f8802091c8341bcc4b1210e78921c578 *DESCRIPTION
65f1afc4148fc8dd0929a4c16dee81fe *LICENSE
7bbd67e30d2b46c76de789712ca43b91 *NAMESPACE
33cfaeb02ac91cd0af83f00aff32aeca *NEWS.md
80f193decf1f42484c20c160bc6a0a51 *R/adhoc-imports.R
e34c92abe0313f7f2f9b0ca2431447d3 *R/baker.R
8cb398bae58f3e919660e68875f5333e *R/clean-perch-data.R
079fba42ee91c8ce4b300683066de2e4 *R/compute_functionals_of_model.R
b9ebf2b2410483f0a80dda72794927b8 *R/eda.R
2e6abde8d22581ee01839661b46c2bb2 *R/example_data.R
c4f4546aa7b4e35bc71f9c2b8ee081f4 *R/nplcm-read-folder.R
f5f90e8216ebcd8c2798ade7d77c25c7 *R/nplcm.R
e358b92fe9d02b3ccb416e8f8e20dfeb *R/plot-etiology-regression.R
c5dba3574e1e23013cc38ff66fbb87d8 *R/plot-model-check.R
1d438f062432e8b9adf3317c926c81e1 *R/plot-panels.R
db6e4b53fea338420e2f134f609afd3e *R/set-prior.R
ebf034b79fa08fe2e4aa1b487ca88195 *R/simulate-nplcm.R
701c6159085c1890def0ee8232574645 *R/summarize_results.R
a6732806cbf6f2c4fa9c67fe08ef931b *R/utils.R
e55de9c175c1a8519ea1b497b867d494 *R/write-model.R
bdbfb278e1ae1d2ecd5c064f88a336bc *README.md
fb43034471f6e68c60f0f4ebd242cb2b *build/vignette.rds
77b99cf0dc1fe22706f75e55da67109f *data/data_nplcm_noreg.rda
4f37117594450682c3d5f352b6a88620 *data/data_nplcm_reg_nest.rda
57b3fe637c989e74422931ba097bbbf1 *data/pathogen_category_perch.rda
91d6758e5d1aa1d6912a1f3d9008041d *data/pathogen_category_simulation.rda
8e431af1bee5907c56c74dd862f73899 *inst/CITATION
ca07b99a2febcf2f2c97831ad402cf68 *inst/WORDLIST
be582cd5dec844af68606293fba9722e *inst/doc/baker_demo.R
e46804591243036b0cab998a3649b0eb *inst/doc/baker_demo.Rmd
a6157d764dc408f3a3eaca2303a62d93 *inst/doc/baker_demo.html
a98c2320a5975aa6fe9048488c28bd77 *inst/example/plot_associations.R
5b955e29072eee7ee84083ab80631ccb *inst/example/simulate_data_example_nplcm_noreg.R
c745e9253a718be4f8431ae7d215dd27 *inst/example/simulate_data_example_nplcm_reg_nest.R
cc7a45774809c8c1cb77c22b1ecdf031 *inst/example_data/pathogen_category_simulation.csv
bd830b7f8a9f146f2cc2a9a30a94a3c4 *inst/figs/legends_visualize_etiology_regression.png
d9fd53d4b09f2f6eb47e981d39f73002 *inst/figs/visualize_etiology_regression_SITE=1.pdf
71699d1d8c6bc98f00936c9afb1b538f *man/H.Rd
daf1d96b0bbe97843fdbd436e2dfad25 *man/I2symb.Rd
beb37b450c1a355bc4128acf61489bb1 *man/Imat2cat.Rd
1be936b34e83debd9b74d026724c8a67 *man/NA2dot.Rd
f02410ccfb4427db43834eb8ef832a60 *man/add_meas_BrS_case_Nest_Slice.Rd
