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| Package: GillespieSSA2 | ||
| Type: Package | ||
| Title: Gillespie's Stochastic Simulation Algorithm for Impatient People | ||
| Version: 0.2.4 | ||
| Authors@R: c( | ||
| person( | ||
| "Robrecht", | ||
| "Cannoodt", | ||
| email = "rcannood@gmail.com", | ||
| role = c("aut", "cre"), | ||
| comment = c(ORCID = "0000-0003-3641-729X") | ||
| ) | ||
| ) | ||
| Description: A fast, scalable, and versatile framework for simulating large | ||
| systems with Gillespie's Stochastic Simulation Algorithm ('SSA'). | ||
| This package is the spiritual successor to the 'GillespieSSA' package | ||
| originally written by Mario Pineda-Krch. Benefits of this package | ||
| include major speed improvements (>100x), easier to understand documentation, | ||
| and many unit tests that try to ensure the package works as intended. | ||
| License: GPL (>= 3) | ||
| LazyData: TRUE | ||
| Depends: R (>= 3.0) | ||
| Imports: assertthat, dplyr, dynutils, Matrix, methods, purrr, Rcpp (>= | ||
| 0.12.3), readr, rlang, stringr, tidyr | ||
| Suggests: ggplot2, GillespieSSA, knitr, rmarkdown, testthat (>= 2.1.0) | ||
| LinkingTo: Rcpp | ||
| VignetteBuilder: knitr | ||
| RoxygenNote: 6.1.1 | ||
| Encoding: UTF-8 | ||
| NeedsCompilation: yes | ||
| Packaged: 2019-08-05 14:21:48 UTC; rcannood | ||
| Author: Robrecht Cannoodt [aut, cre] (<https://orcid.org/0000-0003-3641-729X>) | ||
| Maintainer: Robrecht Cannoodt <rcannood@gmail.com> | ||
| Repository: CRAN | ||
| Date/Publication: 2019-08-05 16:20:02 UTC |
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| 191d22809821009d1f96c27c4e0c90aa *DESCRIPTION | ||
| 884b7995647e5e5882fe3011464a100c *NAMESPACE | ||
| 344f4c2a677a88d06a644c80f502739d *R/RcppExports.R | ||
| 923d2489eda49166bdd0cfd4b74286bb *R/compile_reactions.R | ||
| 8187cadc939326b491c14d43b5db902a *R/ode_em.R | ||
| 2258529f29949f8295fbd6511399efea *R/package.R | ||
| 29c88d8ada2ce642e79c72cd95c598d2 *R/port_reactions.R | ||
| 20e60bf0e3cbe5102622be377a595b99 *R/reaction.R | ||
| c21bd34e407b6fb9ea2b30394ae65d5a *R/ssa_btl.R | ||
| f795e74184f331a7f8b2c10da7c8ba2e *R/ssa_etl.R | ||
| b7b8f91d2169ae81380dc6a6688cb423 *R/ssa_exact.R | ||
| 22e74d4118b9cf37ecaf2fe701d7015a *R/ssa_method.R | ||
| 19df42238b05fa2def48090062960dd9 *R/ssa_plot.R | ||
| 57de42552ac338979f9b272a04443de7 *R/ssa_simulation.R | ||
| acbf8be5ab92cc08b9c202088cbcab07 *R/zzz.R | ||
| 89e541d0bb325872128159c1451a6104 *README.md | ||
| e94abedc8576c708a265d455f0cd4228 *build/partial.rdb | ||
| 49decf5be23809b1d5abb3daa8a47c22 *build/vignette.rds | ||
| a5a42033585d4d7e7fb6a395bc0553bc *inst/NEWS | ||
| b04418b0496196c4010578ea3aa0e176 *inst/NEWS.md | ||
| c407323c01d4cb29a0912d25439cb66f *inst/doc/an_introduction.R | ||
| 2e880d98e5cfe831cfb9509005ebd6bd *inst/doc/an_introduction.Rmd | ||
| 6213c5e6991969d791f4e2c5cf2699b1 *inst/doc/an_introduction.html | ||
| 057aef922cfb277ecd4852a3064edff3 *inst/doc/converting_from_GillespieSSA.R | ||
| cd92c2357999e9fa000834f2bf159aa0 *inst/doc/converting_from_GillespieSSA.Rmd | ||
| adedb2b75ce1b608daec3d281d51e321 *inst/doc/converting_from_GillespieSSA.html | ||
| 7346ce9627be9c43cc417f6f4dcb5f97 *inst/doc/decaying_dimer.R | ||
| bc2936c466cd068dd2a19585878fd133 *inst/doc/decaying_dimer.Rmd | ||
| 9a7ca6f895d096808cf17b4fa495fb89 *inst/doc/decaying_dimer.html | ||
| 4792a0ea62b530ca2964f6ee6d2717fb *inst/doc/epi_chain.R | ||
| afec1c7d4d4604ab05532bfa4f915592 *inst/doc/epi_chain.Rmd | ||
| bbb7a13c706915b745316a98b162296e *inst/doc/epi_chain.html | ||
| 0493c7e0abbeb5444b40266223dd3401 *inst/doc/linear_chain.R | ||
| 2d52d621734b6049cb2329bc2ca87681 *inst/doc/linear_chain.Rmd | ||
| aaa8a86b0f0006b24bc68597a002f895 *inst/doc/linear_chain.html | ||
| bba0b2ecc5cbd5a6e18b01bb984298e7 *inst/doc/logistic_growth.R | ||
| effb05388f34ff7e3e44528d816e99d4 *inst/doc/logistic_growth.Rmd | ||
| 91980f913149c2e8ab502a7f91d3efed *inst/doc/logistic_growth.html | ||
| 7bd92f48fdf2d443871b27ebb7dba577 *inst/doc/lotka_predator_prey.R | ||
| 1f11dc84adfe1275ddccedd70499c9d8 *inst/doc/lotka_predator_prey.Rmd | ||
| 3cb025155813d83f2ba59a74b335b30b *inst/doc/lotka_predator_prey.html | ||
| eef3750b1060f35e41c5033e04b408ee *inst/doc/radioactive_decay.R | ||
| d942088d72be1c22c1a69ed91d2b2fc6 *inst/doc/radioactive_decay.Rmd | ||
| 0c0a579c2cc94995d5d5fe6bffd770bb *inst/doc/radioactive_decay.html | ||
| d018e124f94236384709b2a435ac8208 *inst/doc/rm_predator_prey.R | ||
| 4b2aab709a1d040e68976c1ab154b20d *inst/doc/rm_predator_prey.Rmd | ||
| 11c59447672d1ceef0ebf68a263d1abc *inst/doc/rm_predator_prey.html | ||
| 94ab5b395ecb972e2550c6ea542a563d *inst/doc/sir.R | ||
| 6d7c039d97e12d246b67e02b4b186ef3 *inst/doc/sir.Rmd | ||
| 932d828fe4b36ddc1a06b251a97bcc2c *inst/doc/sir.html | ||
| 885656c8fdf1ba13aede0673c30a019c *man/GillespieSSA2.Rd | ||
| 1de755ee9b886a3dbb8330cd00808603 *man/autoplot.ssa.Rd | ||
| 0f73e5544604b26d5333992f28745472 *man/compile_reactions.Rd | ||
| fd4c47d761c9f639c188d297da449d64 *man/figures/dependencies.png | ||
| 47b54f1c878c06fc218c268b82d13ef4 *man/ode_em.Rd | ||
| c0210cda6bede49cfe3187de64b0563b *man/port_reactions.Rd | ||
| d25d966dbf3fed048815f86e37d149e1 *man/print_ssa.Rd | ||
| 7f5d1b74229be68010f7b88b1ae41ae9 *man/reaction.Rd | ||
| 1521290994d19e02cadd0a409702e598 *man/ssa.Rd | ||
| 032520bc72e0f9ca30b91dbdea4c414c *man/ssa_btl.Rd | ||
