Files in slequime/nosoi
A Forward Agent-Based Transmission Chain Simulator
.Rbuildignore
.dockerignore
.github/.gitignore
.github/workflows/R-CMD-check-no-force-suggest.yaml
.github/workflows/R-CMD-check.yaml
.github/workflows/test-coverage.yaml
.gitignore
.travis.yml
DESCRIPTION
LICENSE
NAMESPACE
NEWS.md
R/.DS_Store
R/.Rapp.history
R/dual-continuous.R
R/dual-discrete.R
R/dual-none.R
R/nosoiSim.R
R/nosoi_sanityChecks-Messages.R
R/nosoi_step1-makeMoves.R
R/nosoi_step2-MeetTransmit.R
R/nosoi_tablesManagment.R
R/nosoi_utilityFunctions.R
R/output_nosoiSummary.R
R/output_treeGenerator.r
R/output_utilityFunctions.R
R/single-continuous.R
R/single-discrete.R
R/single-none.R
README.md
_pkgdown.yml
cran-comments.md
docs/404.html
docs/LICENSE-text.html
docs/_config.yml
docs/_pkgdown.yml
docs/apple-touch-icon-120x120.png
docs/apple-touch-icon-152x152.png
docs/apple-touch-icon-180x180.png
docs/apple-touch-icon-60x60.png
docs/apple-touch-icon-76x76.png
docs/apple-touch-icon.png
docs/articles/continuous.html
docs/articles/continuous_files/figure-html/RW-1-1.png
docs/articles/continuous_files/figure-html/RasterCode2-1.png
docs/articles/continuous_files/figure-html/nContact2-1.png
docs/articles/continuous_files/figure-html/nContact2.B-1.png
docs/articles/continuous_files/figure-html/pExit2-1.png
docs/articles/continuous_files/figure-html/pExit2-dual-1.png
docs/articles/continuous_files/figure-html/pTrans3-1.png
docs/articles/continuous_files/figure-html/pTrans3.B-1.png
docs/articles/discrete.html
docs/articles/discrete_files/figure-html/nContact2-1.png
docs/articles/discrete_files/figure-html/nContact2.B-1.png
docs/articles/discrete_files/figure-html/pExit2-dual-1.png
docs/articles/discrete_files/figure-html/pTrans3-1.png
docs/articles/discrete_files/figure-html/pTrans3.B-1.png
docs/articles/discrete_files/figure-html/setupMatrix-1.png
docs/articles/examples/Africa_pop_2015.tif.zip
docs/articles/examples/dengue.html
docs/articles/examples/dengue_files/figure-html/air1-1.png
docs/articles/examples/dengue_files/figure-html/air2-1.png
docs/articles/examples/dengue_files/figure-html/air4-1.png
docs/articles/examples/dengue_files/figure-html/avgTemp2-1.png
docs/articles/examples/dengue_files/figure-html/avgTemp3-1.png
docs/articles/examples/dengue_files/figure-html/avgTemp5-1.png
docs/articles/examples/dengue_files/figure-html/figureDynamics1-1.png
docs/articles/examples/dengue_files/figure-html/figureDynamics2-1.png
docs/articles/examples/dengue_files/figure-html/generalEpi2-1.png
docs/articles/examples/dengue_files/figure-html/generalEpi3-1.png
docs/articles/examples/dengue_files/figure-html/pTrans3-1.png
docs/articles/examples/dengue_files/figure-html/treeC-1.png
docs/articles/examples/dengue_files/figure-html/treeC2-1.png
docs/articles/examples/dengue_files/figure-html/visualisationMatrix-1.gif
docs/articles/examples/dengue_files/header-attrs-2.7/header-attrs.js
docs/articles/examples/ebola-like.gif
docs/articles/examples/ebola.html
docs/articles/examples/ebola_files/figure-html/cumulativeDynamics-1.png
docs/articles/examples/ebola_files/figure-html/cumulativeDynamics-2.png
docs/articles/examples/ebola_files/figure-html/generalEpi3-1.png
docs/articles/examples/ebola_files/figure-html/importRaster-1.png
docs/articles/examples/ebola_files/figure-html/sdMove2-1.png
docs/articles/examples/ebola_files/figure-html/tincubDemo-1.png
docs/articles/examples/ebola_files/figure-html/transmissionTree-Full2-1.png
docs/articles/examples/ebola_files/figure-html/transmissionTree-Full3-1.png
docs/articles/examples/ebola_files/figure-html/treeC-1.png
docs/articles/examples/ebola_files/figure-html/treeC2-1.png
docs/articles/examples/ebola_files/header-attrs-2.7/header-attrs.js
docs/articles/examples/transmission-nosoi.mp4
docs/articles/examples/vector-competence.html
docs/articles/examples/vector-competence_files/figure-html/Output1-1.png
docs/articles/examples/vector-competence_files/figure-html/nContact2-1.png
docs/articles/examples/vector-competence_files/figure-html/pTrans.B-1.png
docs/articles/examples/vector-competence_files/figure-html/pTrans3-1.png
docs/articles/examples/vector-competence_files/figure-html/popDemo-1.png
docs/articles/examples/vector-competence_files/header-attrs-2.7/header-attrs.js
docs/articles/examples/viz.html
docs/articles/examples/viz_files/figure-html/plotcontinuous-1.png
docs/articles/examples/viz_files/figure-html/plotcontinuous2-1.gif
docs/articles/examples/viz_files/figure-html/treeA-1.png
docs/articles/examples/viz_files/figure-html/visualisation-1.png
docs/articles/examples/viz_files/figure-html/visualisation1-1.png
docs/articles/examples/viz_files/figure-html/visualisationMatrix-1.gif
docs/articles/examples/viz_files/figure-html/visualisationMatrix2-1.gif
docs/articles/examples/viz_files/header-attrs-2.7/header-attrs.js
docs/articles/examples/viz_stat.html
docs/articles/index.html
docs/articles/none.html
docs/articles/none_files/figure-html/nContact2-1.png
docs/articles/none_files/figure-html/nContact2.B-1.png
docs/articles/none_files/figure-html/pExit2-dual-1.png
docs/articles/none_files/figure-html/pTrans3-1.png
docs/articles/none_files/figure-html/pTrans3.B-1.png
docs/articles/nosoi.html
docs/articles/nosoi_files/figure-html/setupMatrix-1.png
docs/articles/output.html
docs/articles/output_files/figure-html/figureDynamics-1.png
docs/articles/output_files/figure-html/figureDynamics-2.png
docs/articles/output_files/figure-html/figureDynamics1-1.png
docs/articles/output_files/figure-html/figureDynamics1_actual-1.png
docs/articles/output_files/figure-html/figureDynamics2-1.png
docs/articles/output_files/figure-html/figureDynamics2_actual-1.png
docs/articles/output_files/figure-html/figureR0-1.png
docs/articles/output_files/figure-html/figureR0_actual-1.png
docs/articles/output_files/figure-html/treeA-1.png
docs/articles/output_files/figure-html/treeA_actual-1.png
docs/articles/output_files/figure-html/treeB-1.png
docs/articles/output_files/figure-html/treeB_actual-1.png
docs/articles/output_files/figure-html/treeC-1.png
docs/articles/output_files/figure-html/treeC_actual-1.png
docs/authors.html
docs/docsearch.css
docs/docsearch.js
docs/favicon-16x16.png
docs/favicon-32x32.png
docs/favicon.ico
docs/index.html
docs/link.svg
docs/logo.png
docs/logo.svg
docs/news/index.html
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/CoreSanityChecks.html
docs/reference/FunctionSanityChecks.html
docs/reference/MatrixSanityChecks.html
docs/reference/RasterSanityChecks.html
docs/reference/SingleNone.html
docs/reference/add_node_tip.html
docs/reference/applyFunctionToHosts.html
docs/reference/cumulativeInfected.html
docs/reference/drawBernouilli.html
docs/reference/dualContinuous.html
docs/reference/dualDiscrete.html
docs/reference/dualNone.html
docs/reference/endMessage.html
docs/reference/figures/logo.png
docs/reference/figures/logo.svg
docs/reference/getCumulative.html
docs/reference/getDynamic.html
docs/reference/getExitingMoving.html
docs/reference/getHostData.html
docs/reference/getHostInfo.html
docs/reference/getPositionInfected.html
docs/reference/getR0.html
docs/reference/getTableHosts.html
docs/reference/getTableState.html
docs/reference/getTransmissionTree-1.png
docs/reference/getTransmissionTree-2.png
docs/reference/getTransmissionTree-3.png
docs/reference/getTransmissionTree.html
docs/reference/get_node.html
docs/reference/get_other_count.html
docs/reference/get_position.html
docs/reference/get_state.html
docs/reference/index.html
docs/reference/iniTable.html
docs/reference/iniTableState.html
docs/reference/keep.tip.treedata.html
docs/reference/keepState.html
docs/reference/makeMoves.html
docs/reference/meetTransmit.html
docs/reference/merge_host_tables.html
docs/reference/moveFunction.continuous.html
docs/reference/moveFunction.discrete.html
docs/reference/moveFunction.singleContinuous.html
docs/reference/moveFunction.singleDiscrete.html
docs/reference/moveRotateContinuous.html
docs/reference/newLine.html
docs/reference/newLineState.html
docs/reference/nosoiSim.html
docs/reference/nosoiSimConstructor.html
docs/reference/nosoiSimOneConstructor.html
docs/reference/nosoiSummary.html
docs/reference/numberInfected.html
docs/reference/numberInfectedBGW.html
docs/reference/numberInfectedStates.html
docs/reference/outputWrapper.html
docs/reference/paramConstructor.html
docs/reference/parseFunction.html
docs/reference/progressMessage.html
docs/reference/sampleTransmissionTree-1.png
docs/reference/sampleTransmissionTree-2.png
docs/reference/sampleTransmissionTree-3.png
docs/reference/sampleTransmissionTree.html
docs/reference/sampleTransmissionTreeFromExiting-1.png
docs/reference/sampleTransmissionTreeFromExiting-2.png
docs/reference/sampleTransmissionTreeFromExiting-3.png
docs/reference/sampleTransmissionTreeFromExiting.html
docs/reference/sampleTransmissionTreeFromTheDead.html
docs/reference/singleContinuous-1.png
docs/reference/singleContinuous.html
docs/reference/singleDiscrete.html
docs/reference/updateHostCount.html
docs/reference/updateTableState.html
docs/reference/writeInfected.html
inst/CITATION
inst/WORDLIST
man/.DS_Store
man/CoreSanityChecks.Rd
man/FunctionSanityChecks.Rd
man/MatrixSanityChecks.Rd
man/RasterSanityChecks.Rd
man/SingleNone.Rd
man/add_node_tip.Rd
man/applyFunctionToHosts.Rd
man/cumulativeInfected.Rd
man/drawBernouilli.Rd
man/dualContinuous.Rd
man/dualDiscrete.Rd
man/dualNone.Rd
man/endMessage.Rd
man/figures/logo.png
man/getCumulative.Rd
man/getDynamic.Rd
man/getExitingMoving.Rd
man/getHostData.Rd
man/getPositionInfected.Rd
man/getR0.Rd
man/getTableHosts.Rd
man/getTableState.Rd
man/getTransmissionTree.Rd
man/get_node.Rd
man/get_other_count.Rd
man/get_position.Rd
man/get_state.Rd
man/iniTable.Rd
man/iniTableState.Rd
man/keep.tip.treedata.Rd
man/keepState.Rd
man/makeMoves.Rd
man/meetTransmit.Rd
man/merge_host_tables.Rd
man/moveFunction.continuous.Rd
man/moveFunction.discrete.Rd
man/moveRotateContinuous.Rd
man/newLine.Rd
man/newLineState.Rd
man/nosoiSim.Rd
man/nosoiSimConstructor.Rd
man/nosoiSimOneConstructor.Rd
man/nosoiSummary.Rd
man/numberInfected.Rd
man/numberInfectedBGW.Rd
man/numberInfectedStates.Rd
man/paramConstructor.Rd
man/parseFunction.Rd
man/progressMessage.Rd
man/sampleTransmissionTree.Rd
man/sampleTransmissionTreeFromExiting.Rd
man/singleContinuous.Rd
man/singleDiscrete.Rd
man/updateHostCount.Rd
man/updateTableState.Rd
man/writeInfected.Rd
nosoi.Rproj
pkgdown/favicon/apple-touch-icon-120x120.png
pkgdown/favicon/apple-touch-icon-152x152.png
pkgdown/favicon/apple-touch-icon-180x180.png
pkgdown/favicon/apple-touch-icon-60x60.png
pkgdown/favicon/apple-touch-icon-76x76.png
pkgdown/favicon/apple-touch-icon.png
pkgdown/favicon/favicon-16x16.png
pkgdown/favicon/favicon-32x32.png
pkgdown/favicon/favicon.ico
tests/manual/BGW.R
tests/manual/readme.md
tests/testthat.R
tests/testthat/testDualContinuous.R
tests/testthat/testDualDiscrete.R
tests/testthat/testDualNone.R
tests/testthat/testErrors.R
tests/testthat/testParsing.R
tests/testthat/testSingleContinuous.R
tests/testthat/testSingleDiscrete.R
tests/testthat/testSingleNone.R
tests/testthat/testTransmissionTree.R
vignettes/.gitignore
vignettes/continuous.Rmd
vignettes/discrete.Rmd
vignettes/examples/avgTemp_data.csv
vignettes/examples/country_code.csv
vignettes/examples/dengue.Rmd
vignettes/examples/ebola.Rmd
vignettes/examples/transmission-nosoi.mp4
vignettes/examples/vector-competence.Rmd
vignettes/examples/viz.Rmd
vignettes/none.Rmd
vignettes/nosoi.Rmd
vignettes/output.Rmd
