Author: Robin Denz

`adjustedCurves`

is an R-Package which can be used to
calculate and plot confounder-adjusted survival curves + confidence
intervals as well as cause-specific confounder-adjusted cumulative
incidence functions + confidence intervals using a variety of methods.
It provides a convenient wrapper around existing R-Packages on the topic
and adds additional methods and functionality on top of it. Those
additional features include the calculation of adjusted restricted mean
survival times and testing whether two confounder-adjusted survival
curves are different in a given interval.

Detailed descriptions of each method can be found in the literature cited in the documentation.

Currently this package is not available on CRAN, but can be installed
easily using the `devtools`

R-Package:

```
library(devtools)
::install_github("https://github.com/RobinDenz1/adjustedCurves") devtools
```

or the `remotes`

R-Package:

```
library(remotes)
::install_github("https://github.com/RobinDenz1/adjustedCurves") remotes
```

If you encounter any bugs or have any specific feature requests, please file an Issue.

This minimal example shows how to calculate and plot adjusted
survival curves using *Direct Adjustment* with this package:

```
library(adjustedCurves)
library(survival)
# simulate some data as example
set.seed(31)
<- sim_confounded_surv(n=250, max_t=1.2, group_beta=0)
sim_dat $group <- as.factor(sim_dat$group)
sim_dat
# estimate a cox-regression for the outcome
<- coxph(Surv(time, event) ~ x1 + x2 + x4 + x5 + group,
cox_mod data=sim_dat, x=TRUE)
# use it to calculate adjusted survival curves
<- adjustedsurv(data=sim_dat,
adjsurv variable="group",
ev_time="time",
event="event",
method="direct",
outcome_model=cox_mod,
conf_int=TRUE)
# plot with confidence intervals
plot(adjsurv, conf_int=TRUE)
```

Here is an example of how to calculate and plot adjusted survival
curves using *Inverse Probability of Treatment Weighting*:

```
# estimate a treatment assignment model
<- glm(group ~ x2 + x3 + x5 + x6, data=sim_dat,
glm_mod family="binomial"(link="logit"))
# use it to calculate adjusted survival curves
<- adjustedsurv(data=sim_dat,
adjsurv variable="group",
ev_time="time",
event="event",
method="iptw_km",
treatment_model=glm_mod,
conf_int=TRUE)
# plot with confidence intervals
plot(adjsurv, conf_int=TRUE)
```

It is also possible to plot the difference between two curves using
the `plot_curve_diff()`

function:

`plot_curve_diff(adjsurv, conf_int=TRUE, color="blue")`

To test whether the two adjusted survival curves are different in a
specified interval (here 0 to 0.75), the `adjustedsurv`

call
has to be made with `bootstrap=TRUE`

:

```
<- adjustedsurv(data=sim_dat,
adjsurv variable="group",
ev_time="time",
event="event",
method="direct",
outcome_model=cox_mod,
conf_int=TRUE,
bootstrap=TRUE,
n_boot=1000)
<- adjusted_curve_test(adjsurv, from=0, to=0.75)
adj_test summary(adj_test)
```

More examples can be found in the documentation and the vignettes.

The main paper associated with this R-Package is:

Robin Denz, Renate Klaaßen-Mielke, and Nina Timmesfeld (2022). *A
Comparison of Different Methods to Adjust Survival Curves for
Confounders*. arXiv:2203.10002v1

In addition, the relevant primary literature of the respective method should be cited. This can be found in the documentation of the method.

© 2021 Robin Denz

The contents of this repository are distributed under the GNU General Public License. You can find the full text of this License in this github repository. Alternatively, see http://www.gnu.org/licenses/.