Files in skgallagher/TBornotTB
Analyze Tuberculosis Patients in Maryland
.RData
.Rbuildignore
.Rhistory
.Rinstignore
.Rproj.user/C501EB0B/console06/INDEX001
.Rproj.user/C501EB0B/cpp-definition-cache
.Rproj.user/C501EB0B/pcs/debug-breakpoints.pper
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.Rproj.user/C501EB0B/persistent-state
.Rproj.user/C501EB0B/rmd-outputs
.Rproj.user/C501EB0B/saved_source_markers
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.Rproj.user/C501EB0B/sources/prop/INDEX
.Rproj.user/shared/notebooks/patch-chunk-names
.Rproj.user/shared/notebooks/paths
.gitignore
.travis.yml
DESCRIPTION
LICENSE
LICENSE.md
NAMESPACE
R/#loglike-faster2.R#
R/RcppExports.R
R/TBornotTB-package.R
R/impute-root.R
R/impute-root.R~
R/likelihood-outside.R
R/likelihood-outside.R~
R/likelihood-sampler.R
R/likelihood-sampler.R~
R/likelihood.R
R/loglike-doubly-trunc.R
R/loglike-faster2.R
R/loglike_faster.R
R/partitions.R
R/sample-trees-fast.R
R/sample-trees-many-index-cases.R
R/simulate-branching-process.R
R/simulate-conditional-bp.R
R/simulate-flip-til-failure.R
R/simulate_outbreak.R
R/summarize-uniform-trees.R
R/table-data.R
R/table-weights.R
R/tree-sampler-with-outside-gen.R
R/utils-pipe.R
R/weighted-sampling.R
README.md
TBornotTB.Rproj
data-raw/DATASET.R
data-raw/TBdataset-clean.csv
data-raw/TBdataset.xlsx
data-raw/zcta_county_rel_10.txt
data/clusts_tb.rda
data/idistrib1e4.rda
data/tb_clean.rda
inst/cointack2.R
inst/data/i_distrib_tables-1000.RDS
inst/data/i_distrib_tables-10000.RDS
inst/paper_eda/duration-size.pdf
inst/paper_eda/eda.R
inst/paper_eda/hiv-smear.pdf
inst/rstan/poisson-stan.R
inst/rstan/poisson.rds
inst/rstan/poisson.stan
inst/rstan/test-rstan.R
inst/rstan/test.stan
inst/tree_sampling/#outside-v2.R#
inst/tree_sampling/compare-tree-sampling-methods.R
inst/tree_sampling/i-distrib-tables.R
inst/tree_sampling/likelihood-multi-roots.R
inst/tree_sampling/likelihood-multi-roots.R~
inst/tree_sampling/outside-v2.R
inst/tree_sampling/outside-v2.R~
inst/tree_sampling/outside_sim.RDS
inst/tree_sampling/part-sampling.R
inst/tree_sampling/tree-sample-test-many-roots.R
inst/tree_sampling/tree-sample-test.R
inst/tree_sampling/tree-sample-test2.R
inst/tree_sampling/tree-sample-test3.R
inst/tree_sampling/tree-sample-test4.R
inst/tree_sampling/tree_report.Rmd
inst/tree_sampling/tree_report.log
inst/tree_sampling/tree_report.pdf
man/assign_infector.Rd
man/assign_smear.Rd
man/cluster_like_smear.Rd
man/count_infections.Rd
man/draw_n_gen.Rd
man/draw_part.Rd
man/draw_part_from_list.Rd
man/flip_til_failure.Rd
man/format_to_outsider.Rd
man/generate_part_list.Rd
man/generate_parts.Rd
man/generation_infection.Rd
man/get_i.Rd
man/get_weight_list.Rd
man/get_weights_from_table.Rd
man/idistrib1e4.Rd
man/impute_root.Rd
man/impute_root_inner.Rd
man/iter_est_ws.Rd
man/like_sampled_cond.Rd
man/likelihood_weighted.Rd
man/loglike_all_clusts.Rd
man/loglike_clust_cond.Rd
man/loglike_cluster_summary.Rd
man/loglike_cond_fast.Rd
man/loglike_fast.Rd
man/loglike_obs_data.Rd
man/loglike_weighted_total.Rd
man/move_up_gen.Rd
man/part_to_cluster.Rd
man/pipe.Rd
man/prob_trans.Rd
man/sample_connections.Rd
man/sample_i.Rd
man/sample_tree_perm.Rd
man/sample_uniform_trees.Rd
man/sample_uniform_trees_nx.Rd
man/sample_uniform_trees_nxo.Rd
man/sample_unique_perms.Rd
man/sample_unique_perms_o.Rd
man/simulate_cond_bp.Rd
man/simulate_flip_til_failure.Rd
man/simulate_many_cond_bp.Rd
man/simulate_outbreak.Rd
man/summarize_clusters.Rd
man/summarize_cond_trees.Rd
man/unique_perm.Rd
src/.gitignore
src/RcppExports.cpp
src/rcpp_hello_world.cpp
tests/testthat.R
tests/testthat/#test-likelihood-sampler.R#
tests/testthat/test-impute-root.R
tests/testthat/test-impute-root.R~
tests/testthat/test-likelihood-outside.R
tests/testthat/test-likelihood-outside.R~
tests/testthat/test-likelihood-sampler.R
tests/testthat/test-likelihood-sampler.R~
tests/testthat/test-likelihood.R
tests/testthat/test-loglike-doubly-trunc.R
tests/testthat/test-loglike-faster2.R
tests/testthat/test-loglike_faster.R
tests/testthat/test-partitions.R
tests/testthat/test-sample-trees-fast.R
tests/testthat/test-sample-trees-many-index-cases.R
tests/testthat/test-simulate-conditional-bp.R
tests/testthat/test-simulate-flip-til-failure.R
tests/testthat/test-simulate_outbreak.R
tests/testthat/test-table-weights.R
tests/testthat/test-tree-sampler-with-outside-gen.R
tests/testthat/test-weighted-sampling.R
vignettes/.gitignore
vignettes/outside-transmission-exported_files/figure-html/unnamed-chunk-5-1.png
vignettes/outside-transmission-v2.Rmd
vignettes/outside-transmission-v2.Rmd~
vignettes/outside-transmission.Rmd
vignettes/outside-transmission_files/MathJax.js
vignettes/tb_md.Rmd
