Several times I had to correct database tables with a character primary key (which is ok, if not all other tables had numeric …). In order to get the necessary numeric format I inserted another variable with the correct format and transformed the character variable to numeric using the CDbl() Function.
The syntax for the CDbl function is: CDbl([MyString])
I did forget it again and could not find any documentation. Googling the topic gave a lot of fruitless hits, so here it is.
Note: This initial blog post is discontinued. If you want to have the latest development of the function have a look at the static page PlotHR
Usually a Cox-regression is achieved in R by library(survival)
model <- coxph ( SuvivalObject ~ Covariate1 + Covariate2 + Factor1 + Factor2 , data = Dataset )
The covariates can be enclosed in other funtions:
factors should be enclosed by factor()
strata, which allow to adjust for a factor without getting an estimate, should be enclosed by strata()
non-log linear continuous terms can be enclosed by pspline()
In the latter case the model might look like model <- coxph (SurvivalObject ~ pspline(Covariate1) + Covariate2 + factor(Factor1) + strata(Factor2) , data = Dataset )
The functional form of the covariates (including the factors) can now be plotted with termplot(model)
Though the termplot() function fails with plotting just one covariate and leaves no cusomization.
The function plotHR() plots the functional form of the desired term: plotHR(model)
plots the first term in the model by default but other terms can be accessed by calling their number (e.g. the second one): plotHR(model , terms = 2)
In order to use the function you have to “source” it into R. It is the same procedure as calling a package, but using “source” instead of “library”.
Paste the function syntax into a textfile and safe it (as plot.HR.R) on your harddisk, remember the path and include source("C:Path/to/plotHR_0.6.R")
before using the function.
Note: I have rewritten the function several times since I wrote the initial post … using version numbers now …
V0.6 – removed the y.log option, since the scale should be logaritmic anyway. Later I will also rewrite the x.log option, since the feature is already incorporated in the plot.default() function. I also removed the dottet line at HR=1 level, since some complained about it overstating the importance of the log(HR) intercept. I included it, since it gives a hint about the significance of the smooth term, in case the confidence intervalls cross over the line… Those who miss it can add manually lines( h = 0 , type = 2 )
I rewrote the “rugs” option. Try rugs = "density" It is still “beta”ish, but some like it.
V0.5 – bug fix for the y-scale and slight adjustment of the default plotting colors (paler CI shade and stronger term-line)
V0.4 – the y-scale should be logarithmic; a HR of 0.5 (50% reduced Hazard) should show the same distance from HR = 1 as a doubled Hazard (HR = 2); this is now default. The linear scale I used initially is biased in this concern (Hat-tip: Arve Ulvik, Eva Pedersen and Roy Nilsen). The option y.log allows both ways (linear and log-scale); the axis labels denote Hazard Ratio instead of log(HR).
Just playing around the other day to get the default plot.density() function a bit more like publishing quality. Above is my favorite so far. Further down are two more spartanic versions.
In this connection I also wrote my first function. When I get more customed to R I will package my ideas into an R library – but later…
There is the possibility to call R-functions without embedding the code into your analysis script, but I did not look that up yet, so embedding the following code into your script (at the beginning) and then using densityplot(Dataset$Coviate)
will do the job, where Dataset and Covariate have to be replaced by the according values of course.
Some might find the colored area to much, although IMHO it puts the focus on the fact that one is looking at areas when ploting a density. But then something similar without the color fill. Not a function just a few lines of code to embed and adjust to the script: