Last data update: 2014.03.03
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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
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