RxODE: Facilities for Simulating from ODE-Based Models

Facilities for running simulations from ordinary differential equation (ODE) models, such as pharmacometrics and other compartmental models. A compilation manager translates the ODE model into C, compiles it, and dynamically loads the object code into R for improved computational efficiency. An event table object facilitates the specification of complex dosing regimens (optional) and sampling schedules. NB: The use of this package requires both C and Fortran compilers, for details on their use with R please see Section 6.3, Appendix A, and Appendix D in the "R Administration and Installation" manual.

Author
Melissa Hallow [aut], Wenping Wang [aut, cre]
Date of publication
2016-11-13 23:37:18
Maintainer
Wenping Wang <wwang8198@gmail.com>
License
GPL (>= 2)
Version
0.5-5
URLs

View on CRAN

Man pages

eventTable
Create an event table object
genShinyApp.template
Generate an example (template) of a dosing regimen shiny app
rx.initCmpMgr
A compilation manager for RxODE models
RxODE
Create an ODE-based model specification

Files in this package

RxODE
RxODE/inst
RxODE/inst/Changes.txt
RxODE/inst/TODO.txt
RxODE/inst/Porting
RxODE/inst/tran.g
RxODE/inst/pkpd.g
RxODE/inst/common
RxODE/inst/common/call_dvode.c
RxODE/inst/THANKS
RxODE/inst/driver_parsetree_no_inp.c
RxODE/inst/Install-windows.Rmd
RxODE/inst/tran.c
RxODE/inst/doc
RxODE/inst/doc/RxODE-intro.html
RxODE/inst/doc/index.html
RxODE/inst/doc/RxODE-syntax.html
RxODE/inst/doc/RxODE-intro.R
RxODE/inst/doc/RxODE-syntax.R
RxODE/inst/doc/RxODE-intro.Rmd
RxODE/inst/doc/RxODE-syntax.Rmd
RxODE/tests
RxODE/tests/test-multi.R
RxODE/tests/Examples
RxODE/tests/Examples/RxODE.Rout.save
RxODE/tests/Examples/eventTable.Rout.save
RxODE/tests/test-basic.R
RxODE/tests/test3.1.R
RxODE/tests/test3.2.R
RxODE/tests/test-parsing.R
RxODE/src
RxODE/src/Makefile
RxODE/src/install.libs.R
RxODE/src/ode
RxODE/src/ode/Makefile
RxODE/src/ode/opkda2.f
RxODE/src/ode/dlsoda.f
RxODE/src/ode/dop853.c
RxODE/src/ode/opkda1_abbr.f
RxODE/src/ode/dop853.h
RxODE/src/ode/vode.f
RxODE/src/Makefile.win
RxODE/src/dparser
RxODE/src/dparser/4calc.in
RxODE/src/dparser/util.c
RxODE/src/dparser/index.html
RxODE/src/dparser/orig-Makefile
RxODE/src/dparser/gram.h
RxODE/src/dparser/write_tables.c
RxODE/src/dparser/dparse_tables.h
RxODE/src/dparser/gramgram.h
RxODE/src/dparser/COPYRIGHT
RxODE/src/dparser/gram.c
RxODE/src/dparser/tests
RxODE/src/dparser/tests/g20.test.g.1
RxODE/src/dparser/tests/sample.test.g.12.check
RxODE/src/dparser/tests/g48.test.g.1
RxODE/src/dparser/tests/sample.test.g.16.check
RxODE/src/dparser/tests/g40.test.g.1.check
RxODE/src/dparser/tests/g44.test.g.1.check
RxODE/src/dparser/tests/g48.test.g
RxODE/src/dparser/tests/sample.test.g.10.check
RxODE/src/dparser/tests/g38.test.g.1.flags
RxODE/src/dparser/tests/sample.test.g.15.check
RxODE/src/dparser/tests/sample.test.g.33.check
RxODE/src/dparser/tests/sample.test.g.28
RxODE/src/dparser/tests/g47.test.g
RxODE/src/dparser/tests/sample.test.g.28.check
RxODE/src/dparser/tests/g29.test.g.1.check
RxODE/src/dparser/tests/g1.test.g.1.check
RxODE/src/dparser/tests/sample.test.g.13
RxODE/src/dparser/tests/g49.test.g.1
RxODE/src/dparser/tests/g51.test.g.1
RxODE/src/dparser/tests/g15.test.g.1
RxODE/src/dparser/tests/sample.test.g.1
RxODE/src/dparser/tests/utf8.test.g.1
RxODE/src/dparser/tests/g50.test.g
RxODE/src/dparser/tests/g11.test.g.3
RxODE/src/dparser/tests/g3.test.g
RxODE/src/dparser/tests/g45.test.g.1.check
RxODE/src/dparser/tests/g39.test.g.1
RxODE/src/dparser/tests/sample.test.g.20
RxODE/src/dparser/tests/python.test.g.1
RxODE/src/dparser/tests/sample.test.g.10
RxODE/src/dparser/tests/g23.test.g.1.check
RxODE/src/dparser/tests/g43.test.g.3
RxODE/src/dparser/tests/sample.test.g.32
RxODE/src/dparser/tests/g25.test.g.1
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RxODE/src/dparser/tests/sample.test.g.3
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RxODE/src/dparser/tests/g33.test.g.1
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RxODE/src/dparser/tests/g42.test.g.1
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RxODE/src/dparser/tests/sample.test.g.5
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RxODE/src/dparser/tests/g10.test.g.1
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RxODE/src/dparser/tests/g28.test.g
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RxODE/src/dparser/tests/g40.test.g
RxODE/src/dparser/tests/g18.test.g.1
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RxODE/src/dparser/tests/sample.test.g.21.check
RxODE/src/dparser/tests/g42.include.g
RxODE/src/dparser/tests/g7.test.g.2
RxODE/src/dparser/tests/g19.test.g.1.check
RxODE/src/dparser/tests/utf8.test.g.1.check
RxODE/src/dparser/tests/sample.test.g.8
RxODE/src/dparser/tests/g5.test.g
RxODE/src/dparser/tests/g47.test.g.1
RxODE/src/dparser/tests/g11.test.g.1.check
RxODE/src/dparser/tests/g33.test.g.1.check
RxODE/src/dparser/tests/g30.test.g.1.check
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RxODE/src/dparser/tests/g5.test.g.1.check
RxODE/src/dparser/tests/g5.test.g.1
RxODE/src/dparser/tests/g23.test.g.1
RxODE/src/dparser/tests/g2.test.g.1
RxODE/src/dparser/tests/sample.test.g.27.check
RxODE/src/dparser/tests/g35.test.g
RxODE/src/dparser/tests/g46.test.g
RxODE/src/dparser/tests/g27.test.g.1.check
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RxODE/src/dparser/tests/g25.test.g.1.check
RxODE/src/dparser/tests/sample.test.g.2
RxODE/src/dparser/tests/g33.test.g
RxODE/src/dparser/tests/sample.test.g.7
RxODE/src/dparser/tests/sample.test.g.9
RxODE/src/dparser/tests/g2.test.g.1.check
RxODE/src/dparser/tests/g47.test.g.1.check
RxODE/src/dparser/tests/sample.test.g.5.check
RxODE/src/dparser/tests/g34.test.g.1.check
RxODE/src/dparser/tests/g8.test.g
RxODE/src/dparser/tests/g29.test.g.1
RxODE/src/dparser/tests/sample.test.g.11
RxODE/src/dparser/tests/g1.test.g
RxODE/src/dparser/tests/g41.test.g
RxODE/src/dparser/tests/g9.test.g
RxODE/src/dparser/tests/g13.test.g.1.check
RxODE/src/dparser/tests/sample.test.g.25.check
RxODE/src/dparser/tests/sample.test.g.31.check
RxODE/src/dparser/tests/g38.test.g.flags
RxODE/src/dparser/tests/g17.test.g.1
RxODE/src/dparser/tests/sample.test.g.9.check
RxODE/src/dparser/tests/g25.test.g
RxODE/src/dparser/tests/g26.test.g.1.check
RxODE/src/dparser/tests/g43.test.g
RxODE/src/dparser/tests/sample.test.g.25
RxODE/src/dparser/tests/sample.test.g
RxODE/src/dparser/tests/g37.test.g
RxODE/src/dparser/tests/g35.test.g.1.check
RxODE/src/dparser/tests/g12.test.g.1.check
RxODE/src/dparser/tests/g43.test.g.1
RxODE/src/dparser/tests/sample.test.g.6
RxODE/src/dparser/tests/sample.test.g.16
RxODE/src/dparser/tests/sample.test.g.17.check
RxODE/src/dparser/tests/g43.test.g.2.check
RxODE/src/dparser/tests/g42.test.g
RxODE/src/dparser/tests/python.test.g.1.check
RxODE/src/dparser/tests/g9.test.g.1.check
RxODE/src/dparser/tests/sample.test.g.1.check
RxODE/src/dparser/tests/sample.test.g.29.check
RxODE/src/dparser/tests/g51.test.g.1.check
RxODE/src/dparser/tests/g7.test.g.2.check
RxODE/src/dparser/tests/ansic.test.g
RxODE/src/dparser/tests/g28.test.g.1.check
RxODE/src/dparser/tests/bnf.g.1
RxODE/src/dparser/tests/g14.test.g
RxODE/src/dparser/tests/sample.test.g.0.check
RxODE/src/dparser/tests/g18.test.g
RxODE/src/dparser/tests/g31.test.g.1.check
RxODE/src/dparser/tests/g4.test.g
RxODE/src/dparser/tests/g26.test.g.1
RxODE/src/dparser/tests/sample.test.g.26
RxODE/src/dparser/tests/sample.test.g.18
RxODE/src/dparser/tests/g32.test.g
RxODE/src/dparser/tests/g50.test.g.1
RxODE/src/dparser/tests/sample.test.g.19
RxODE/src/dparser/tests/sample.test.g.13.check
RxODE/src/dparser/tests/g13.test.g
RxODE/src/dparser/tests/g36.test.g.1
RxODE/src/dparser/tests/g3.test.g.1
RxODE/src/dparser/tests/g14.test.g.1.check
RxODE/src/dparser/tests/sample.test.g.15
RxODE/src/dparser/tests/sample.test.g.23.check
RxODE/src/dparser/tests/g6.test.g.1
RxODE/src/dparser/tests/g21.test.g.1.check
RxODE/src/dparser/tests/g17.test.g.1.check
RxODE/src/dparser/tests/g43.test.g.2
RxODE/src/dparser/tests/g21.test.g.1
RxODE/src/dparser/tests/python.test.g
RxODE/src/dparser/tests/g6.test.g.1.check
RxODE/src/dparser/tests/g50.test.g.1.check
RxODE/src/dparser/tests/g20.test.g.1.check
RxODE/src/dparser/tests/g23.test.g
RxODE/src/dparser/tests/g39.test.g.1.check
RxODE/src/dparser/tests/sample.test.g.19.check
RxODE/src/dparser/tests/g16.test.g.1
RxODE/src/dparser/tests/sample.test.g.24.check
RxODE/src/dparser/tests/g6.test.g
RxODE/src/dparser/tests/g28.test.g.1
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RxODE/src/dparser/tests/g32.test.g.1.check
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RxODE/src/dparser/tests/g38.test.g.1.check
RxODE/src/dparser/tests/g35.test.g.1
RxODE/src/dparser/tests/g24.test.g
RxODE/src/dparser/tests/g22.test.g.1
RxODE/src/dparser/tests/g16.test.g.1.check
RxODE/src/dparser/tests/g45.test.g.1
RxODE/src/dparser/tests/g8.test.g.1
RxODE/src/dparser/tests/sample.test.g.4
RxODE/src/dparser/tests/sample.test.g.33
RxODE/src/dparser/tests/g31.test.g.1
RxODE/src/dparser/tests/g27.test.g.1
RxODE/src/dparser/tests/g38.test.g.1
RxODE/src/dparser/tests/g13.test.g.1
RxODE/src/dparser/tests/g31.test.g
RxODE/src/dparser/tests/sample.test.g.14
RxODE/src/dparser/tests/sample.test.g.31
RxODE/src/dparser/tests/sample.test.g.7.check
RxODE/src/dparser/tests/ansic.test.g.2.check
RxODE/src/dparser/tests/g32.test.g.1
RxODE/src/dparser/tests/g37.test.g.1
RxODE/src/dparser/tests/g44.test.g
RxODE/src/dparser/tests/g9.test.g.1
RxODE/src/dparser/tests/g45.test.g
RxODE/src/dparser/tests/g7.test.g.1.check
RxODE/src/dparser/tests/ansic.test.g.1
RxODE/src/dparser/tests/g22.test.g
RxODE/src/dparser/tests/g43.test.g.1.check
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RxODE/src/dparser/tests/sample.test.g.18.check
RxODE/src/dparser/tests/g14.test.g.1
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RxODE/src/dparser/tests/g27.test.g
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RxODE/src/dparser/tests/g46.test.g.1
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RxODE/src/dparser/tests/g24.test.g.1
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RxODE/src/dparser/tests/sample.test.g.2.check
RxODE/src/dparser/tests/sample.test.g.11.check
RxODE/src/dparser/tests/g43.test.g.3.flags
RxODE/src/dparser/tests/sample.test.g.29
RxODE/src/dparser/tests/ansic.test.g.1.check
RxODE/src/dparser/read_binary.h
RxODE/src/dparser/verilog
RxODE/src/dparser/verilog/Makefile
RxODE/src/dparser/verilog/main.c
RxODE/src/dparser/verilog/ambig.c
RxODE/src/dparser/verilog/vparse.c
RxODE/src/dparser/verilog/verilog.g
RxODE/src/dparser/verilog/README
RxODE/src/dparser/verilog/verilog_tests
RxODE/src/dparser/verilog/vparse.h
RxODE/src/dparser/read_binary.c
RxODE/src/dparser/sample_parser.c
RxODE/src/dparser/baseline
RxODE/src/dparser/python
RxODE/src/dparser/python/dparser.i
RxODE/src/dparser/python/index.html
RxODE/src/dparser/python/swigpyrun.h
RxODE/src/dparser/python/tests
RxODE/src/dparser/python/tests/test4.py
RxODE/src/dparser/python/tests/test6.py
RxODE/src/dparser/python/tests/test5.py
RxODE/src/dparser/python/tests/test3.py
RxODE/src/dparser/python/tests/test.py
RxODE/src/dparser/python/tests/test2.py
RxODE/src/dparser/python/tests/test7.py
RxODE/src/dparser/python/pydparser.c
RxODE/src/dparser/python/pydparser.h
RxODE/src/dparser/python/README
RxODE/src/dparser/python/setup.py
RxODE/src/dparser/python/dparser.py
RxODE/src/dparser/python/make_tables.c
RxODE/src/dparser/python/dparser_wrap.c
RxODE/src/dparser/python/py_dparser_manual.html
RxODE/src/dparser/python/contrib
RxODE/src/dparser/python/contrib/dparserpy.el
RxODE/src/dparser/python/contrib/dparserpy-syntax_error.py
RxODE/src/dparser/python/dparser_swigc.py
RxODE/src/dparser/test_parser.c
RxODE/src/dparser/lex.h
RxODE/src/dparser/my.g
RxODE/src/dparser/scan.h
RxODE/src/dparser/sample.g
RxODE/src/dparser/D_BUILD_VERSION
RxODE/src/dparser/dsymtab.h
RxODE/src/dparser/arg.h
RxODE/src/dparser/Makefile.org
RxODE/src/dparser/symtab.c
RxODE/src/dparser/README
RxODE/src/dparser/arg.c
RxODE/src/dparser/make_dparser.c
RxODE/src/dparser/faq.html
RxODE/src/dparser/mkdparse.c
RxODE/src/dparser/lr.c
RxODE/src/dparser/4calc.g
RxODE/src/dparser/make_dparser.cat
RxODE/src/dparser/parser_tests
RxODE/src/dparser/parse.h
RxODE/src/dparser/make_dparser.1
RxODE/src/dparser/util.h
RxODE/src/dparser/scan.c
RxODE/src/dparser/lex.c
RxODE/src/dparser/d.h
RxODE/src/dparser/lr.h
RxODE/src/dparser/driver_parsetree.c
RxODE/src/dparser/manual.html
RxODE/src/dparser/grammar.g.c
RxODE/src/dparser/my.c
RxODE/src/dparser/mkdparse.h
RxODE/src/dparser/write_tables.h
RxODE/src/dparser/parse.c
RxODE/src/dparser/dparse_tree.c
RxODE/src/dparser/dparse.h
RxODE/src/dparser/grammar.g
RxODE/src/dparser/Makefile.new
RxODE/src/dparser/CHANGES
RxODE/src/dparser/version.c
RxODE/src/dparser/dparse_tree.h
RxODE/src/tran.c
RxODE/src/tran.g.d_parser.c
RxODE/NAMESPACE
RxODE/demo
RxODE/demo/demo1.R
RxODE/demo/00Index
RxODE/R
RxODE/R/genShinyApp.template.R
RxODE/R/RxODE.R
RxODE/R/eventTable.R
RxODE/vignettes
RxODE/vignettes/RxODE-intro.html
RxODE/vignettes/RxODE-syntax.html
RxODE/vignettes/Model_schematic_w500.png
RxODE/vignettes/RxODE-intro.Rmd
RxODE/vignettes/RxODE-syntax.Rmd
RxODE/MD5
RxODE/build
RxODE/build/vignette.rds
RxODE/DESCRIPTION
RxODE/man
RxODE/man/genShinyApp.template.Rd
RxODE/man/eventTable.Rd
RxODE/man/rx.initCmpMgr.Rd
RxODE/man/RxODE.Rd