| 36b134ba50341247c4f15abc0328e0a1 *man/ssa_etl.Rd | ||
| ca1bc07dc11c6a0af5bdec024514398a *man/ssa_exact.Rd | ||
| 952211738b7fdb7459ba8be08513b543 *src/RcppExports.cpp | ||
| 19b51f2f7daeb0a4f71a053cadb53a42 *src/ode_em.cpp | ||
| 9e1d45a2fe4d7c5632cf4c333f90e1ef *src/ssa_btl.cpp | ||
| 22d3daae3990928fce6fffbb657a1396 *src/ssa_etl.cpp | ||
| 3b960fed578440c1e0bd9013ee0ec7e5 *src/ssa_exact.cpp | ||
| b461dd928b90cb3c7ad01db3c01e7869 *src/ssa_method.cpp | ||
| ecab019f3b376fe4149f3425293c4016 *src/ssa_method.h | ||
| f1210d19d1f247c1370cddaf6654dd3a *src/ssa_simulation.cpp | ||
| d9da71bc3aae5d5795002c21aaa03d9c *src/test_helper_funs.cpp | ||
| 519f20d4b66bf43e926da24ee495c7bf *src/utils.cpp | ||
| bde4cd198553f4f2f2bb64ade0b2f79e *src/utils.h | ||
| 1f805c4be7c74e9df39994f09c36fa25 *tests/testthat.R | ||
| 6736703cf1e7eb6d5149f0547e6ae31e *tests/testthat/helper-test_propensity.R | ||
| 3f38c64eff5561aafca0ad2172b8874e *tests/testthat/helper-test_ssa_step.R | ||
| 9598bac6aa535675370ee8e7fabeb5fe *tests/testthat/test-compile_reactions.R | ||
| abb0748b010db2641b963047e151e6dc *tests/testthat/test-ode_em.R | ||
| ed1ac27aaa28558d05f8ba4ee2327c4e *tests/testthat/test-reaction.R | ||
| ccd175ee8cdc55dd8d20576058ecbc45 *tests/testthat/test-ssa.R | ||
| 9bf4dc603912d1257df777b56624f433 *tests/testthat/test-ssa_btl.R | ||
| 36fc2bb46a63705dfb136b951eea2c6f *tests/testthat/test-ssa_etl.R | ||
| 95e9d9020887f6a76fcf9cf6471f3667 *tests/testthat/test-ssa_exact.R | ||
| 2e880d98e5cfe831cfb9509005ebd6bd *vignettes/an_introduction.Rmd | ||
| cd92c2357999e9fa000834f2bf159aa0 *vignettes/converting_from_GillespieSSA.Rmd | ||
| bc2936c466cd068dd2a19585878fd133 *vignettes/decaying_dimer.Rmd | ||
| afec1c7d4d4604ab05532bfa4f915592 *vignettes/epi_chain.Rmd | ||
| 2d52d621734b6049cb2329bc2ca87681 *vignettes/linear_chain.Rmd | ||
| effb05388f34ff7e3e44528d816e99d4 *vignettes/logistic_growth.Rmd | ||
| 1f11dc84adfe1275ddccedd70499c9d8 *vignettes/lotka_predator_prey.Rmd | ||
| d942088d72be1c22c1a69ed91d2b2fc6 *vignettes/radioactive_decay.Rmd | ||
| 4b2aab709a1d040e68976c1ab154b20d *vignettes/rm_predator_prey.Rmd | ||
| 6d7c039d97e12d246b67e02b4b186ef3 *vignettes/sir.Rmd |
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| # Generated by roxygen2: do not edit by hand | ||
|
|
||
| S3method(print,SSA_method) | ||
| S3method(print,SSA_reaction) | ||
| export(autoplot.ssa) | ||
| export(compile_reactions) | ||
| export(ode_em) | ||
| export(port_reactions) | ||
| export(reaction) | ||
| export(ssa) | ||
| export(ssa_btl) | ||
| export(ssa_etl) | ||
| export(ssa_exact) | ||
| importFrom(Matrix,Matrix) | ||
| importFrom(Rcpp,cpp_object_initializer) | ||
