baker-package	baker-package
add_meas_BrS_case_Nest_Slice	add_meas_BrS_case_Nest_Slice
add_meas_BrS_case_Nest_Slice_jags	add_meas_BrS_case_Nest_Slice_jags
add_meas_BrS_case_NoNest_reg_discrete_predictor_Slice_jags	add_meas_BrS_case_NoNest_reg_discrete_predictor_Slice_jags
add_meas_BrS_case_NoNest_reg_Slice_jags	add_meas_BrS_case_NoNest_reg_Slice_jags
add_meas_BrS_case_NoNest_Slice	add_meas_BrS_case_NoNest_Slice
add_meas_BrS_case_NoNest_Slice_jags	add_meas_BrS_case_NoNest_Slice_jags
add_meas_BrS_ctrl_Nest_Slice	add_meas_BrS_ctrl_Nest_Slice
add_meas_BrS_ctrl_NoNest_reg_discrete_predictor_Slice_jags	add_meas_BrS_ctrl_NoNest_reg_discrete_predictor_Slice_jags
add_meas_BrS_ctrl_NoNest_reg_Slice_jags	add_meas_BrS_ctrl_NoNest_reg_Slice_jags
add_meas_BrS_ctrl_NoNest_Slice	add_meas_BrS_ctrl_NoNest_Slice
add_meas_BrS_param_Nest_reg_Slice_jags	add_meas_BrS_param_Nest_reg_Slice_jags
add_meas_BrS_param_Nest_Slice	add_meas_BrS_param_Nest_Slice
add_meas_BrS_param_Nest_Slice_jags	add_meas_BrS_param_Nest_Slice_jags
add_meas_BrS_param_NoNest_reg_discrete_predictor_Slice_jags	add_meas_BrS_param_NoNest_reg_discrete_predictor_Slice_jags
add_meas_BrS_param_NoNest_reg_Slice_jags	add_meas_BrS_param_NoNest_reg_Slice_jags
add_meas_BrS_param_NoNest_Slice	add_meas_BrS_param_NoNest_Slice
add_meas_BrS_param_NoNest_Slice_jags	add_meas_BrS_param_NoNest_Slice_jags
add_meas_BrS_subclass_Nest_Slice	add_meas_BrS_subclass_Nest_Slice
add_meas_SS_case	add_meas_SS_case
add_meas_SS_param	add_meas_SS_param
as.matrix_or_vec	as.matrix_or_vec
assign_model	assign_model
baker	baker-package
beta_parms_from_quantiles	beta_parms_from_quantiles
beta_plot	beta_plot
bin2dec	bin2dec
check_dir_create	check_dir_create
clean_combine_subsites	clean_combine_subsites
clean_perch_data	clean_perch_data
combine_data_nplcm	combine_data_nplcm
compute_logOR_single_cause	compute_logOR_single_cause
compute_marg_PR_nested_reg	compute_marg_PR_nested_reg
compute_marg_PR_nested_reg_array	compute_marg_PR_nested_reg_array
create_bugs_regressor_Eti	create_bugs_regressor_Eti
create_bugs_regressor_FPR	create_bugs_regressor_FPR
data_nplcm_noreg	data_nplcm_noreg
data_nplcm_reg_nest	data_nplcm_reg_nest
delete_start_with	delete_start_with
dm_Rdate_Eti	dm_Rdate_Eti
dm_Rdate_FPR	dm_Rdate_FPR
expit	expit
extract_data_raw	extract_data_raw
get_coverage	get_coverage
get_direct_bias	get_direct_bias
get_fitted_mean_nested	get_fitted_mean_nested
get_fitted_mean_no_nested	get_fitted_mean_no_nested
get_individual_data	get_individual_data
get_individual_prediction	get_individual_prediction
get_latent_seq	get_latent_seq
get_marginal_rates_nested	get_marginal_rates_nested
get_marginal_rates_no_nested	get_marginal_rates_no_nested
get_metric	get_metric
get_pEti_samp	get_pEti_samp
get_plot_num	get_plot_num
get_plot_pos	get_plot_pos
get_postsd	get_postsd
get_top_pattern	get_top_pattern
H	H
has_non_basis	has_non_basis
I2symb	I2symb
Imat2cat	Imat2cat
init_latent_jags_multipleSS	init_latent_jags_multipleSS
insert_bugfile_chunk_noreg_etiology	insert_bugfile_chunk_noreg_etiology
insert_bugfile_chunk_noreg_meas	insert_bugfile_chunk_noreg_meas
insert_bugfile_chunk_reg_discrete_predictor_etiology	insert_bugfile_chunk_reg_discrete_predictor_etiology
