An R package for Cox-type models with interval-censored data
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DESCRIPTION
INSTALL
NAMESPACE
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README.md

README.md

coxinterval

An R package for Cox-type models with interval-censored data

Requirements

Required software for coxinterval is summarized as follows. System-specific notes for each item are provided below.

  1. Development tools for R, including GNU make
  2. 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.

Linux

  1. Install the r-base-dev package. For further details, see the R download documentation for your Linux distribution.

Mac

  1. 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.

Windows

  1. Install Rtools. From a command prompt run set PATH and ensure that the value for the PATH environment variable includes the folders for both R and Rtools binaries. If not, update PATH using 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%
  2. Install 32-bit CPLEX. Note that this means that the package's CPLEX-dependent functions are limited to 32-bit R.

Installing

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

In the interest of easy installation over complete portability, the package's Makevars files uses non-standard GNU make extensions to locate CPLEX's default directory, which depends on the system.

  • Linux: /opt/*/ILOG/CPLEX*
  • Mac: /Users/*/Applications/IBM/ILOG/CPLEX*
  • Windows 64-bit: C:/PROGRA~2/IBM/ILOG/CPLEX*
  • Windows 32-bit: C:/PROGRA~1/IBM/ILOG/CPLEX*

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 <CPLEXLIBDIR>/cplex<version>.lib.

Installing on systems without GNU make

Precede the install instructions with:

  1. Extract the source from the package tarball
  2. Revise the coxinterval/src/Makevars file according to the template below
  3. 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 =