6ae5caae4a8bb7b9cf57a639df2bc197 *man/add_meas_BrS_case_Nest_Slice_jags.Rd
976ca75428d71af43a19ae831e994eab *man/add_meas_BrS_case_NoNest_Slice.Rd
66bc0d598bd3a17df91c1d901cda2b69 *man/add_meas_BrS_case_NoNest_Slice_jags.Rd
5d00025354c9ed86baec94353ff9e7ce *man/add_meas_BrS_case_NoNest_reg_Slice_jags.Rd
b52700ba3dab7786854e7f110748c7c4 *man/add_meas_BrS_case_NoNest_reg_discrete_predictor_Slice_jags.Rd
3d88b113522ff8a3045205eb5996a8ab *man/add_meas_BrS_ctrl_Nest_Slice.Rd
d3a4b5663b903d81eb9574553b3c510d *man/add_meas_BrS_ctrl_NoNest_Slice.Rd
b049c0d593aa1d0aecc50258c9002755 *man/add_meas_BrS_ctrl_NoNest_reg_Slice_jags.Rd
18ae0b5418f741185ab31b0eb03e7a8b *man/add_meas_BrS_ctrl_NoNest_reg_discrete_predictor_Slice_jags.Rd
cb37b801871fd6639fb142d713b5e894 *man/add_meas_BrS_param_Nest_Slice.Rd
5897f2317efc3c2d28288438c873c760 *man/add_meas_BrS_param_Nest_Slice_jags.Rd
3551bc7d2d98bcaf9c08551efb459d41 *man/add_meas_BrS_param_Nest_reg_Slice_jags.Rd
8bb845dcc6af5894e81299a3c0cac672 *man/add_meas_BrS_param_NoNest_Slice.Rd
e4231240d85eba9200f7352df674116d *man/add_meas_BrS_param_NoNest_Slice_jags.Rd
34dc147c6c4a911eaa34c4005afc868a *man/add_meas_BrS_param_NoNest_reg_Slice_jags.Rd
e228b121ff9856189787a8f972d6d0f8 *man/add_meas_BrS_param_NoNest_reg_discrete_predictor_Slice_jags.Rd
2a0b7709ba5c7758f0c39f5a1af08905 *man/add_meas_BrS_subclass_Nest_Slice.Rd
46f97653640c6a8ca1d468c65931eda8 *man/add_meas_SS_case.Rd
8f84fe626098ae1f81f4b16f85d16d4a *man/add_meas_SS_param.Rd
d32e7630236e55df235cc1b51ca89837 *man/as.matrix_or_vec.Rd
5e4ae369f06c3b881e9a81d919df9cb5 *man/assign_model.Rd
e18db6bc6e139bf60bcc5fde5e602ca9 *man/baker.Rd
e5892b488b5205d9745dfad566d64491 *man/beta_parms_from_quantiles.Rd
30bdf91ddc1e4cc46eab2b00552e8d10 *man/beta_plot.Rd
ef0b0bce0e990a0af4b0493d1df552fd *man/bin2dec.Rd
75aff8ffa7d6aab52a2887e5755e3cca *man/check_dir_create.Rd
e0c4c4cf9c583a8c978d28cdf3df818a *man/clean_combine_subsites.Rd
2e820b4348960d2ae043b4d92c17901d *man/clean_perch_data.Rd
b1c79fb9018a53c1f6bff41dff360101 *man/combine_data_nplcm.Rd
d6eccab9b4efc5abacf28f0856e60fc3 *man/compute_logOR_single_cause.Rd
fc2fd08846237e8581dc08f889063215 *man/compute_marg_PR_nested_reg.Rd
6338706227210bdd77e5a2fdfad88067 *man/compute_marg_PR_nested_reg_array.Rd
7cb2d7670e7aa18919b6fddf3758fa65 *man/create_bugs_regressor_Eti.Rd
5d804f7c4205af47af2ab77fb4ba0a32 *man/create_bugs_regressor_FPR.Rd
