2224e2433f46cc92bc0acc18e4d86a51 *DESCRIPTION
562876877024ec28e9ed773f445317c7 *LICENSE
759828dabdcd6caeda4279aee46fd4bd *NAMESPACE
43e0cc89da42eee063cef9111d4f8721 *NEWS.md
c24743898d8315003bedaf57d470d831 *R/adaptive_sampling.R
fcc6216f9bbf7801da758f174e157a79 *R/algorithm_comparison_helpers.R
02c0757084d216318a3756f674fa6d42 *R/core.R
edebfaf1a8d533198a02636077622fc1 *R/data.R
1ac557cca744c50c0ea7e6aec42db4ea *R/data_preprocessing.R
cd487e18a2afcdae34cce4681d7542f3 *R/diagnostics.R
28fb6c4155ae1bcef87ee11f2a8981af *R/error_metrics.R
bd89d1b3a0accbdc19d7eb92fa90b30f *R/experiments.R
3a8eea90651d2a8cdf51884d4f08cd52 *R/globals.R
e5ae0dbf6e580bf5e2f03772e43542de *R/procrustes.R
b4c8aac3259f989b5bfaa31e0145a9b0 *R/topolow-package.R
c9ccd4d9f092ad37122a13137acb1099 *R/transformations.R
bc30206bbc04992641547b35206d7e91 *R/utils.R
537c1ec1410a5badecd9b59bba265a8b *R/visualization.R
946a2f0fcfc293d3f57249edc8c578d5 *README.md
cb3b20077bebc5da31fc1b46c657c0ff *build/partial.rdb
6235fc722c05a5c1c2bfd5fb172bbcc6 *build/topolow-manual.pdf
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
8857508cc8ef75eeee33502501ca3370 *inst/extdata/diag_chain1.csv
1f09ac251359a4eef910b36bf854d6b2 *inst/extdata/diag_chain2.csv
ae6b087570c70bf4196dc913cc35a633 *inst/extdata/diag_chain3.csv
5dbe6ee8ebedbcfdff2acce43e796320 *inst/extdata/example_titer_data.csv
c1119b9f40da4b13583a4a8ec6dc924c *inst/extdata/initial_samples_example.csv
f02387cb68d80838fbfd2e45a89fc052 *inst/extdata/sample_params.csv
aa6a98b004d25ca75110eb4dd2e2c698 *inst/scripts/check_dependencies.R
f91c91560d3d40c9cb1f7634b4a88998 *man/adaptive_MC_sampling.Rd
625d29b0f82642574013c892f0be911c *man/add_noise_bias.Rd
48daa39936a206099b83356a4f5f01da *man/analyze_network_structure.Rd
bdcae5f29667791031005ae595ae2396 *man/calculate_annual_distances.Rd
86aac397d3d6d2a621e1f810eb57dbca *man/calculate_cumulative_distances.Rd
90e7659383c562fdf134cd5dd84ce315 *man/calculate_diagnostics.Rd
5b752730061a536126cdfff83ca8596c *man/calculate_prediction_interval.Rd
65dc82b0e1baebe9dd082ad39f67ff2a *man/calculate_procrustes_difference.Rd
be5654c0212ecc796ce33c32b8aa8dfd *man/calculate_procrustes_significance.Rd
69388d0c4cf27686112ed327eaa20ff0 *man/calculate_weighted_marginals.Rd
71529b4080b50549ff5ad26f767cf489 *man/check_gaussian_convergence.Rd
9856dea885007f2865d3aee85f17a87b *man/clean_data.Rd
a2fff914ee4365d6ad46a735ab901cfb *man/color_palettes.Rd
62a3405173a3885220ebbea7d781e325 *man/coordinates_to_matrix.Rd
c3ce345edac5271c4398c9194e203b0a *man/create_and_optimize_RACMACS_map.Rd
ad06467c2bdf02e454cf02e9411be94a *man/create_base_theme.Rd
d404e93ea2a7561e60a63439e1fb44cf *man/create_cv_folds.Rd
dd8b258acc1e17cc3a1686b9d4b85d2c *man/create_diagnostic_plots.Rd
b4dd737f42146fdc2a59aad966b42f7b *man/create_topolow_map.Rd
614a631f44f75cfc266060b3e8c99edd *man/denv_data.Rd
5de3597e6a5ee21a3d844602fc3548d7 *man/detect_outliers_mad.Rd
6caca5a95764966be0dc47b302372f4b *man/dist_to_titer_table.Rd
8675b14fb5ebf3a32c61541f4807084e *man/error_calculator_comparison.Rd
528a5abffc943671cd8898e3bc6f0413 *man/example_positions.Rd
e09eeeacb379d160d2a0b3731b41ba47 *man/find_mode.Rd
0d1af734712a35543ba86b94681d94ed *man/generate_complex_data.Rd
ed0a3271c85ac16ba951214e22c7f4d5 *man/generate_kde_samples.Rd
598ced738af58e76e19cf83b8cfa5875 *man/generate_synthetic_datasets.Rd
39663062510e658a8d287c625800714b *man/generate_unique_string.Rd
1e7231a58805074ea2f9d8f215d30332 *man/get_grid.Rd
9a8a1bc7c01a09b2e78b925bbe3f99c8 *man/ggsave_white_bg.Rd
6f33cab3af5943254bdd64dfbe0617f7 *man/gmultiple.Rd
