* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘baker’ ...
** package ‘baker’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘baker’
finding HTML links ... done
H html
I2symb html
Imat2cat html
NA2dot html
add_meas_BrS_case_Nest_Slice html
add_meas_BrS_case_Nest_Slice_jags html
add_meas_BrS_case_NoNest_Slice html
add_meas_BrS_case_NoNest_Slice_jags html
add_meas_BrS_case_NoNest_reg_Slice_jags
html
add_meas_BrS_case_NoNest_reg_discrete_predictor_Slice_jags
html
add_meas_BrS_ctrl_Nest_Slice html
add_meas_BrS_ctrl_NoNest_Slice html
add_meas_BrS_ctrl_NoNest_reg_Slice_jags
html
add_meas_BrS_ctrl_NoNest_reg_discrete_predictor_Slice_jags
html
add_meas_BrS_param_Nest_Slice html
add_meas_BrS_param_Nest_Slice_jags html
add_meas_BrS_param_Nest_reg_Slice_jags
html
add_meas_BrS_param_NoNest_Slice html
add_meas_BrS_param_NoNest_Slice_jags html
add_meas_BrS_param_NoNest_reg_Slice_jags
html
add_meas_BrS_param_NoNest_reg_discrete_predictor_Slice_jags
html
add_meas_BrS_subclass_Nest_Slice html
add_meas_SS_case html
add_meas_SS_param html
as.matrix_or_vec html
assign_model html
baker html
beta_parms_from_quantiles html
beta_plot html
bin2dec html
check_dir_create html
clean_combine_subsites html
clean_perch_data html
combine_data_nplcm html
compute_logOR_single_cause html
compute_marg_PR_nested_reg html
compute_marg_PR_nested_reg_array html
create_bugs_regressor_Eti html
create_bugs_regressor_FPR html
data_nplcm_noreg html
data_nplcm_reg_nest html
delete_start_with html
dm_Rdate_Eti html
dm_Rdate_FPR html
expit html
extract_data_raw html
get_coverage html
get_direct_bias html
get_fitted_mean_nested html
get_fitted_mean_no_nested html
get_individual_data html
get_individual_prediction html
get_latent_seq html
get_marginal_rates_nested html
get_marginal_rates_no_nested html
get_metric html
get_pEti_samp html
get_plot_num html
get_plot_pos html
get_postsd html
get_top_pattern html
has_non_basis html
init_latent_jags_multipleSS html
insert_bugfile_chunk_noreg_etiology html
insert_bugfile_chunk_noreg_meas html
insert_bugfile_chunk_reg_discrete_predictor_etiology
html
insert_bugfile_chunk_reg_discrete_predictor_nonest_meas
html
insert_bugfile_chunk_reg_etiology html
insert_bugfile_chunk_reg_nest_meas html
insert_bugfile_chunk_reg_nonest_meas html
is.error html
is_discrete html
is_intercept_only html
is_jags_folder html
is_length_all_one html
jags2_baker html
line2user html
loadOneName html
logOR html
logit html
logsumexp html
lookup_quality html
make_filename html
make_foldername html
make_list html
make_meas_object html
make_numbered_list html
make_template html
marg_H html
match_cause html
merge_lists html
my_reorder html
nplcm html
nplcm_fit_NoReg html
nplcm_fit_Reg_Nest html
nplcm_fit_Reg_NoNest html
nplcm_fit_Reg_discrete_predictor_NoNest
html
nplcm_read_folder html
null_as_zero html
order_post_eti html
overall_uniform html
parse_nplcm_reg html
pathogen_category_perch html
pathogen_category_simulation html
plot.nplcm html
plot_BrS_panel html
plot_SS_panel html
plot_case_study html
plot_check_common_pattern html
plot_check_pairwise_SLORD html
plot_etiology_regression html
plot_etiology_strat html
plot_leftmost html
plot_logORmat html
plot_panels html
plot_pie_panel html
plot_subwt_regression html
print.nplcm html
print.summary.nplcm.no_reg html
print.summary.nplcm.reg_nest html
print.summary.nplcm.reg_nest_strat html
print.summary.nplcm.reg_nonest html
print.summary.nplcm.reg_nonest_strat html
read_meas_object html
rvbern html
s_date_Eti html
s_date_FPR html
set_prior_tpr_BrS_NoNest html
set_prior_tpr_SS html
set_strat html
show_dep html
show_individual html
simulate_brs html
simulate_latent html
simulate_nplcm html
simulate_ss html
softmax html
subset_data_nplcm_by_index html
summarize_BrS html
summarize_SS html
summary.nplcm html
sym_diff_month html
symb2I html
tsb html
unfactor html
unique_cause html
unique_month html
visualize_case_control_matrix html
visualize_season html
write.model html
write_model_NoReg html
write_model_Reg_Nest html
write_model_Reg_NoNest html
write_model_Reg_discrete_predictor_NoNest
html
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (baker)