Example programs for the book "Nonparametric Estimation under Shape Constraints" (2014), Piet Groeneboom and Geurt Jongbloed. Cambridge University Press, 2014.

For running the R scripts, like MLEThai.R in the directory Rcpp_scripts/CompetingRisk_bootstrap, one needs three files: the R script, the input file (for the present directory this is: dataThai.txt) and the C++ file (in this case icm.cpp). One needs to put the three files, R script, C++ file (which has the extension .cpp) and input file (with extension .txt), into one directory, just like it is done in the repository. The bootstrap procedure draws 1000 bootstrap samples and computes 95% confidence intervals for the hazards.

One needs recent versions of R and then the examples run in any case on Mac, Windows and Linux (also on virtual versions of these sytems). One also needs the Rcpp package for the command "sourceCpp", which makes the connection between the C++ code and R. If one gets an error message of the type "sourceCpp cannot be found", the script will not work and one probably has to update one's version of R. Windows users may also need to install the latest version of Rtools (http://cran.r-project.org/bin/windows/Rtools/index.html).

Mac users may have to use Xcode, or at least the corresponding command line tools, see (with advices for Windows, Mac and Linux users): https://support.rstudio.com/hc/en-us/articles/200486498-Package-Development-Prerequisites. Mac users who use the GUI application, given on http://dutiosc.twi.tudelft.nl/~pietg/software.html do not have to download extra tools.

The directory CompetingRisk_nongrouped_data has the data file in a format where the observation times are non-unique and where the ties at the observations are computed by the program. The directory CompetingRisk_grouped_data has the data file in a format where the observation times are unique and where the number of observations of a certain type are given at each observation. Note the different structures of the input files in the grouped and non-grouped directories!

In copying the files from the site, one should push the button "raw" above the file in GitHub, to avoid getting html code instead of the file one needs. For more information on the present examples, see Software.pdf. The sources of the GUI Mac application are also kept on the present site in the directory MacGui.