7a0b7bc640d2592029013f0c5c614add *man/h3n2_data.Rd
6d2b9a7a94bb2a3649048af3eb3f4038 *man/hiv_titers.Rd
842e26624d1be091a9da22c66599e01b *man/hiv_viruses.Rd
2f47804b8a44f970801a7faf13f2c6b9 *man/increase_na_percentage.Rd
09a138003e7bab04bd82144cdae8259b *man/initial_parameter_optimization.Rd
acbfebacd7a1055247b8be061c0ac83e *man/likelihood_function.Rd
0912ddc3cde6e1a1739e969d9f20001f *man/log_transform_parameters.Rd
7fac607c21db7c23318129ffb8bc516c *man/long_to_matrix.Rd
6fa87b12a43943f7786f76080717eb7e *man/make_interactive.Rd
cdfd83eaac8e66eba78b2a912f5a3c39 *man/new_aesthetic_config.Rd
fbc32fdb28ab990bed474891c958aa39 *man/new_annotation_config.Rd
859e67a07e4f605288dd317a351db99c *man/new_dim_reduction_config.Rd
41219cebf35e362b8244c3d99d425773 *man/new_layout_config.Rd
8492a313c0a3115a869a2dfd0f592f7d *man/only_virus_vs_as.Rd
50098f4575ecf2bab1fe69df230b5df6 *man/parameter_sensitivity_analysis.Rd
6509a3c58049a05c08f49144d01e28dc *man/plot.parameter_sensitivity.Rd
e736a68e0e907d7b806b99735b614aef *man/plot.profile_likelihood.Rd
e8c276266b391e413b42e8e3b2db90c8 *man/plot.topolow_amcs_diagnostics.Rd
795e242426fb1f75c5862f24a4462298 *man/plot.topolow_convergence.Rd
4a948a0199168c4e560c09ca08f8006e *man/plot_3d_mapping.Rd
0cbb464b3153101b4d3d5113ba941c29 *man/plot_cluster_mapping.Rd
83c5a01d77e585e7e9f4c50d384318c7 *man/plot_distance_heatmap.Rd
b6c3c9453e5aa6761cc7bf50036d50be *man/plot_network_structure.Rd
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dd4706ef56357cc54af1ca3d3ada48dc *man/prepare_heatmap_data.Rd
72d6d7ad0cb79988fef1181b4d2dd180 *man/print.parameter_sensitivity.Rd
7dd5603f3635f482b79df7077d7081fd *man/print.profile_likelihood.Rd
60decfb1b3495c3f0046f75de43f0fed *man/print.topolow.Rd
3fac30ac6709a5c78710e651464a1ba0 *man/print.topolow_amcs_diagnostics.Rd
310af0a0bc9eb241dd33ef032c32e894 *man/print.topolow_convergence.Rd
5e32f1dc032598d478dfd622daabf48f *man/process_antigenic_data.Rd
6c651949d40774789d84262883e897d9 *man/process_distance_matrix.Rd
804f8c504cb57fa71968ec3fc08c6ed1 *man/profile_likelihood.Rd
10c28b1ed582be552c1868b153c920b5 *man/profile_likelihood_result.Rd
96a052096040fc31c352a6724ed1d676 *man/prune_distance_network.Rd
93a0a78143d699b2f4a59f72ddda2458 *man/reduce_dimensions.Rd
6b19509fc638a45ec0179e716dfe8021 *man/run_adaptive_sampling.Rd
c0796b215c65667f7341051c7cc33969 *man/sample_from_distribution.Rd
b69d402cbef10f5b3c0245c88e15b980 *man/save_plot.Rd
670d813be6347342c082a72376696494 *man/scale_to_original_distances.Rd
cb38fc6e24c4f65a7794756884685ff7 *man/scatterplot_fitted_vs_true.Rd
9b3bd062782a7f0fcb97363059c469ee *man/summary.topolow.Rd
9f90164bc43b68150bf0d6dc6a91ab13 *man/symmetric_to_nonsymmetric_matrix.Rd
28d38a5a0b57dab1f3f3f934507a7611 *man/topolow-package.Rd
baf01a2fbdce6b3be1fbb9045b698e41 *man/unweighted_kde.Rd
865ace470a8bedc3552f8d78c67ee82d *man/validate_antigenic_data.Rd
a4771ed9c04e5e57438af733b681773b *man/validate_topolow_df.Rd
e013f4173f3ea5dfca1d57d2ae18ed9d *man/vectorized_process_distance_matrix.Rd
fc1ec05907d8b380c375cc0153a0206a *man/weighted_kde.Rd
dacd82a7c7649aec76075afae56a5187 *man/yy_to_yyyy.Rd
793a3b4b2b65893b20f22527b5e2a2d5 *tests/testthat.R
d56302484677a930b4058fcb6e7e49fc *tests/testthat/model_parameters/test_amc_model_parameters.csv
3a40894fb5c9a8006771336acfe0b1ac *tests/testthat/test-core.R
47a4e654ccca532f70d09f6e7edb5112 *tests/testthat/test-data-preprocessing.R
cc250e0b3fe9ac50f408518c9f7bd0df *tests/testthat/test-data.R
c0c43562741c4bdaf005a7d6237d300f *tests/testthat/test-integration.R
669ed7d6fb335beafbbcb2d9ec86a551 *tests/testthat/test-visualization.R
