ecohealthalliance/metaflu: Functions for Avian Influenza Metapopulation Simulation

Implements Hosseini et al (2050) avian influenza metapopulation model for use in the African Sustainable Livestock 2050 project.

Install the latest version of this package by entering the following in R:
install.packages("devtools")
library(devtools)
install_github("ecohealthalliance/metaflu")
Date of publicationNone
Maintainer
LicenseMIT + file LICENSE
Version0.1.0
https://github.com/noamross/metaflu

View on GitHub

Files

.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
LICENSE
LICENSE.md
NAMESPACE
R/RcppExports.R R/metaflu-package.R R/simulate.R R/summarizing_functions.R
README.Rmd
README.md
inst/deploy_pages.sh
inst/experiments/01-growth-initial.Rmd
inst/experiments/01-growth-initial.html
inst/experiments/01-growth-initial_cache/html/__packages
inst/experiments/01-growth-initial_cache/html/basic-run_fd5d548c471b2aeac2e39ee01f28c208.RData
inst/experiments/01-growth-initial_cache/html/basic-run_fd5d548c471b2aeac2e39ee01f28c208.rdb
inst/experiments/01-growth-initial_cache/html/basic-run_fd5d548c471b2aeac2e39ee01f28c208.rdx
inst/experiments/01-growth-initial_cache/html/growth-run_a4218776a85894f33a58622549985859.RData
inst/experiments/01-growth-initial_cache/html/growth-run_a4218776a85894f33a58622549985859.rdb
inst/experiments/01-growth-initial_cache/html/growth-run_a4218776a85894f33a58622549985859.rdx
inst/experiments/01-growth-initial_cache/html/network-setup_005d4f66f259c517129bd89b93d2a45b.RData
inst/experiments/01-growth-initial_cache/html/network-setup_005d4f66f259c517129bd89b93d2a45b.rdb
inst/experiments/01-growth-initial_cache/html/network-setup_005d4f66f259c517129bd89b93d2a45b.rdx
inst/experiments/01-growth-initial_cache/html/parameter-setup_23f7d29fd524baf4dda7613053e15de0.RData
inst/experiments/01-growth-initial_cache/html/parameter-setup_23f7d29fd524baf4dda7613053e15de0.rdb
inst/experiments/01-growth-initial_cache/html/parameter-setup_23f7d29fd524baf4dda7613053e15de0.rdx
inst/experiments/01-growth-initial_cache/html/patch-functions_2b8fc4e9a693b6a38cb78ee46fb5565c.RData
inst/experiments/01-growth-initial_cache/html/patch-functions_2b8fc4e9a693b6a38cb78ee46fb5565c.rdb
inst/experiments/01-growth-initial_cache/html/patch-functions_2b8fc4e9a693b6a38cb78ee46fb5565c.rdx
inst/experiments/01-growth-initial_cache/html/plots-basic_11a0e0809f39906219e79e5bcc537ed8.RData
inst/experiments/01-growth-initial_cache/html/plots-basic_11a0e0809f39906219e79e5bcc537ed8.rdb
inst/experiments/01-growth-initial_cache/html/plots-basic_11a0e0809f39906219e79e5bcc537ed8.rdx
inst/experiments/01-growth-initial_cache/html/plots-growth_ee9c724171ee93fe6d6cc59144732723.RData
inst/experiments/01-growth-initial_cache/html/plots-growth_ee9c724171ee93fe6d6cc59144732723.rdb
inst/experiments/01-growth-initial_cache/html/plots-growth_ee9c724171ee93fe6d6cc59144732723.rdx
inst/experiments/01-growth-initial_files/figure-html/plots-basic-1.png
inst/experiments/01-growth-initial_files/figure-html/plots-growth-1.png
inst/experiments/02-growth-non-linear.Rmd
inst/experiments/02-growth-non-linear.html
inst/experiments/02-growth-non-linear_cache/html/__packages
inst/experiments/02-growth-non-linear_cache/html/basic-run_1429014cc6124a82288705abc964bb44.RData
