Too crude to be true? The key to programming is being lazy; it has actually been called a virtue by some.
When I discovered the update() function it blew me away. Within short I had created a monster based upon this tiny function, allowing quick and easy output of regression tables that contain crude and adjusted estimates. In this post I’ll show you how to tame the printCrudeAndAdjusted() function in my Gmisc-package and show a little behind the scenes. Although not always present I think a regression table that shows both the crude and adjusted estimates conveys important information.
The crude is also referred to as un-adjusted and if this sharply drops in the adjusted model we can suspect that there is a strong confounder that steals some of the effect that this variable has. A simple walk-through We will start with basic usage of the function. If the names are a little to shorthand and we want prettier names it is easy to set the label of the name using the Hmisc label() function:
Showing results from Cox PH Models in R with simPH. Update 2 February 2014: A new version of simPH (Version 1.0) will soon be available for download from CRAN.
It allows you to plot using points, ribbons, and (new) lines. See the updated package description paper for examples. Note that the ribbons argument will no longer work as in the examples below. Please use type = 'ribbons' (or 'points' or 'lines'). Effectively showing estimates and uncertainty from Cox Proportional Hazard (PH) models, especially for interactive and non-linear effects, can be challenging with currently available software. So, I’ve been putting together the simPH R package to hopefully make it easier to show results from Cox PH models.
Here I want to give an overview of how to use simPH. General Steps There are three steps to use simPH: A Few Examples Here are some basic examples that illustrate the process and key syntax. Linear effects Let’s look at a simple example with a linear non-interactive effect. Notice that the argument spin = TRUE. Interactions. Survival - Which model should I use for Cox proportional hazards with paired data. Cluster() or frailty() in coxph. Good looking survival curves – ‘ggsurv’ function.
This is a guest post by Edwin Thoen Currently I am doing my master thesis on multi-state models.
Survival analysis was my favourite course in the masters program, partly because of the great survival package which is maintained by Terry Therneau. The only thing I am not so keen on are the default plots created by this package, by using plot.survfit. Although the plots are very easy to produce, they are not that attractive (as are most R default plots) and legends has to be added manually. I come across them all the time in the literature and wondered whether there was a better way to display survival. Once the function is loaded, we can get going, we use the lung data set from the survival package for illustration. Censored observations are denoted by red crosses, by default a confidence interval is plotted and the axes are labeled. The multi-stratum curves are by default of different colors, the standard ggplot colours.
That’s better. Finally we can also adjust the plot itself. Coxph and loglik converged before variable X. R - How to extract values from survfit object. Dealing with non-proportional hazards in R. Since I’m frequently working with large datasets and survival data I often find that the proportional hazards assumption for the Cox regressions doesn’t hold.
In my most recent study on cardiovascular deaths after total hip arthroplasty the coefficient was close to zero when looking at the period between 5 and 21 years after surgery. Grambsch and Thernau’s test for non-proportionality hinted though of a problem and as I explored it there was a clear correlation between mortality and hip arthroplasty surgery. The effect increased over time, just as we had originally thought, see below figure. In this post I’ll try to show how I handle with non-proportional hazards in R.
Why should we care? As we scale up to larger datasets we are increasingly looking at smaller effects. Missing the exposure In the example above I would have missed the fact that a hip implant may affect mortality in the long run. Insufficient adjustment for confounding What is the Cox model all about? Drop unused variables. Timedep.