1f112ae86871a94c1873d975561b658f *DESCRIPTION
34688085eb4431ba9441cdd9f44515d8 *LICENSE
40af6319010642b5ea03c92b37109f4d *NAMESPACE
6ac93ae64f71ea27e18acde6c377f088 *NEWS.md
8a958d37509be9cb6dfcfaa23fc6475c *R/RcppExports.R
545cd4082b886d11567fdace3f23db2a *R/adaptive_sampling.R
fcc6216f9bbf7801da758f174e157a79 *R/algorithm_comparison_helpers.R
233237e909035b13a051c600330911d6 *R/core.R
edebfaf1a8d533198a02636077622fc1 *R/data.R
a080d9d8e408eba9cf8aed79af2f93d7 *R/data_preprocessing.R
417169d18f2f5675563ab64fa516003d *R/diagnostics.R
fc8d0b15bbe6106a527e97a12df06977 *R/error_metrics.R
946b97dd69d55e3025d5e9849a2a4d72 *R/euclidify_diagnostics.R
4304162d99954058c2b027dbdb215f42 *R/globals.R
923ec6a16ba0a4a9e4a186f364e34b54 *R/topolow-package.R
a4b6e54d747ae647719674224bb254a5 *R/utils.R
ef81d8712bfc822a933ed7344c064fff *R/visualization.R
e16395618c550dee0a8a9c2c6aa062e9 *README.md
ba582b375e5afde780e991c9b7711c6a *build/partial.rdb
7513aca20adf0a0b3ca3584e78d59e96 *build/vignette.rds
65ce905ca3bcb699bfa56add2a98f50c *data/denv_data.rda
87ba0a85b241b26c5743a07662c772b5 *data/example_positions.rda
1118223fc00b22f692e418943d290ec5 *data/h3n2_data.rda
56ce310a3f3edee4c3691c64cb37ee37 *data/hiv_titers.rda
934d7b417f943eb319b5aaa8b1e9cc23 *data/hiv_viruses.rda
86f430dc8c944a99294d9f90f3293f67 *inst/CITATION
ca67a321f749a64fb97032ab3e520f07 *inst/WORDLIST
627da9235255185b4b92c6507db3007e *inst/doc/Comprehensive_Evaluation.R
a7e6bfb8d0fe62eeacb86fe18d664fb6 *inst/doc/Comprehensive_Evaluation.Rmd
854900f9d53293af000a2ee6ce93a555 *inst/doc/Comprehensive_Evaluation.html
be1809ba812ea1417c995bc7971380cb *inst/extdata/diag_chain1.csv
35d626b5f8d2a57a1b2ba63a750960cd *inst/extdata/diag_chain2.csv
a9bf5642808d62c8553aada2d596853f *inst/extdata/diag_chain3.csv
5dbe6ee8ebedbcfdff2acce43e796320 *inst/extdata/example_titer_data.csv
7269a288efdc65b4956c2f6c8661cea8 *inst/extdata/initial_samples_example.csv
f02387cb68d80838fbfd2e45a89fc052 *inst/extdata/sample_params.csv
275f4672e38f4c95a363b32c05619e2b *inst/scripts/check_dependencies.R
c2499afa6c75f812a1f6aae59c225266 *man/Euclidify.Rd
a87f65fd9699f6d7220cec2842787f3f *man/adaptive_MC_sampling.Rd
26b441572360c01ad752b2d19b304ad2 *man/analyze_network_structure.Rd
eb71b25ca10d530aa0d8461d792216e3 *man/calculate_diagnostics.Rd
95b9f42ec5f119dee01c85529426cd87 *man/calculate_prediction_interval.Rd
3f34f5120b8bdbef11071273ea4e185c *man/calculate_weighted_marginals.Rd
b23b144c3269c8c0be441f09d25f1aec *man/check_gaussian_convergence.Rd
2af50dec137f3d14610e9f4648c54a17 *man/check_matrix_connectivity.Rd
cbb1efd29f04b9d24040dc958b9fa23e *man/clean_data.Rd
3fa34608e4582168cbd30d15c435abee *man/color_palettes.Rd
b72a521e012188ceb612c72f05d5642c *man/compute_kernel_velocity.Rd
42303b811022727463a2a0012cab1b3a *man/coordinates_to_matrix.Rd
2c4487568f94d055e308dd0dc2fb4521 *man/create_base_theme.Rd
b5e023aa4f819bad9422e6f2f41fbfd0 *man/create_cv_folds.Rd
ad66a202d5cf43580f1088b6c951d6e0 *man/create_diagnostic_plots.Rd
e56b7f44b6dd6677e4311ac6af0c244c *man/create_diagnostic_report.Rd
