SimInf

Package: SimInf
Title: A Framework for Data-Driven Stochastic Disease Spread
Simulations
Version: 2.0.0
Author: Stefan Widgren (National Veterinary Institute, Sweden),
Pavol Bauer (Uppsala University, Sweden),
Stefan Engblom (Uppsala University, Sweden)
Maintainer: Stefan Widgren <stefan.widgren@gmail.com>
Description: Livestock movements are important for the spread of many
infectious diseases between herds. The package provides an
efficient and flexible framework for stochastic disease spread
modelling that integrates within-herd disease dynamics as
continuous-time Markov chains and livestock movements between
herds as scheduled events. The core simulation solver is
implemented in C and uses 'OpenMP' (if available) to divide work
over multiple processors. The package contains template models and
can be extended with user defined models.
Acknowledgements: This work was financially supported by the Swedish
Research Council within the UPMARC Linnaeus center of
Excellence (Pavol Bauer and Stefan Engblom), The Swedish
Research Council Formas (Stefan Engblom and Stefan Widgren),
and The Swedish Board of Agriculture (Stefan Widgren).
License: GPL-3
URL: https://github.com/stewid/SimInf
BugReports: https://github.com/stewid/SimInf/issues
Type: Package
LazyData: true
Biarch: true
NeedsCompilation: yes
SystemRequirements: GNU Scientific Library (GSL)
Depends: R (>= 3.0.2), methods
Imports: graphics, Matrix
Collate: 'AllGenerics.R' 'check_arguments.R' 'scheduled_events.R'
'siminf_model.R' 'SISe.R' 'SISe3.R' 'SISe3_sp.R' 'SISe_sp.R'
'SimInf.R' 'demo_model.R' 'dependencies.R' 'distance.R'
'run_outer.R'
RoxygenNote: 5.0.1
Packaged: 2016-05-03 19:11:45 UTC; stefan
Repository: CRAN
Date/Publication: 2016-05-04 07:56:46

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'SimInf' ...
** package 'SimInf' successfully unpacked and MD5 sums checked
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for gcc option to support OpenMP... -fopenmp
checking whether OpenMP will work in a package... yes
checking for cblas_dgemm in -lgslcblas... yes
checking for gsl_blas_dgemm in -lgsl... yes
configure: creating ./config.status
config.status: creating R/dependencies.R
config.status: creating src/Makevars
** libs
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -Icore -Imisc -Imodels -fopenmp -I/usr/local/include -I/usr/local/include   -fopenmp -fpic  -g -O2  -c siminf.c -o siminf.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -Icore -Imisc -Imodels -fopenmp -I/usr/local/include -I/usr/local/include   -fopenmp -fpic  -g -O2  -c core/siminf_solver.c -o core/siminf_solver.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -Icore -Imisc -Imodels -fopenmp -I/usr/local/include -I/usr/local/include   -fopenmp -fpic  -g -O2  -c misc/siminf_arg.c -o misc/siminf_arg.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -Icore -Imisc -Imodels -fopenmp -I/usr/local/include -I/usr/local/include   -fopenmp -fpic  -g -O2  -c misc/siminf_forward_euler_linear_decay.c -o misc/siminf_forward_euler_linear_decay.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -Icore -Imisc -Imodels -fopenmp -I/usr/local/include -I/usr/local/include   -fopenmp -fpic  -g -O2  -c misc/siminf_ldata.c -o misc/siminf_ldata.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -Icore -Imisc -Imodels -fopenmp -I/usr/local/include -I/usr/local/include   -fopenmp -fpic  -g -O2  -c models/SISe.c -o models/SISe.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -Icore -Imisc -Imodels -fopenmp -I/usr/local/include -I/usr/local/include   -fopenmp -fpic  -g -O2  -c models/SISe3.c -o models/SISe3.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -Icore -Imisc -Imodels -fopenmp -I/usr/local/include -I/usr/local/include   -fopenmp -fpic  -g -O2  -c models/SISe3_sp.c -o models/SISe3_sp.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -Icore -Imisc -Imodels -fopenmp -I/usr/local/include -I/usr/local/include   -fopenmp -fpic  -g -O2  -c models/SISe_sp.c -o models/SISe_sp.o
gcc -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o SimInf.so siminf.o core/siminf_solver.o misc/siminf_arg.o misc/siminf_forward_euler_linear_decay.o misc/siminf_ldata.o models/SISe.o models/SISe3.o models/SISe3_sp.o models/SISe_sp.o -fopenmp -lgsl -lgslcblas -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/SimInf/libs
** R
** data
*** moving datasets to lazyload DB
** preparing package for lazy loading
Creating a generic function for 'plot' from package 'graphics' in package 'SimInf'
** help
*** installing help indices
  converting help for package 'SimInf'
    finding HTML links ... done
    SISe-class                              html  
    SISe                                    html  
    SISe3-class                             html  
    SISe3                                   html  
    SISe3_sp-class                          html  
    SISe3_sp                                html  
    SISe_sp-class                           html  
    SISe_sp                                 html  
    SimInf                                  html  
    check_end_t_arg                         html  
    check_gdata_arg                         html  
    check_infectious_pressure_arg           html  
    check_integer_arg                       html  
    demo_model                              html  
    distance_matrix                         html  
    events_SISe3                            html  
    have_openmp                             html  
    infected-methods                        html  
    is_wholenumber                          html  
    plot-methods                            html  
    prevalence-methods                      html  
    run-methods                             html  
    run_outer-methods                       html  
    scheduled_events-class                  html  
    scheduled_events                        html  
    show-scheduled_events-method            html  
    show-siminf_model-method                html  
    siminf_model-class                      html  
    siminf_model                            html  
    summary-scheduled_events-method         html  
    summary-siminf_model-method             html  
    susceptible-methods                     html  
    u0_SISe3                                html  
** building package indices
** testing if installed package can be loaded
* DONE (SimInf)
Making 'packages.html' ... done