| importFrom(Rcpp,loadModule) | ||
| importFrom(Rcpp,sourceCpp) | ||
| importFrom(assertthat,assert_that) | ||
| importFrom(dplyr,bind_rows) | ||
| importFrom(dplyr,first) | ||
| importFrom(dplyr,last) | ||
| importFrom(dplyr,mutate) | ||
| importFrom(dynutils,"%all_in%") | ||
| importFrom(dynutils,inherit_default_params) | ||
| importFrom(dynutils,is_sparse) | ||
| importFrom(dynutils,safe_tempdir) | ||
| importFrom(methods,is) | ||
| importFrom(methods,new) | ||
| importFrom(purrr,"%>%") | ||
| importFrom(purrr,discard) | ||
| importFrom(purrr,is_scalar_character) | ||
| importFrom(purrr,is_scalar_double) | ||
| importFrom(purrr,is_scalar_integer) | ||
| importFrom(purrr,is_scalar_logical) | ||
| importFrom(purrr,keep) | ||
| importFrom(purrr,map) | ||
| importFrom(purrr,map_chr) | ||
| importFrom(purrr,map_df) | ||
| importFrom(purrr,map_int) | ||
| importFrom(purrr,set_names) | ||
| importFrom(purrr,walk) | ||
| importFrom(readr,write_lines) | ||
| importFrom(rlang,is_formula) | ||
| importFrom(rlang,is_integerish) | ||
| importFrom(stringr,str_count) | ||
| importFrom(stringr,str_extract_all) | ||
| importFrom(stringr,str_replace) | ||
| importFrom(stringr,str_replace_all) | ||
| importFrom(stringr,str_split) | ||
| importFrom(tidyr,gather) | ||
| useDynLib(GillespieSSA2) |
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|---|---|---|
| @@ -0,0 +1,27 @@ | ||
| # Generated by using Rcpp::compileAttributes() -> do not edit by hand | ||
| # Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393 | ||
|
|
||
| make_ode_em <- function(tau, noise_strength) { | ||
| .Call('_GillespieSSA2_make_ode_em', PACKAGE = 'GillespieSSA2', tau, noise_strength) | ||
| } | ||
|
|
||
| make_ssa_btl <- function(mean_firings) { | ||
| .Call('_GillespieSSA2_make_ssa_btl', PACKAGE = 'GillespieSSA2', mean_firings) | ||
| } | ||
|
|
||
| make_ssa_etl <- function(tau) { | ||
| .Call('_GillespieSSA2_make_ssa_etl', PACKAGE = 'GillespieSSA2', tau) | ||
| } | ||
|
|
||
| make_ssa_exact <- function() { | ||
| .Call('_GillespieSSA2_make_ssa_exact', PACKAGE = 'GillespieSSA2') | ||
| } | ||
|
|
||
| test_ssa_method_cpp <- function(ssa_alg, state, propensity, nu_i, nu_p, nu_x) { | ||
| .Call('_GillespieSSA2_test_ssa_method_cpp', PACKAGE = 'GillespieSSA2', ssa_alg, state, propensity, nu_i, nu_p, nu_x) | ||
| } | ||
|
|
||
| test_propensity_cpp <- function(num_functions, propensity_funs, params, buffer_size, propensity_size, state, sim_time) { | ||
| .Call('_GillespieSSA2_test_propensity_cpp', PACKAGE = 'GillespieSSA2', num_functions, propensity_funs, params, buffer_size, propensity_size, state, sim_time) | ||
| } | ||
|
|
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