# 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 …

Usage:

`plotHR( model , terms = 1 , se = TRUE , rug = "ticks" , x.log = FALSE , xlab = "" , ylab = "Hazard Ratio" , main = NULL , xlim = NULL , ylim = NULL, col.term = "#08519C", lwd.term = 3, col.se = "#DEEBF7", cex = 1 , bty = "n" , axes = TRUE )`

- model – a coxph model
- terms – integer; the number of the term to plot
- se – logical TRUE/FALSE; plotting the CI
- rug – “ticks” or “density”; rug plot or density plot at x-axis. Any other value for “rug” will omit the rugplot.
- x.log – logical TRUE/FALSE; log-transformed exposure variable
- xlab – character; x-axis label
- ylab – character; y-axis label
- main – character; main plot title
- xlim – 2×1 column vector; x-range of plot
- ylim – 2×1 column vector; y-range of plot
- col.term – color of HR-curve
- lwd.term – line width of HR-curve
- col.se – color of CI (if plotted)
- cex – numeric; size factor of labels
- bty – specifies the boxtype around the plot. See
`?plot.default`