inst/experiments/02-growth-non-linear_cache/html/basic-run_1429014cc6124a82288705abc964bb44.rdb
inst/experiments/02-growth-non-linear_cache/html/basic-run_1429014cc6124a82288705abc964bb44.rdx
inst/experiments/02-growth-non-linear_cache/html/growth-run_0fada9212392d22b3626b6bff763a9b8.RData
inst/experiments/02-growth-non-linear_cache/html/growth-run_0fada9212392d22b3626b6bff763a9b8.rdb
inst/experiments/02-growth-non-linear_cache/html/growth-run_0fada9212392d22b3626b6bff763a9b8.rdx
inst/experiments/02-growth-non-linear_cache/html/network-setup_665cd51da76f22ed02fb79304f96bcc2.RData
inst/experiments/02-growth-non-linear_cache/html/network-setup_665cd51da76f22ed02fb79304f96bcc2.rdb
inst/experiments/02-growth-non-linear_cache/html/network-setup_665cd51da76f22ed02fb79304f96bcc2.rdx
inst/experiments/02-growth-non-linear_cache/html/parameter-setup_8296a98b68ce3818a7d956bae931adf9.RData
inst/experiments/02-growth-non-linear_cache/html/parameter-setup_8296a98b68ce3818a7d956bae931adf9.rdb
inst/experiments/02-growth-non-linear_cache/html/parameter-setup_8296a98b68ce3818a7d956bae931adf9.rdx
inst/experiments/02-growth-non-linear_cache/html/patch-functions_fe66afe2c87decb45f683a7504e702c8.RData
inst/experiments/02-growth-non-linear_cache/html/patch-functions_fe66afe2c87decb45f683a7504e702c8.rdb
inst/experiments/02-growth-non-linear_cache/html/patch-functions_fe66afe2c87decb45f683a7504e702c8.rdx
inst/experiments/02-growth-non-linear_cache/html/plots-basic_dfb6383d67e9d310059ca7ef4f3b04d1.RData
inst/experiments/02-growth-non-linear_cache/html/plots-basic_dfb6383d67e9d310059ca7ef4f3b04d1.rdb
inst/experiments/02-growth-non-linear_cache/html/plots-basic_dfb6383d67e9d310059ca7ef4f3b04d1.rdx
inst/experiments/02-growth-non-linear_cache/html/plots-growth_d9f2f245b61e3f5601675cd9e5ff3262.RData
inst/experiments/02-growth-non-linear_cache/html/plots-growth_d9f2f245b61e3f5601675cd9e5ff3262.rdb
inst/experiments/02-growth-non-linear_cache/html/plots-growth_d9f2f245b61e3f5601675cd9e5ff3262.rdx
inst/experiments/02-growth-non-linear_files/figure-html/plots-basic-1.png
inst/experiments/02-growth-non-linear_files/figure-html/plots-growth-1.png
inst/experiments/03-growth-clustered.Rmd
inst/experiments/03-growth-clustered.html
inst/experiments/03-growth-clustered_cache/html/__packages
inst/experiments/03-growth-clustered_cache/html/basic-run_8076c7b4f4bb7c4b420bccb7ba0f1bc6.RData
inst/experiments/03-growth-clustered_cache/html/basic-run_8076c7b4f4bb7c4b420bccb7ba0f1bc6.rdb
inst/experiments/03-growth-clustered_cache/html/basic-run_8076c7b4f4bb7c4b420bccb7ba0f1bc6.rdx
inst/experiments/03-growth-clustered_cache/html/growth-run_2260d4e51e08b2c7796726f9dae166e8.RData
inst/experiments/03-growth-clustered_cache/html/growth-run_2260d4e51e08b2c7796726f9dae166e8.rdb
inst/experiments/03-growth-clustered_cache/html/growth-run_2260d4e51e08b2c7796726f9dae166e8.rdx
inst/experiments/03-growth-clustered_cache/html/network-setup_090fa6d5132a2ab9c4ac9b3c1dc7f669.RData
inst/experiments/03-growth-clustered_cache/html/network-setup_090fa6d5132a2ab9c4ac9b3c1dc7f669.rdb
inst/experiments/03-growth-clustered_cache/html/network-setup_090fa6d5132a2ab9c4ac9b3c1dc7f669.rdx
inst/experiments/03-growth-clustered_cache/html/parameter-setup_27c1768c494425437f31bd7cab17942e.RData
