I've drawn figure in R with lwd=1, e.g.pdf('test.pdf')plot(1:10, type='o', lwd=2, axes=F)box(lwd=1, col='red')dev.off()And then you open the PDF in Illustrator, you will see the border width is 0.75pt, and the line is 1.5pt, which seems that the unit ... [Read more...]

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When learning a new language I try to make an effort to write it like a native developer. R has one language feature that has been severely testing my desire to write like a native and this afternoon I realized that most of the people reading my code will also ... [Read more...]

The animation embedded in this post was done using R and the iGraph package and was, frankly, a great deal more work than I thought it would be when I started. What kept me going was a desire to express a wish for the New Year while also experimenting with ... [Read more...]

In case you missed it, a new paper was published in Nature Biotechnology on a method for detecting isoform-level differential expression with RNA-seq Data:Trapnell, Cole, et al. "Differential analysis of gene regulation at transcript resolution with RN... [Read more...]

This video covers how to run SQL queries using the ‘sqldf’ package within R. This sqldf tutorial was part of a Keystone Solutions podcast discussion about data science and what skills beginning analysts should be learning to improve their skill set. The example files from this tutorial can be downloaded ... [Read more...]

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Florence Nightingale is held as a heroine for the British people because of her work during the Crimean War. However, she would not have been so fairly recognised if she had not been also a superb statistician: in a brilliant … Continue reading → [Read more...]

I’ve been dreaming on writing a manuscript about who are the pollinators for a while, but it looks I’m not going to have the time soon, so here is an early draft of what the main figure should look like: It’s surprisingly … Continue reading → [Read more...]

experimental.  the behavioral risk factor surveillance system (brfss) aggregates behavioral health data from 400,000 adults via telephone every year.  it's um *clears throat* the largest telephone survey in the world and it's gotta lotta uses... [Read more...]

The second R UseR meetup was 16 october. Kutergin Alex presented an overview of the packages for high-performance computing. HPC in R from arbuzov1989 [Read more...]

I learned of the passing of Albert Hirschman on December 11, and while better and more instructive tributes to his life can be read elsewhere, I wanted to focus on a little piece of Hirschman’s work that I use all the time: the (inverse) Herfindahl–Hirschman Index. The HHI is ... [Read more...]

Historical Value at Risk (VaR) is very popular because it is easy and intuitive: use the empirical distribution of some specific number of past returns for the portfolio. Previously “The estimation of Value at Risk and Expected Shortfall” included an R function to estimate historical VaR. Generating portfolios A useful ... [Read more...]

The example is more of a statistical exercise that  shows the true significance and the density curve of simulated random normal data.  The code can be changed to generate data using either a different mean and standard deviation or a different distribution altogether. This extends the idea of estimating pi ... [Read more...]

Of course, a picture on a computer monitor is a coloured plot of x and y coordinates or pixels. Still, I was smitten by David Sparks' posts on is.r(), where he shows how easy it is to read images into R to analyse them. In two posts [1], [2] he replicates ... [Read more...]

It's winter break… and as any academic knows, breaks are “a good time to get work done.” For the Christmas break, many of us have to travel home to see family members. One of the great privileges of being an academic is that you don't necessarily need to be in ... [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. In [1]: import pandas as pd In [2]: import statsmodels.api as sm In [3]: data = pd.read_table('/home/liuwensui/Documents/data/csdata.txt') In [4]: Y = data.LEV_LT3 In [5]: X = sm.add_constant(data[['COLLAT1', 'SIZE1', 'PROF2', 'LIQ', 'IND3A']]) In [6]: # Discrete Dependent Variable Models with Logit Link In [7]: mod = sm.Logit(Y, X) In [8]: res = mod.fit() Optimization terminated successfully. Current function value: 882.448249 Iterations 8 In [9]: print res.summary() Logit Regression Results ============================================================================== Dep. Variable: LEV_LT3 No. Observations: 4421 Model: Logit Df Residuals: 4415 Method: MLE Df Model: 5 Date: Sun, 16 Dec 2012 Pseudo R-squ.: 0.04022 Time: 23:40:40 Log-Likelihood: -882.45 converged: True LL-Null: -919.42 LLR p-value: 1.539e-14 ============================================================================== coef std err z P>|z| [95.0% Conf. Int.] ------------------------------------------------------------------------------ COLLAT1 1.2371 0.260 4.756 0.000 0.727 1.747 SIZE1 0.3590 0.037 9.584 0.000 0.286 0.432 PROF2 -3.1431 0.739 -4.254 0.000 -4.591 -1.695 LIQ -1.3825 0.357 -3.867 0.000 -2.083 -0.682 IND3A 0.5466 0.141 3.867 0.000 0.270 0.824 const -7.2498 [...] [Read more...]

Well, that’s embarrassing. A little tweak to my dark matter model resulted in a leaderboard score in the top 10. The only problem is that the contest closed about an hour ago. I ran this final prediction earlier today but then simply forgot to go back to it and submit!! ... [Read more...]

I outlined some personal suggestions for those interested in learning R. Refer to the new page  titled “Quick Start R“. …Continue reading » [Read more...]

First off, I'd really like to give a shout-out to the brave people who have created and maintain this great package - the fame is yours!So, while exploring the capabilities of the package some issues with the ITIS-Server arose and with large datasets things weren't working out quite well ... [Read more...]