Man pages for zhenkewu/nplcm
Nested Partially-Latent Class Models (nplcm)

assign_modelChoose a model to fit
beta_parms_from_quantilesPick parameters in the Beta distribution to match the...
beta_plotPlot beta density
bin2decConvert 0/1 binary coded sequence into decimal digits
check_common_patternPosterior predictive checking for the nested partially class...
check_common_pattern_two_foldersPosterior predictive checking for the nested partially class...
check_pairwise_logORPosterior predictive checking for nested partially latent...
check_pairwise_logOR_two_foldersPosterior predictive checking for nested partially latent...
clean_combine_subsitesCombine subsites in raw PERCH data set
clean_perch_dataClean PERCH data
create_bugs_regressor_Eticreate regressor summation equation used in regression for...
create_bugs_regressor_FPRcreate regressor summation equation used in regression for...
delete_start_withDeletes a pattern from the start of a string, or each of a...
dm_Rdate_EtiMake etiology design matrix for dates with R format.
dm_Rdate_FPRMake FPR design matrix for dates with R format.
expitexpit function
extract_data_rawConvert raw data sheet to analyzable format
get_mseObtain MSE, bias-squared and variance of posterior from nplcm...
getPckgGet package from CRAN website
I2symbConvert 0/1 coding to pathogen/combinations
Imat2catConvert a matrix of binary indicators to categorial variables
is_discreteCheck if covariates are discrete
is.errorTest for 'try-error' class
load_or_installLoad or install a package
logitlogit function
logORcalculate pairwise log odds ratios
make_filenameCreate new file name
make_foldernameCreate new folder name
make_listTakes any number of R objects as arguments and returns a list...
my_reorderReorder the measurement dimensions to match the order for...
NA2dotconvert 'NA' to '.'
nplcmFit nested partially latent class models (high-level)
nplcm_fit_NoReg_BrSandSS_NestFit nested partially-latent class model (low-level)
nplcm_fit_NoReg_BrSandSS_Nest_SSonlyFit nested partially-latent class model (low-level)
nplcm_fit_NoReg_BrSandSS_NoNestFit nested partially-latent class model (low-level)
nplcm_fit_NoReg_BrSandSS_NoNest_SSonlyFit nested partially-latent class model (low-level)
nplcm_fit_NoReg_BrS_NestFit nested partially-latent class model (low-level)
nplcm_fit_NoReg_BrS_NoNestFit nested partially-latent class model (low-level)
nplcm_fit_Reg_BrS_NoNestFit nested partially-latent class model with regression...
nplcm_fit_Strat_BrS_NoNestFit nested partially-latent class model with stratification...
nplcm_read_folderRead data and other model information from a folder that...
null_as_zeroConvert 'NULL' to zero.
plot_BrS_panelPlot bronze-standard (BrS) panel
plot_etiology_music_sheetcompare the posterior distribution of population etiologies...
plot_group_etiologyPlot viral etiology posterior and distribution within...
plot_individual_diagnosisIndividual prediction from nested partially-latent class...
plot_individual_diagnosis_two_foldersIndividual prediction from nested partially-latent class...
plot_logORmatVisualize pairwise log odds ratios (LOR) for data that are...
plot_pie_panelPlot etiology (pie) panel
plot_pie_panel_two_foldersPlot etiology (pie) panel
plot_skylineDistribution of individual prediction for each pathogen sort...
plot_SS_panelPlot silver-standard (SS) panel
plot_three_panelPlot three-panel figures for nested partially-latent model...
plot_three_panel_two_foldersPlot three-panel figures for nested partially-latent model...
rvbernSample a vector of Bernoulli variables.
set_prior_etiSet the etiology prior
set_prior_tprSet true positive rate (TPR) prior ranges
set_stratStratification setup by covaraites
simulate_nplcmSimulation data from nested partially-latent class model...
simulate_nplcm_known_ISimulation case data from nested partially-latent class model...
sort_data_frameOrder rows of data frame according to variable combinations.
symb2IConvert names of pathogen/combinations into 0/1 coding
sym_diff_monthget symmetric difference of months from two vector of...
unfactorConvert factor to numeric without losing information on the...
unique_monthGet unique month from Date
visualize_case_control_matrixVisualize matrix for a quantity measured on cases and...
zhenkewu/nplcm documentation built on May 28, 2017, 1:43 p.m.