insert_bugfile_chunk_reg_discrete_predictor_nonest_meas	insert_bugfile_chunk_reg_discrete_predictor_nonest_meas
insert_bugfile_chunk_reg_etiology	insert_bugfile_chunk_reg_etiology
insert_bugfile_chunk_reg_nest_meas	insert_bugfile_chunk_reg_nest_meas
insert_bugfile_chunk_reg_nonest_meas	insert_bugfile_chunk_reg_nonest_meas
is.error	is.error
is_discrete	is_discrete
is_intercept_only	is_intercept_only
is_jags_folder	is_jags_folder
is_length_all_one	is_length_all_one
jags2_baker	jags2_baker
line2user	line2user
loadOneName	loadOneName
logit	logit
logOR	logOR
logsumexp	logsumexp
lookup_quality	lookup_quality
make_filename	make_filename
make_foldername	make_foldername
make_list	make_list
make_meas_object	make_meas_object
make_numbered_list	make_numbered_list
make_template	make_template
marg_H	marg_H
match_cause	match_cause
merge_lists	merge_lists
my_reorder	my_reorder
NA2dot	NA2dot
nplcm	nplcm
nplcm_fit_NoReg	nplcm_fit_NoReg
nplcm_fit_Reg_discrete_predictor_NoNest	nplcm_fit_Reg_discrete_predictor_NoNest
nplcm_fit_Reg_Nest	nplcm_fit_Reg_Nest
nplcm_fit_Reg_NoNest	nplcm_fit_Reg_NoNest
nplcm_read_folder	nplcm_read_folder
null_as_zero	null_as_zero
order_post_eti	order_post_eti
overall_uniform	overall_uniform
parse_nplcm_reg	parse_nplcm_reg
pathogen_category_perch	pathogen_category_perch
pathogen_category_simulation	pathogen_category_simulation
plot.nplcm	plot.nplcm
plot_BrS_panel	plot_BrS_panel
plot_case_study	plot_case_study
plot_check_common_pattern	plot_check_common_pattern
plot_check_pairwise_SLORD	plot_check_pairwise_SLORD
plot_etiology_regression	plot_etiology_regression
plot_etiology_strat	plot_etiology_strat
plot_leftmost	plot_leftmost
plot_logORmat	plot_logORmat
plot_panels	plot_panels
plot_pie_panel	plot_pie_panel
plot_SS_panel	plot_SS_panel
plot_subwt_regression	plot_subwt_regression
print.nplcm	print.nplcm
print.summary.nplcm.no_reg	print.summary.nplcm.no_reg
print.summary.nplcm.reg_nest	print.summary.nplcm.reg_nest
print.summary.nplcm.reg_nest_strat	print.summary.nplcm.reg_nest_strat
print.summary.nplcm.reg_nonest	print.summary.nplcm.reg_nonest
print.summary.nplcm.reg_nonest_strat	print.summary.nplcm.reg_nonest_strat
read_meas_object	read_meas_object
rvbern	rvbern
set_prior_tpr_BrS_NoNest	set_prior_tpr_BrS_NoNest
set_prior_tpr_SS	set_prior_tpr_SS
set_strat	set_strat
show_dep	show_dep
show_individual	show_individual
simulate_brs	simulate_brs
simulate_latent	simulate_latent
simulate_nplcm	simulate_nplcm
simulate_ss	simulate_ss
softmax	softmax
subset_data_nplcm_by_index	subset_data_nplcm_by_index
summarize_BrS	summarize_BrS
summarize_SS	summarize_SS
summary.nplcm	summary.nplcm
symb2I	symb2I
sym_diff_month	sym_diff_month
s_date_Eti	s_date_Eti
s_date_FPR	s_date_FPR
tsb	tsb
unfactor	unfactor
unique_cause	unique_cause
unique_month	unique_month
visualize_case_control_matrix	visualize_case_control_matrix
visualize_season	visualize_season
write.model	write.model
write_model_NoReg	write_model_NoReg
write_model_Reg_discrete_predictor_NoNest	write_model_Reg_discrete_predictor_NoNest
write_model_Reg_Nest	write_model_Reg_Nest
write_model_Reg_NoNest	write_model_Reg_NoNest