inst/experiments/03-growth-clustered_cache/html/parameter-setup_27c1768c494425437f31bd7cab17942e.rdb
inst/experiments/03-growth-clustered_cache/html/parameter-setup_27c1768c494425437f31bd7cab17942e.rdx
inst/experiments/03-growth-clustered_cache/html/patch-functions_fb3f451b8d8b44b37917e2a20f9077e0.RData
inst/experiments/03-growth-clustered_cache/html/patch-functions_fb3f451b8d8b44b37917e2a20f9077e0.rdb
inst/experiments/03-growth-clustered_cache/html/patch-functions_fb3f451b8d8b44b37917e2a20f9077e0.rdx
inst/experiments/03-growth-clustered_cache/html/plots-basic_d3aa79a28140c4e8f3801a0d41d8aa3b.RData
inst/experiments/03-growth-clustered_cache/html/plots-basic_d3aa79a28140c4e8f3801a0d41d8aa3b.rdb
inst/experiments/03-growth-clustered_cache/html/plots-basic_d3aa79a28140c4e8f3801a0d41d8aa3b.rdx
inst/experiments/03-growth-clustered_cache/html/plots-growth_4847b39bc0c6b1df7515743ee880c33a.RData
inst/experiments/03-growth-clustered_cache/html/plots-growth_4847b39bc0c6b1df7515743ee880c33a.rdb
inst/experiments/03-growth-clustered_cache/html/plots-growth_4847b39bc0c6b1df7515743ee880c33a.rdx
inst/experiments/03-growth-clustered_files/figure-html/plots-basic-1.png
inst/experiments/03-growth-clustered_files/figure-html/plots-growth-1.png
inst/experiments/04-paired-networks.Rmd
inst/experiments/04-paired-networks.html
inst/experiments/05-external-infection.Rmd
inst/experiments/05-external-infection.html
inst/experiments/06-culling.Rmd
inst/experiments/06-culling.html
inst/experiments/07-delayed-culling.Rmd
inst/experiments/07-delayed-culling.html
inst/experiments/08-cull-time-analysis.Rmd
inst/experiments/doubling-initial_cache/html/__packages
inst/experiments/doubling-initial_cache/html/basic-run_3f243a00113f5c92d8d618a721e4f139.RData
inst/experiments/doubling-initial_cache/html/basic-run_3f243a00113f5c92d8d618a721e4f139.rdb
inst/experiments/doubling-initial_cache/html/basic-run_3f243a00113f5c92d8d618a721e4f139.rdx
inst/experiments/doubling-initial_cache/html/growth-run_245a723e1214e4555e149cd91a01093d.RData
inst/experiments/doubling-initial_cache/html/growth-run_245a723e1214e4555e149cd91a01093d.rdb
inst/experiments/doubling-initial_cache/html/growth-run_245a723e1214e4555e149cd91a01093d.rdx
inst/experiments/doubling-initial_cache/html/network-setup_d0022bcf7425e01d99306dd21ba6afef.RData
inst/experiments/doubling-initial_cache/html/network-setup_d0022bcf7425e01d99306dd21ba6afef.rdb
inst/experiments/doubling-initial_cache/html/network-setup_d0022bcf7425e01d99306dd21ba6afef.rdx
inst/experiments/doubling-initial_cache/html/parameter-setup_82a637b576b673625978acb8afe5b6d8.RData
inst/experiments/doubling-initial_cache/html/parameter-setup_82a637b576b673625978acb8afe5b6d8.rdb
inst/experiments/doubling-initial_cache/html/parameter-setup_82a637b576b673625978acb8afe5b6d8.rdx
inst/experiments/doubling-initial_cache/html/patch-functions_9baec858b4d834fc07600f9db315723d.RData
inst/experiments/doubling-initial_cache/html/patch-functions_9baec858b4d834fc07600f9db315723d.rdb
inst/experiments/doubling-initial_cache/html/patch-functions_9baec858b4d834fc07600f9db315723d.rdx
inst/experiments/doubling-initial_cache/html/plot-basic_a2edbbbe1460ca810946e393aa308c45.RData
