An R package for Cox-type models with interval-censored data
Required software for coxinterval is summarized as follows. System-specific notes for each item are provided below.
- Development tools for R, including GNU make
- C API for CPLEX available with IBM ILOG CPLEX Optimization Studio 12.5+. Members of IBM's Academic Initiative can obtain CPLEX at no charge. Without CPLEX, coxinterval offers reduced functionality.
- Install the r-base-dev package. For further details, see the R download documentation for your Linux distribution.
- Install software listed in the tools section of the Mac OS X R download documentation. With R 3+, this amounts to the GNU Fortran compiler gfortran.
Install Rtools. From a command prompt run
set PATHand ensure that the value for the
PATHenvironment variable includes the folders for both R and Rtools binaries. If not, update
PATHusing the Windows command
set. For example:
set PATH=C:/Rtools/bin;C:/Rtools/gcc-4.6.3/bin;%PATH% set PATH=C:/Program Files/R/R-3.1.0/bin;%PATH%
Install 32-bit CPLEX. Note that this means that the package's CPLEX-dependent functions are limited to 32-bit R.
To install from CRAN, run in an R session:
> install.packages("coxinterval", type = "source")
To install a development release from GitHub, download the package tarball to your R session working directory and run:
> install.packages("coxinterval_<version>.tar.gz", repos = NULL, type = "source")
Overriding installer defaults
- Windows 64-bit:
- Windows 32-bit:
With custom or multiple installations of CPLEX, a directory must specified in POSIX-like format with the
CPLEXDIR environment variable. For example, on a 64-bit Windows system,
install.packages could be preceded with:
> Sys.setenv(CPLEXDIR = "C:/PROGRA~2/IBM/ILOG/CPLEX_Studio126")
The CPLEX-related compiler variables can also be set directly, but the provided values are not validated. Continuing the above example:
> Sys.setenv(CPLEXINCVARS = paste('-I"', Sys.getenv("CPLEXDIR"), '/cplex/include"', sep = "")) > Sys.setenv(CPLEXLIBVARS = paste('-L"', Sys.getenv("CPLEXDIR"), '/cplex/lib/x86_windows_vs2010/stat_mda" -lcplex1260 -lm', sep = ""))
Note the use of quotes for correct reference to directory names. These are unnecessary on (mostly) POSIX-compliant systems like Linux and Mac.
GNU make extensions are further used to locate CPLEX's include and library directories. In general these have the form
CPLEXINCDIR = <CPLEXDIR>/cplex/include CPLEXLIBDIR = <CPLEXDIR>/cplex/lib/<machine or compiler>/<library format>
respectively, where the include directory points to the header file
<CPLEXINCDIR>/ilcplex/cplex.h. The choice of the library format has no consequence for CPLEX's C API. Under Linux and Mac adequate linking option settings are
-lcplex -lm. With Windows it is necessary to specify the CPLEX version number in the library name:
-lcplex<version> -lm, where
<version> can be obtained from the library file name
Installing on systems without GNU make
Precede the install instructions with:
- Extract the source from the package tarball
- Revise the
coxinterval/src/Makevarsfile according to the template below
- Rebuild the package tarball with
R CMD build coxinterval
Makevars template for systems with CPLEX:
CPLEXDIR = <add-on software directory>/ibm/ILOG/CPLEX_Studio<version> CPLEXINCDIR = $(CPLEXDIR)/cplex/include CPLEXLIBDIR = $(CPLEXDIR)/cplex/lib/<machine>/<library format> CPLEXINCVARS = -I$(CPLEXINCDIR) CPLEXLIBVARS = -L$(CPLEXLIBDIR) -lcplex -lm PKG_CPPFLAGS = $(SHLIB_PTHREAD_FLAGS) $(CPLEXINCVARS) PKG_LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) $(SHLIB_PTHREAD_FLAGS) \ $(CPLEXLIBVARS)
Without CPLEX, the first five lines can be replaced with:
CPLEXINCVARS = CPLEXLIBVARS =