2cfce598e563bee0b5244ea043c064b5 *man/data_nplcm_noreg.Rd
14287260ee1ae40e7c45bfbd97b80896 *man/data_nplcm_reg_nest.Rd
4979c0d0280c4061f809b0e756fb27db *man/delete_start_with.Rd
02401ccdbdf969e125ba1c4621a0687c *man/dm_Rdate_Eti.Rd
603bd7024cada1a10f39ff126d69f318 *man/dm_Rdate_FPR.Rd
e3a6a69656629b955ce77376d4517834 *man/expit.Rd
a87eca1b59b5f5103992d8fdd5433c12 *man/extract_data_raw.Rd
db96ae4eed5037bd7ca666e31206780e *man/figures/nplcm_functional_dependence.png
b97474dd9e90f538cca4e77540ac507d *man/get_coverage.Rd
e7e00a97649e8b44d6307c465757d3c3 *man/get_direct_bias.Rd
fe41ff4ceadf9dbed7416520b110fe76 *man/get_fitted_mean_nested.Rd
4f4bbb6bb2f9316536189286e69603fa *man/get_fitted_mean_no_nested.Rd
22dd3929578f6e0d4e85aef072013320 *man/get_individual_data.Rd
886d9eac78fbdc89e51aa70086796053 *man/get_individual_prediction.Rd
34290fa104bb18f42d83b6b90ab54b74 *man/get_latent_seq.Rd
cb48c8e8728c0463af22650ea37b24b8 *man/get_marginal_rates_nested.Rd
02d68bdad90db99867cf938e4921d255 *man/get_marginal_rates_no_nested.Rd
38fd448b08d40862ba69d9d9743a6e3a *man/get_metric.Rd
ce6ec08aec98f28818d7f58ba242e1d5 *man/get_pEti_samp.Rd
92d30f4a2b58538b74bbf6555cc5a432 *man/get_plot_num.Rd
07f97d4b7ffd8ce318927a5ac7b0f233 *man/get_plot_pos.Rd
94aa3a1afd42aa97e4b1e3b125050090 *man/get_postsd.Rd
3712ceeaa3cc69234b5d4967601e5f32 *man/get_top_pattern.Rd
e037b6bdbaa74b55ac3839a82af5f3f3 *man/has_non_basis.Rd
747d64061b37bde9f38f6bb03c0d4d79 *man/init_latent_jags_multipleSS.Rd
0c6173ec634a5eb7d17f7d6879c85455 *man/insert_bugfile_chunk_noreg_etiology.Rd
ace1d812eef9718bcec2a4bd835e1655 *man/insert_bugfile_chunk_noreg_meas.Rd
2bfbc1988741cb43a00c317c8feb19fa *man/insert_bugfile_chunk_reg_discrete_predictor_etiology.Rd
e831b0c1b34df92b637c739a813253b7 *man/insert_bugfile_chunk_reg_discrete_predictor_nonest_meas.Rd
463167d71b0be045c3b7bf522cf1047f *man/insert_bugfile_chunk_reg_etiology.Rd
925442020463553bbb9d59ca5491ca4b *man/insert_bugfile_chunk_reg_nest_meas.Rd
62437531a7ed5b1b9eb6354dae316d52 *man/insert_bugfile_chunk_reg_nonest_meas.Rd
f870fa260d94ca45d1626c7e80924f5b *man/is.error.Rd
28eec42988bc6a7da13f6d3a19802eb0 *man/is_discrete.Rd
5c128ec924c347bcb4831ce7d0cdcd10 *man/is_intercept_only.Rd
7ed07e4e12d739301538e5c304f58702 *man/is_jags_folder.Rd
c08509d77f57f976fbdab6891aa81b59 *man/is_length_all_one.Rd
34dcda5d47acb3267b72b2c590c790bc *man/jags2_baker.Rd
