7baa6fbd464d9719ed7495f98b685ce0 *DESCRIPTION
b9b00ddd3b4ad56555a544aa4e02101c *LICENSE
792ab6e954adcd0f250bcf31bab388df *NAMESPACE
1a346ce763868c05e1331712375e9112 *NEWS.md
e4a9e2e5f64799b40de28f15a2c20324 *R/RcppExports.R
9363d79935b1e89094ced5475d0a29bd *R/assess_bayespim_convergence.R
3e1b65e058402986b4dad9fc704cc2e7 *R/augment_w.R
2636e43c756bb29f9b600688a5df9bcc *R/bayespim.R
652c2483a9894c84dbaacb64f548bb25 *R/bayespim_analysis_chains.R
cca8f496fd062df3b6307f3bba736ae5 *R/bayespim_combined_draw_matrix.R
c36dff6d32910878f5353e6dd58bbb4c *R/bayespim_convergence_chain_matrices.R
6a2e5b29874fd46b962435ca258c62eb *R/bayespim_convergence_criteria.R
d874fce9aa8c0b75d7769d07d97ccd94 *R/bayespim_covariate_scaling.R
842f69646cdf11a629133d6e0dc66471 *R/bayespim_design_ncol.R
c563ebad8e0cf4ef0fa7282935451629 *R/bayespim_package.R
00a24c90dbfdb0a0d0d02d36e62e44a9 *R/bayespim_parameter_diagnostic.R
de92d14647eb3c71bac4798d31da6872 *R/bayespim_parameter_draw_matrix.R
02ab57c434c6e1f1fbb643c811d661cb *R/bayespim_parameter_metadata.R
fed549f6c1c49d588787a41cf5b8cf3e *R/bayespim_subset_chain_iterations.R
7b6746642dcf22c900423a9b2a83fb38 *R/bayespim_summary_block_table.R
2e4fe503df6c6e8a93373cd55c175623 *R/bayespim_summary_draw_counts.R
b742d8fbe0911c69729f367b822f5edd *R/bayespim_transform_coefficients.R
dfb6b16bbf3f915146d277b7223e7450 *R/bayespim_validate_probs.R
f361bf42af27e372c4d3f06e1d222501 *R/bayespim_validate_warmup.R
91b82988a11091db29360226d789a9f3 *R/bind_mcmc_lists.R
75322c3b75f48add2e05cfa30021ca10 *R/cor2cov.R
7ecc5ee24324e21c70873239c9122aaf *R/dist_wrappers.R
e1e635e406ea4800aba2967114f8f69d *R/dloglog.R
6cff799178e1f1e184485adbc7c2533a *R/fc_beta.R
cf282921f5c30fce0f19d70eeb78fe97 *R/fc_beta_g_exp_haar.R
351b553906ec2c727dde680ff01086c5 *R/find_ab.R
67501b532ff08d40e3a2a86f4af4f799 *R/format_bayespim_convergence_table.R
f2de67a2d3e0798ce9fd12e9b6eb52cf *R/format_bayespim_summary_draw_counts.R
da9573ff46008de3da1e773b615f7a92 *R/gen_data.R
4ef0dc8f8616a8bc2a24abda8bb490ba *R/geom.R
ac9db52cc4ad7e72e06d6061433527ce *R/geom_inf.R
6a54bd7ea01d96e53ca1988aa099b36c *R/get_ic.R
0707e320cc9161271249b2b30c2876d4 *R/handle_bayespim_convergence.R
6a5e65c6738048596a284b9907069046 *R/ini_bayespim.R
a0080b58c03a5f99ddc7836e49a49c99 *R/ini_gibbs.R
761d7fd24a110b25cb85ed20e2d188d2 *R/l_obs_2s.R
3422986b9f72903c4f94b20d5ded0c7a *R/ll_aft.R
250bb2cfe9f569ec4d7d8c1ab31c3c70 *R/ll_aft_ic.R
3e601da0ce38f93296fc85b9a1d698f1 *R/log_aft_prior.R
ce6b7aed36bff8758efaec1b4e1be238 *R/log_pst.R
15ee6298d13fbd6b70102b4c27d6bc7d *R/log_pst_component.R
893cda48f750aad1b0495bca833286c6 *R/logsdiff.R
847c8e89dc38b57af80057679884b7c7 *R/mod-data.R
ed5b5bfdfdec89a2d3eeb0820189cf9a *R/p_v_obs.R
ad5ac7d067a412957f05ebdcd7dbebfb *R/p_v_obs_2.R
4e7afa10bed0fd64de8172b24229f8d3 *R/ploglog.R
167c4eefefc7020d35451ef3084358d8 *R/plot.bayespim.R
1bb4b15a8183ce56c805f93332f48e23 *R/plot.ppCIF.R
96f89027fc3718eb04018866a1e3d0cf *R/ppCIF.R
08bb3f5f920964de29050bba98533887 *R/prepare_bayespim_data.R
0274dae8c42e936afd41a467d318899b *R/print_bayespim_convergence.R
2d4a32ed3fc84cccaa7aa5e3818a7d44 *R/pst_kappa_no_prev.R
9790232145d829eb6890d64ed242c119 *R/q_ev.R
72b3d909cd0b7bd512e4484f7c52714f *R/qlog.R
19a936fbb6f974b040e509c3ffb41594 *R/qloglog.R
1fd131e6cd1e6b7dcf2244fc7a59f886 *R/r_ev.R
100fca447274f4b27f6180c89e9bd2e8 *R/r_trdist.R
b11246f361c2386044d1a28c33fce15d *R/rlog.R
2649376df0c0a70f8003b53f07125e38 *R/rloglog.R