inst/experiments/doubling-initial_cache/html/plot-basic_a2edbbbe1460ca810946e393aa308c45.rdb
inst/experiments/doubling-initial_cache/html/plot-basic_a2edbbbe1460ca810946e393aa308c45.rdx
inst/experiments/doubling-initial_cache/html/plot-growth_07f27e0c358c39ab397db8f5fa989b70.RData
inst/experiments/doubling-initial_cache/html/plot-growth_07f27e0c358c39ab397db8f5fa989b70.rdb
inst/experiments/doubling-initial_cache/html/plot-growth_07f27e0c358c39ab397db8f5fa989b70.rdx
inst/experiments/doubling-initial_cache/html/plots-basic_4b9ba09cd5fb631294362ce41aa60bae.RData
inst/experiments/doubling-initial_cache/html/plots-basic_4b9ba09cd5fb631294362ce41aa60bae.rdb
inst/experiments/doubling-initial_cache/html/plots-basic_4b9ba09cd5fb631294362ce41aa60bae.rdx
inst/experiments/doubling-initial_cache/html/plots-growth_0f717fc434cf055454a69b6794f405a6.RData
inst/experiments/doubling-initial_cache/html/plots-growth_0f717fc434cf055454a69b6794f405a6.rdb
inst/experiments/doubling-initial_cache/html/plots-growth_0f717fc434cf055454a69b6794f405a6.rdx
inst/experiments/explore_culling.R
inst/experiments/growth-non-linear_cache/html/__packages
inst/experiments/growth-non-linear_cache/html/basic-run_d3d6761123f5f1756221ce9ffffacc06.RData
inst/experiments/growth-non-linear_cache/html/basic-run_d3d6761123f5f1756221ce9ffffacc06.rdb
inst/experiments/growth-non-linear_cache/html/basic-run_d3d6761123f5f1756221ce9ffffacc06.rdx
inst/experiments/growth-non-linear_cache/html/growth-run_2da6addc755048c9c44bf0ca356f2412.RData
inst/experiments/growth-non-linear_cache/html/growth-run_2da6addc755048c9c44bf0ca356f2412.rdb
inst/experiments/growth-non-linear_cache/html/growth-run_2da6addc755048c9c44bf0ca356f2412.rdx
inst/experiments/growth-non-linear_cache/html/network-setup_cc08ee2440a0f2d6ded25cf2cceac0b0.RData
inst/experiments/growth-non-linear_cache/html/network-setup_cc08ee2440a0f2d6ded25cf2cceac0b0.rdb
inst/experiments/growth-non-linear_cache/html/network-setup_cc08ee2440a0f2d6ded25cf2cceac0b0.rdx
inst/experiments/growth-non-linear_cache/html/parameter-setup_b5b9d47f5ae286e99dbb7c7396cf340f.RData
inst/experiments/growth-non-linear_cache/html/parameter-setup_b5b9d47f5ae286e99dbb7c7396cf340f.rdb
inst/experiments/growth-non-linear_cache/html/parameter-setup_b5b9d47f5ae286e99dbb7c7396cf340f.rdx
inst/experiments/growth-non-linear_cache/html/patch-functions_9759d05c79caa6231f66eee491465419.RData
inst/experiments/growth-non-linear_cache/html/patch-functions_9759d05c79caa6231f66eee491465419.rdb
inst/experiments/growth-non-linear_cache/html/patch-functions_9759d05c79caa6231f66eee491465419.rdx
inst/experiments/growth-non-linear_cache/html/plots-basic_012e49e4cdad0e947151a1ba1aabc0a2.RData
inst/experiments/growth-non-linear_cache/html/plots-basic_012e49e4cdad0e947151a1ba1aabc0a2.rdb
inst/experiments/growth-non-linear_cache/html/plots-basic_012e49e4cdad0e947151a1ba1aabc0a2.rdx
inst/experiments/growth-non-linear_cache/html/plots-growth_cad47ef4ca06cfb307fef3e89b9b7a4f.RData
inst/experiments/growth-non-linear_cache/html/plots-growth_cad47ef4ca06cfb307fef3e89b9b7a4f.rdb
inst/experiments/growth-non-linear_cache/html/plots-growth_cad47ef4ca06cfb307fef3e89b9b7a4f.rdx
inst/experiments/outbreak-test.Rmd
inst/experiments/outbreak-test.html
inst/experiments/outbreak-test_cache/html/__packages