bdd5089955497b6f24cc3562eea97f99 *man/line2user.Rd
e032a49f9426f82d36f9c6b1852191f2 *man/loadOneName.Rd
db17262c999ee982d4eca3be58053b55 *man/logOR.Rd
91fe24310ab03d8f1a150fab12375898 *man/logit.Rd
f091b1a5fe69bef3d44ae575953f77d2 *man/logsumexp.Rd
1d07b3f2c002cbd5013c5a84f3cfb1c6 *man/lookup_quality.Rd
5ce1375de9cc38c08f58f45235f8abfe *man/make_filename.Rd
a7884bd532d33755fd42873a39b75400 *man/make_foldername.Rd
c6998f9b184bc8205e044be6e1cf8ff3 *man/make_list.Rd
448d309c84f99703088efe66772ee98e *man/make_meas_object.Rd
06ddbe77070bffcb21f68807ebcec764 *man/make_numbered_list.Rd
f6408679d212497dc1ce9319c8ad9ce0 *man/make_template.Rd
463722ce6a2d6e7c1041c0f7e28139ce *man/marg_H.Rd
a88b409bb5f83b4987a3da2687a485d8 *man/match_cause.Rd
376e2bccb7ae02ad9256b9101ecaaf52 *man/merge_lists.Rd
a18355cc35e2c32a6b4221d48fd1f3e3 *man/my_reorder.Rd
67b56ed419b5560bc7b9b9f2a07f0cde *man/nplcm.Rd
1024d71d3a7b279e354b062408314653 *man/nplcm_fit_NoReg.Rd
d42adccf806f9b27960c5f8afaad3497 *man/nplcm_fit_Reg_Nest.Rd
83024f062947adc51f2ab2d589044918 *man/nplcm_fit_Reg_NoNest.Rd
9af91e5626162db692524890d62d298b *man/nplcm_fit_Reg_discrete_predictor_NoNest.Rd
9f1b4db3bbceba86a8e65993bbf140a5 *man/nplcm_read_folder.Rd
6fc3d83c8783009c5e483a45aba74320 *man/null_as_zero.Rd
c7bdbe010bcd37b82c744ef8a3d9caf8 *man/order_post_eti.Rd
b5613cc0bcc9e6cb531fda648827837f *man/overall_uniform.Rd
5e4d02701aa6b09f3d88f64da2d379ff *man/parse_nplcm_reg.Rd
8eced9ba71e1397858ce2b9262f3654f *man/pathogen_category_perch.Rd
c3960f9ce19befdc1462c93cabdac266 *man/pathogen_category_simulation.Rd
fc06081ab06d563631d7ff6988af9e48 *man/plot.nplcm.Rd
5c4fe8f44ed1b9e819e5efaf08d6313e *man/plot_BrS_panel.Rd
6b1e94372fbd4d93955a435793cbee5e *man/plot_SS_panel.Rd
5b0c7752ed6891b4699082a505db7a8e *man/plot_case_study.Rd
a5f8b9a286fa6cc2e84440e336cfa202 *man/plot_check_common_pattern.Rd
dbcce0bc0f68bcd3e4fb1e97023874c9 *man/plot_check_pairwise_SLORD.Rd
f0be5003fdc3b2f10b17b04eb9c34b1e *man/plot_etiology_regression.Rd
ba0c7ca2ce988607ae768478581b2691 *man/plot_etiology_strat.Rd
3b9385c889701542346d7a27fec347fd *man/plot_leftmost.Rd
e6fd113f5061267552204711c34f3fd3 *man/plot_logORmat.Rd
111a74dc835dd557c07eb357f8e9f1b7 *man/plot_panels.Rd
3eae20c2b15623ad3d8a7083aee72931 *man/plot_pie_panel.Rd
0bd4ea1c54895257bec1cb47817817c8 *man/plot_subwt_regression.Rd
929afaef75df9fa94e1b3e3d9dd0262d *man/print.nplcm.Rd
