports the date without the day, another as the last business day, and another as the last day of the month. ... [Read more...]

We’re excited to announce the start of our Intro to Data Science with R two-­day corporate training session, held Nov. 6-7 in New York City! Please visit nycdatascience.com for details on the location, time, and course syllabus. The application of R in industries from banking to telecommunications ... [Read more...]

My second-favourite keynote from yesterday's Strata Hadoop World conference was this one, from Pinterest's John Rauser. To many people (especially in the Big Data world), Statistics is a series of complex equations, but a just a little intuition goes a long way to really understanding data. John illustrates this wonderfully ... [Read more...]

Highcharts is the best JavaScript chart library, I feel. By default, there is an export button which can let you save the interactive figure to PNG, JPEG, PDF and SVG format, and one important point is, you can use it in your shiny app through R package rCharts. However, there ... [Read more...]