clean_perch_data: Clean PERCH data

View source: R/clean-perch-data.R

clean_perch_dataR Documentation

Clean PERCH data


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.





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..


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 March 17, 2022, 9:54 p.m.