ff29f1e2b88c64e96e2d51c5fc9083cb *man/print.summary.nplcm.no_reg.Rd
af2c9ba155437c0cb628c3725a537e0c *man/print.summary.nplcm.reg_nest.Rd
55d9a47231b05dc1488c708bbbd7acc2 *man/print.summary.nplcm.reg_nest_strat.Rd
c02bc2d627f1fa54a59c723c4de0126f *man/print.summary.nplcm.reg_nonest.Rd
aed2e0e810e7ca59b76c78dda5b2a2c9 *man/print.summary.nplcm.reg_nonest_strat.Rd
0884d94824c38a1f7884ef863b175b4f *man/read_meas_object.Rd
fa5d86586cf991ff55abf0ac92edce53 *man/rvbern.Rd
fe3ac38bbef8e0f1af3d32e508e03c4a *man/s_date_Eti.Rd
afd230287c0c780971dd3af9d010ff49 *man/s_date_FPR.Rd
1ad2824f798626143807e9cb4b11da76 *man/set_prior_tpr_BrS_NoNest.Rd
d3ea4830d4e79409e32316a2d205007e *man/set_prior_tpr_SS.Rd
ca9248f03520bd6705f283d097bd9dee *man/set_strat.Rd
5d1647094a8a7413a95902a0f113b927 *man/show_dep.Rd
5e06beefa3da049b52bc495e009a9693 *man/show_individual.Rd
78825d96c6283740ece01c0faac032c2 *man/simulate_brs.Rd
a94d755cc38f87329954c987f3cee1a9 *man/simulate_latent.Rd
9c3d45357688a7db70cbf0c632ad2f1f *man/simulate_nplcm.Rd
8653bca1f6b92c39656a82cd82c7bd50 *man/simulate_ss.Rd
0d8d90bf8461af94ff72a93f940fa52e *man/softmax.Rd
f0c35f28ec2b078a888c39f4f2dacd5b *man/subset_data_nplcm_by_index.Rd
87b7f555da4d7830ef46158494ea762b *man/summarize_BrS.Rd
913c5175f0b3ede21f3ac7eb18b2279f *man/summarize_SS.Rd
8725dbbe4da490d3978debcde93a7c4c *man/summary.nplcm.Rd
ea761129eaff02cc87bd2c7ec68bec7b *man/sym_diff_month.Rd
cf8c65e520e84504b0af4e2a71fbb027 *man/symb2I.Rd
a7476a91934ab7dd0b54a28d846637e0 *man/tsb.Rd
1e00d482d7a300862fb44726fbd3c6a7 *man/unfactor.Rd
5ab46b3c0930e3526c58f4d590ebb9fb *man/unique_cause.Rd
8894ecbd2c9deed36be62413db2c136c *man/unique_month.Rd
a2eaa860d4ae49f55e6528a626faa8a4 *man/visualize_case_control_matrix.Rd
6404caf02a7b064d8c8516703b609094 *man/visualize_season.Rd
c7bded7a67095be8136a4be0dafdb587 *man/write.model.Rd
4dcaba05fc1c4085f03c3152cc5e7a2d *man/write_model_NoReg.Rd
109ad4879dce7f34b2c0ef971e310c56 *man/write_model_Reg_Nest.Rd
b83d829bd3c82fddc5b40ccdcd1310e6 *man/write_model_Reg_NoNest.Rd
336c08063b83daafe301c8296b86e6c4 *man/write_model_Reg_discrete_predictor_NoNest.Rd
0622a97a2aaa3c342f09636052c2d7f5 *tests/spelling.R
97f1da6f799db592c97b7f111725639b *tests/testthat.R
4a641a44c2019b14a6aa4baf5db2013a *tests/testthat/test-helpers.R
a7b610b9a41144ffa270ef3f6d186e5e *tests/testthat/test-symbol-conversion.r
e46804591243036b0cab998a3649b0eb *vignettes/baker_demo.Rmd