inst/experiments/outbreak-test_cache/html/basic-run_7659d6f1398fd0138025ccd75bf72420.RData
inst/experiments/outbreak-test_cache/html/basic-run_7659d6f1398fd0138025ccd75bf72420.rdb
inst/experiments/outbreak-test_cache/html/basic-run_7659d6f1398fd0138025ccd75bf72420.rdx
inst/experiments/outbreak-test_cache/html/growth-run_f8eb2c7d7253cc90c3d006b7312db978.RData
inst/experiments/outbreak-test_cache/html/growth-run_f8eb2c7d7253cc90c3d006b7312db978.rdb
inst/experiments/outbreak-test_cache/html/growth-run_f8eb2c7d7253cc90c3d006b7312db978.rdx
inst/experiments/outbreak-test_cache/html/network-setup_c4f4d909cee3388061ca4ce45e138cba.RData
inst/experiments/outbreak-test_cache/html/network-setup_c4f4d909cee3388061ca4ce45e138cba.rdb
inst/experiments/outbreak-test_cache/html/network-setup_c4f4d909cee3388061ca4ce45e138cba.rdx
inst/experiments/outbreak-test_cache/html/parameter-setup_3389f243fe6e2262d3e9cfa91a17f2fc.RData
inst/experiments/outbreak-test_cache/html/parameter-setup_3389f243fe6e2262d3e9cfa91a17f2fc.rdb
inst/experiments/outbreak-test_cache/html/parameter-setup_3389f243fe6e2262d3e9cfa91a17f2fc.rdx
inst/experiments/outbreak-test_cache/html/patch-functions_f253e47134bc05f0a47fa4353f33c4ce.RData
inst/experiments/outbreak-test_cache/html/patch-functions_f253e47134bc05f0a47fa4353f33c4ce.rdb
inst/experiments/outbreak-test_cache/html/patch-functions_f253e47134bc05f0a47fa4353f33c4ce.rdx
inst/experiments/outbreak-test_cache/html/plots-basic_b7892f19d76943ffc45f7ec5eda7ab43.RData
inst/experiments/outbreak-test_cache/html/plots-basic_b7892f19d76943ffc45f7ec5eda7ab43.rdb
inst/experiments/outbreak-test_cache/html/plots-basic_b7892f19d76943ffc45f7ec5eda7ab43.rdx
inst/experiments/outbreak-test_cache/html/plots-growth_f9be694ce0a9922114bbcef10906c8b1.RData
inst/experiments/outbreak-test_cache/html/plots-growth_f9be694ce0a9922114bbcef10906c8b1.rdb
inst/experiments/outbreak-test_cache/html/plots-growth_f9be694ce0a9922114bbcef10906c8b1.rdx
inst/experiments/outbreak-test_files/figure-html/plots-basic-1.png
inst/experiments/outbreak-test_files/figure-html/plots-growth-1.png
inst/make_network_plot.R man/metaflu.Rd man/mf_sim.Rd
metaflu.Rproj
src/.gitignore
src/RcppExports.cpp
src/data_structures.h
src/gillespie.cpp
src/includes.h
src/rates.h
tests/testthat.R
tests/testthat/stored_sim_results.rds
tests/testthat/test_culling.R tests/testthat/test_reproducibility.R
vignettes/.culling_research.Rmd.swp
vignettes/08-detect-culling.Rmd
vignettes/2016-10-08-design_notes.md
vignettes/2016-10-13-first-test.Rmd
vignettes/2016-12-01-figure-experiments.Rmd
vignettes/README.md
vignettes/culling_research.Rmd
vignettes/culling_research.html
vignettes/elsevier-with-titles.csl
vignettes/fig2results.rds
vignettes/growth-scenario.R
vignettes/models.Rmd
vignettes/models.html
vignettes/models.md
vignettes/notebook-template.Rmd
vignettes/notebook-template.html
vignettes/parameters.Rmd
vignettes/parameters.html
vignettes/parameters.md
vignettes/poultry_worker_risk.Rmd
vignettes/poultry_worker_risk.html
vignettes/poultry_worker_risk.md
vignettes/references.bib
vignettes/reproduce-paper.Rmd
vignettes/wild_bird_ecology.Rmd
vignettes/wild_bird_ecology.html
vignettes/wild_bird_ecology.md

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.