clean_perch_data: Clean PERCH data

In zhenkewu/baker: "Nested Partially Latent Class Models"

Clean PERCH data

Description

clean_perch_data transforms a raw data table (row for subjects, column for variables - named as {pathogen name}_{specimen}{test} for lab tests or other covariates) into a list. It is designed for PERCH data format.

Usage

clean_perch_data(clean_options)

Arguments

clean_options

The list of options for cleaning PERCH data. Its elements are defined as follows: raw_meas_dir : The file path to the raw data; case_def : Variable name in raw data for case definition; case_def_val : The value for case definition; ctrl_def : Variable name in raw data for control definition; ctrl_def_val : The value for control definition; X_strat : A vector of variable names for stratifying the data to perform SEPARATE analyses; X_strat_val : A list of values for X_strat. The output data only have individuals with identical(X_strat,X_strat_val)==TRUE. To perform analysis on a single site, say "02GAM", use X_strat="newSITE" and X_strat_val=list("02GAM"); BrS_objects : A list of BrS objects built by make_meas_object(); SS_objects : A list of SS objects built by make_meas_object(); X_extra : A vector of covariate names for regression or visualization; patho_taxo_dir : The file path to the pathogen category or taxonomy information (.csv). The information should be as complete as possible for a particular analysis. If not, the pathogen without taxonomy information could not be assigned to bacterial or viral groups (see plot_group_etiology()); See assign_taxo_cause_list() that requires this taxonomy information. .

Value

A List: list(Mobs,Y,X)

• Mobs A list of bronze- (MBS), silver- (MSS), and gold-standard (MGS, if available) measurements. See the formats of these measurements in extract_data_raw().

• Y 1 for case; 0 for control;

• X Data frame of covariates for cases and controls. The covariate names are specified in X_extra;

This function does not re-order pathogens that only have silver-standard data.

See Also

make_meas_object for wrapping information about a particular type of measurement; extract_data_raw for reading raw data table and organizing them into data_nplcm format. Also see clean_combine_subsites for combining subsites and parse_date_time for parsing date.

zhenkewu/baker documentation built on May 6, 2024, 11:19 p.m.