3ce2a5bd4b7f3d5c9d56c0326250a817 *man/create_topolow_map.Rd
4678674470c94becd07f683829fadd41 *man/denv_data.Rd
0f406c1cf5bccb0bff533adcdd2c1114 *man/detect_outliers_mad.Rd
59cfbfe4a63d70b9b2a3e8beddf4a050 *man/error_calculator_comparison.Rd
630cd139b2b8e3833416593d74de708f *man/euclidean_embedding.Rd
5dbd2cb5dbd66c295c06c2001b366453 *man/example_positions.Rd
27287246b6fceac91418586ea49d6c9e *man/extract_numeric_values.Rd
5065cb42c812c645340e8c0fbe24e111 *man/figures/combined_analysis-1.png
cfe8630f9c4d9a4548ba11e46a198747 *man/figures/distance_preservation-1.png
5d938eb997c67e576186fa50e11cade5 *man/figures/distance_preservation-2.png
d763487d2de58141cd5350fb0a6eea39 *man/figures/distorted_eigenvalues-1.png
859f6f718e5ac03f1b22660b65d95fe1 *man/figures/distorted_performance-1.png
391f696f961e28914508628a7af31b74 *man/figures/lifecycle-deprecated.svg
691b1eb2aec9e1bec96b79d11ba5e631 *man/figures/lifecycle-experimental.svg
ed42e3fbd7cc30bc6ca8fa9b658e24a8 *man/figures/lifecycle-stable.svg
bf2f1ad432ecccee3400afe533404113 *man/figures/lifecycle-superseded.svg
b22583f2f0fd6160df0e9f700274eb32 *man/figures/swiss_eigenvalues-1.png
8186453031841c4dcb9825619f780d9f *man/figures/swiss_performance-1.png
2cceac25fe09b94f83d14df240d1b1c5 *man/generate_kde_samples.Rd
e7e5e806dbbd84809338649a079ba80a *man/get_grid.Rd
115516093d6f7ae6a5f9f2e6845e5737 *man/ggsave_white_bg.Rd
affa6f59c1b43429f305abf2fa176a26 *man/h3n2_data.Rd
98c3204c0a0662b4524c981570f4c9ff *man/hiv_titers.Rd
2f5a0a48cd41dd53d646a5803be9fd76 *man/hiv_viruses.Rd
da2cfda044c606f60321537e3e4ff03c *man/initial_parameter_optimization.Rd
6f7f2ab6db002b56825b4f93f8dcde5e *man/likelihood_function.Rd
13b99948fef791f140ef347eefd0037c *man/list_to_matrix.Rd
2b0936072df59be5a406d702370a0aff *man/log_transform_parameters.Rd
4e59b797362e2a2904411cbef17cc9d8 *man/make_interactive.Rd
0f22af3954245a79b4ae5728174d772a *man/new_aesthetic_config.Rd
8f99d4ef4b38320c90b110d4a5233ca7 *man/new_annotation_config.Rd
91c8bcaf986a4e617059136833e73ed1 *man/new_dim_reduction_config.Rd
fdf4b513e61db3b506b3cc1d03b3acc3 *man/new_layout_config.Rd
abad67f9c66ea0e5e0abaac5d92e8905 *man/parameter_sensitivity_analysis.Rd
e28328f375a01d9c052717af0d5b3634 *man/plot.parameter_sensitivity.Rd
2e64d87c3f08499884cfe8c2a7c2ddec *man/plot.profile_likelihood.Rd
4690d744ac27b9bffa874e5b94c026be *man/plot.topolow_convergence.Rd
fd600bb4e46a799c62f6827887828464 *man/plot.topolow_diagnostics.Rd
3113572e96ef5530cb8bf6e4612d7535 *man/plot_3d_mapping.Rd
3149f556f2065e5782d6331e3de0e04a *man/plot_cluster_mapping.Rd
adf755936b0b66096cf335de958f5c61 *man/plot_cv_errors.Rd
e56ada460e8b69410f92367602448571 *man/plot_embedding_quality.Rd
bdbce0a90c1bb35f3289a6d8c65806e7 *man/plot_euclidify_diagnostics.Rd
fd1768a28b5c2da264e2f42705b1ddfb *man/plot_ll_improvement.Rd
f493f895d840b3b60a70b994ee7f6aa0 *man/plot_mcmc_diagnostics.Rd
1f0817dcc17ba90ea52a60b46b81e752 *man/plot_network_structure.Rd
87546ed1059bfe8f209a66f808c692cb *man/plot_parameter_search.Rd
085b579a25bba2ae5f267cb929348d7f *man/plot_performance_trace.Rd