05f0bc60552a3b34bd9a15b90c453a6e *R/rtruncnorm_inv.R
f6d221e84cda342178100e96ece011fe *R/sample_ppd_mixture.R
b1c60cf8b38e86ad0388d25a8af7942e *R/sample_ppd_nonprevalent.R
8243fe5d76f36b2ee8675a2a72917152 *R/sample_slice_component.R
3ad40dc42dbfb839b08edd453c92f5bb *R/search_prop_sd.R
3fbdf1f5a4c68b4f24122a223b4b661a *R/slice_passthrough.R
2391273a084602e1333c7448b5b1f9cc *R/step_mh.R
b189b1804227f244b69900fcbdd3d0b0 *R/step_slice.R
1ca9604c810bad1a90f3a04cfc5986f0 *R/step_slice_collapsed.R
ac4a4a09bb11a62bf2eaf6dc10374819 *R/summary.bayespim.R
c3314540ed762ad1287ff5bdaaa07447 *R/trans_par.R
fb691087a5b670fdeca1788fc284b93a *R/trans_par_gamma.R
17989d1d1970c181bf1a88ea1c21718c *R/trans_par_gengamma.R
25a8049a36d36c239e8dd0395ae0e7c3 *R/trans_par_ind_norm.R
8f541e854cda792e22665355cab3b3de *R/trim_mcmc.R
939d0ed25249e06620edf0cef705f591 *R/unwrap_bayespim_chains.R
bb92cb6a3fed3c90829dcbd6001c1991 *R/v_to_v_obs.R
63b721b8cfb796b77b946fe719e70b82 *R/validate_bayespim_inputs.R
2bc4b664feeee98a38d8aba8edbf8813 *README.md
533839446f70bde34a1050627ce80586 *build/partial.rdb
07c4f1fab3484a014e884844065cfb32 *build/vignette.rds
59ca3d6fcdebe056cb6b498d89acf5de *data/mod.rda
29bf797f5e45732a8db11b0a6d9d52f1 *inst/WORDLIST
c642263691a6466c37466f9e2e299a7a *inst/doc/BayesPIM_intro.R
2b474ea81699fd066399fd9d02a5928a *inst/doc/BayesPIM_intro.Rmd
5d4b72035fc5ba54376b7bd7968408c7 *inst/doc/BayesPIM_intro.html
26cfec7d2e9a9cfcb68cad1644bc2905 *man/BayesPIM-package.Rd
d7bf4f652a2ddce29589b4954eb799a4 *man/bayespim.Rd
b22f3eea79d6d73fc16b770c32a231bc *man/gen_data.Rd
64eb54274875bd4a4571f89ff152c0db *man/get_ic.Rd
b56157e7e963f3996ef594ea5a7ae625 *man/log_aft_prior.Rd
1ac6240f3c77fa08a00a3e7f81140bc1 *man/mod.Rd
c8be8fbd19ea4e251b1deb845dacb3bf *man/plot.bayespim.Rd
c17126f4cf0fd88bc3af97a3310fbff3 *man/plot.ppCIF.Rd
c79cf4462f954ea3092d5b4afa7674b2 *man/ppCIF.Rd
dc993065bd775e349f816355cc3456b3 *man/search_prop_sd.Rd
0c7ee712df85462ff9a25adb312e3f0b *man/summary.bayespim.Rd
d57faade04be0a760805be85f5b093c9 *man/trim_mcmc.Rd
dd05d96e4e84a71b714ba13ae5f41f43 *src/RcppExports.cpp
ca79e1f7b4c23a9a415397a19d4e62b5 *src/augment_g_collapsed_rcpp.cpp
bbc7ac913ee7695f2b2a5e4ede311af4 *src/fc_kappa_rcpp.cpp
6db28545680c039b3ef52c5ba3ae0140 *src/interval_probs_rcpp.cpp
b0f4d3b24bf352d9cc6aa8ad3e36ba22 *src/look_up_mat_rcpp.cpp
6a7a96d10d76879456e2e71fe9f95813 *src/p_v_obs_rcpp.cpp
19d15fc11be37c5a5797102687b8de98 *src/pdist_rcpp.cpp
dc1c8b6f7327e6963ad420fb4a313bb7 *src/pdist_rcpp.h
30bf560ef165f70c99d9bf9867e0486b *src/sample_k_rcpp.cpp
0524fabde7925f9b084cf22fd96ae4d1 *tests/contract_names.R
5a74597bba4a421b52d36481274d10bf *tests/covariate_scaling_contract.R
b373939a669c0da0c145ee18194cbbf0 *tests/default_sampler_contract.R
b90e88a9853e84fa9513f22db38da09c *tests/gamma_contract.R
d2a1f6cd52f9432974617fa444bcf1fd *tests/gen_data_contract.R
acea43f9110500133bc05d9d3e86238d *tests/gengamma_contract.R
2bb1fa50fab2c6f1b4175558a636c602 *tests/kappa_prior_contract.R
f037274ef9a4cb86843e9676b26af192 *tests/ppcif_contract.R
83f6ca609cb0a7e9697188ca490336d7 *tests/sampler_steps.R
5d8c8228be92daa27bb44fd7b24bc34c *tests/save_every_contract.R
2b474ea81699fd066399fd9d02a5928a *vignettes/BayesPIM_intro.Rmd
84911311ac16a493044b686850b8c8e8 *vignettes/figures/mcmc-traceplot.png
80c2dc71725e9d4c346b8948c83cacaf *vignettes/figures/ppCIF_both.png
2ad71cc934ccdba41b50ddc916a06d33 *vignettes/figures/ppCIF_conditional.png
