Nested Partially-Latent Class Models (nplcm)

assign_model | Choose a model to fit |

beta_parms_from_quantiles | Pick parameters in the Beta distribution to match the... |

beta_plot | Plot beta density |

bin2dec | Convert 0/1 binary coded sequence into decimal digits |

check_common_pattern | Posterior predictive checking for the nested partially class... |

check_common_pattern_two_folders | Posterior predictive checking for the nested partially class... |

check_pairwise_logOR | Posterior predictive checking for nested partially latent... |

check_pairwise_logOR_two_folders | Posterior predictive checking for nested partially latent... |

clean_combine_subsites | Combine subsites in raw PERCH data set |

clean_perch_data | Clean PERCH data |

create_bugs_regressor_Eti | create regressor summation equation used in regression for... |

create_bugs_regressor_FPR | create regressor summation equation used in regression for... |

delete_start_with | Deletes a pattern from the start of a string, or each of a... |

dm_Rdate_Eti | Make etiology design matrix for dates with R format. |

dm_Rdate_FPR | Make FPR design matrix for dates with R format. |

expit | expit function |

extract_data_raw | Convert raw data sheet to analyzable format |

get_mse | Obtain MSE, bias-squared and variance of posterior from nplcm... |

getPckg | Get package from CRAN website |

I2symb | Convert 0/1 coding to pathogen/combinations |

Imat2cat | Convert a matrix of binary indicators to categorial variables |

is_discrete | Check if covariates are discrete |

is.error | Test for 'try-error' class |

load_or_install | Load or install a package |

logit | logit function |

logOR | calculate pairwise log odds ratios |

make_filename | Create new file name |

make_foldername | Create new folder name |

make_list | Takes any number of R objects as arguments and returns a list... |

my_reorder | Reorder the measurement dimensions to match the order for... |

NA2dot | convert 'NA' to '.' |

nplcm | Fit nested partially latent class models (high-level) |

nplcm_fit_NoReg_BrSandSS_Nest | Fit nested partially-latent class model (low-level) |

nplcm_fit_NoReg_BrSandSS_Nest_SSonly | Fit nested partially-latent class model (low-level) |

nplcm_fit_NoReg_BrSandSS_NoNest | Fit nested partially-latent class model (low-level) |

nplcm_fit_NoReg_BrSandSS_NoNest_SSonly | Fit nested partially-latent class model (low-level) |

nplcm_fit_NoReg_BrS_Nest | Fit nested partially-latent class model (low-level) |

nplcm_fit_NoReg_BrS_NoNest | Fit nested partially-latent class model (low-level) |

nplcm_fit_Reg_BrS_NoNest | Fit nested partially-latent class model with regression... |

nplcm_fit_Strat_BrS_NoNest | Fit nested partially-latent class model with stratification... |

nplcm_read_folder | Read data and other model information from a folder that... |

null_as_zero | Convert 'NULL' to zero. |

plot_BrS_panel | Plot bronze-standard (BrS) panel |

plot_etiology_music_sheet | compare the posterior distribution of population etiologies... |

plot_group_etiology | Plot viral etiology posterior and distribution within... |

plot_individual_diagnosis | Individual prediction from nested partially-latent class... |

plot_individual_diagnosis_two_folders | Individual prediction from nested partially-latent class... |

plot_logORmat | Visualize pairwise log odds ratios (LOR) for data that are... |

plot_pie_panel | Plot etiology (pie) panel |

plot_pie_panel_two_folders | Plot etiology (pie) panel |

plot_skyline | Distribution of individual prediction for each pathogen sort... |

plot_SS_panel | Plot silver-standard (SS) panel |

plot_three_panel | Plot three-panel figures for nested partially-latent model... |

plot_three_panel_two_folders | Plot three-panel figures for nested partially-latent model... |

rvbern | Sample a vector of Bernoulli variables. |

set_prior_eti | Set the etiology prior |

set_prior_tpr | Set true positive rate (TPR) prior ranges |

set_strat | Stratification setup by covaraites |

simulate_nplcm | Simulation data from nested partially-latent class model... |

simulate_nplcm_known_I | Simulation case data from nested partially-latent class model... |

sort_data_frame | Order rows of data frame according to variable combinations. |

symb2I | Convert names of pathogen/combinations into 0/1 coding |

sym_diff_month | get symmetric difference of months from two vector of... |

unfactor | Convert factor to numeric without losing information on the... |

unique_month | Get unique month from Date |

visualize_case_control_matrix | Visualize matrix for a quantity measured on cases and... |

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