5d5c7458d83fbff47174a80c2b6b2196 *man/plot_temporal_mapping.Rd
abf91459b7e82d724a8c21f6e43f9f97 *man/prepare_clade_membership.Rd
6a636a0a3858ab8bce77002a2078ac20 *man/print.parameter_sensitivity.Rd
da475c8d028fbc0f6641836b6a72b5aa *man/print.profile_likelihood.Rd
8380789da8e413ca3f367329f5ba5777 *man/print.topolow.Rd
65550cd4106cbc1de3cfe87663eb59cf *man/print.topolow_convergence.Rd
b0b282213b0a9760a5adeadcb7783164 *man/print.topolow_diagnostics.Rd
8889e51551555232e2afa62c8c714bcd *man/process_antigenic_data.Rd
e2e87373f333208de87fbb74f7bd548a *man/profile_likelihood.Rd
fb340e420c7eeda0e9e07242c1a6aea0 *man/profile_likelihood_result.Rd
bf0898dc0dbd915b27ff4dd9234d9edf *man/prune_sparse_matrix.Rd
3786b6af46c257abb913c7c7b9477b49 *man/reduce_dimensions.Rd
4e779a21cdbfd6edf6eca18c792d357f *man/run_adaptive_sampling.Rd
353f967d8be9e709d07f39fc4d6dfe33 *man/sanity_check_subsample.Rd
739a2c8ea9dc20cca0fb600ea7e76e1e *man/save_plot.Rd
b700c6d13c63672565c76e98276a0921 *man/scale_to_original_distances.Rd
1fd05b29d0c6543f2fa3c43861dabfc3 *man/scatterplot_fitted_vs_true.Rd
7fd146c2bd689032467e1ac5cac5894f *man/subsample_dissimilarity_matrix.Rd
60a7a1d465d280ae6349e37143051689 *man/summary.topolow.Rd
bc7e368cdd24f19522b21e6c25e4ceb5 *man/symmetric_to_nonsymmetric_matrix.Rd
25c8341f87ab688484b40bb5adfad6b6 *man/table_to_matrix.Rd
1d8005f2038d23096c3b20c6f7b3c2cd *man/titers_list_to_matrix.Rd
6b791aac81d778f5fc5b103b002432fb *man/topolow-package.Rd
a0f45e51425297e4cfbba20a4df60e23 *man/validate_topolow_df.Rd
3bcbbe179815c0e81fb3bc938b946e66 *man/vectorized_process_distance_matrix.Rd
abe524e02ca16187ffcface4809ea6cb *man/weighted_kde.Rd
96a749771410186fdf0228f9efaedd39 *src/RcppExports.cpp
e666ce15874c875dfe7012ee5de158e0 *src/optimization.cpp
bb89b8fb140e0eed3c163312bbdb33e2 *tests/testthat.R
636218e09783a4dfa3e6e3ad417f5ee5 *tests/testthat/model_parameters/test_amc_model_parameters.csv
30d54ab45ba6df479aebd2144cc0c8e7 *tests/testthat/test-S3-methods.R
1a41eb5140fd52160b3ad804b80afed2 *tests/testthat/test-adaptive-sampling.R
3fd54d06307c3d480b6b39ce94c4be45 *tests/testthat/test-antigenic-cartography.R
e67bac26d1425cde422e77cd942933c8 *tests/testthat/test-core.R
d344f235a57ba28ff7171fdf79992420 *tests/testthat/test-data-preprocessing.R
cc250e0b3fe9ac50f408518c9f7bd0df *tests/testthat/test-data.R
0b27c6f630d90bf51829e37ff59de77c *tests/testthat/test-deprecated.R
9f7c11ea041d6709f0ca962306d1a8b9 *tests/testthat/test-diagnostics.R
e4c0e42f8fc092146a4b1509ef696b70 *tests/testthat/test-edge-cases.R
62bba94ae424f46d49bfb824c39829a8 *tests/testthat/test-euclidify-diagnostics.R
d8944596d43961dff0dbae1f962a1add *tests/testthat/test-integration.R
6469da34994437b78796214c637d826c *tests/testthat/test-subsample.r
ea51fa94ba5e0e036758a0793d43a4cf *tests/testthat/test-transformations.R
4a3f0132cc8717c44636e889adadd737 *tests/testthat/test-utils.R
ae3eab9f3b4c4906e68ebaa0d507ece9 *tests/testthat/test-visualization.R
a7e6bfb8d0fe62eeacb86fe18d664fb6 *vignettes/Comprehensive_Evaluation.Rmd
