Publications by aghaynes
Calculating confidence intervals for proportions
Heres a couple of functions for calculating the confidence intervals for proportions. Firstly I give you the Simple Asymtotic Method: simpasym <- function(n, p, z=1.96, cc=TRUE){ out <- list() if(cc){ out$lb <- p - z*sqrt((p*(1-p))/n) - 0.5/n out$ub <- p + z*sqrt((p*(1-p))/n) + 0.5/n } else { out$lb <- p - z*sqrt((p*...
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“Pretty” table columns
Every now and then you might want to make a nice table to include directly in your documents without having to faff about with columns later in excel or word. Typical issues might be the specification of decimal places, converting a value and proportion/SE column into one to take the form of n (x) or a value and CIs into x (x_min – x_max). I ne...
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Emails from R
There are a few packages for sending email directly from R, but I work in a place where none of these work due to strict network settings. To at least partially circumvent this, here’s some code to produce a PowerShell script to send email(s) via Outlook. The PowerShell script can then be run either by a shell call (again, not possible in my wo...
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Count models in JAGS
Looks like I’ll be diving into some Bayesian analyses using JAGS. This post is primarily intended as a collection of links to [potentially] useful information, but also includes a few initial thoughts (I might update it occasionally with new links). In terms of R packages, a very brief play suggests that R2jags is more user friendly than rjags ...
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Flow charts in R
Flow charts are an important part of a clinical trial report. Making them can be a pain though. One good way to do it seems to be with the grid and Gmisc packages in R. X and Y coordinates can be designated based on the center of the boxes in normalized device coordinates (proportions of the device space – 0.5 is this middle) which saves a lot ...
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grconvertX and grconvertY
These two functions are unbelievably useful for positioning graphical elements (text, axes, labels, …) in R. They allow one to convert coordinates between various different formats. For instance, you can convert your user coordinate (say 5 where x ranges from 0 to 200) to normalized device coordinates (proportional distance across the device) a...
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openrouteservice – geodata!
The openrouteservice provides a new method to get geodata into R. It has an API (or a set of them) and an R package has been written to communicate with said API(s) and is available from GitHub. I’ve just been playing around with the examples on this page, in the thought of using it for a project (more on that later if I get anywhere with it). ...
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Tips for great graphics
R is a great program for generating top-notch graphics. But to get the best out of it, you need to put in a little more work. Here are a few tips for adapting your R graphics to make them look a little better. 1) Dont use the “File/Save as…/” menu. If you set up your graphic in the first place then theres no need to post-process (eg crop, s...
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Intersecting points and overlapping polygons
I’ve been doing some spatial stuff of late and the next little step will involve intersecting points with possibly many overlapping polygons. The sp package has a function called over which returns the polygons that points intersects with. The catch though, is that it only returns the last (highest numerical value) polygon a point overlaps with...
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Merging spatial buffers in R
I’m sure there’s a better way out there, but I struggled to find a way to dissolve polygons that touched/overlapped each other (the special case being buffers). For example, using the osmdata package, we can download the polygons representing hospital buildings in Bern, Switzerland. library(osmdata) library(rgdal) ; library(maptools) ; libr...
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