clean_perch_data function

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.

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.

Returns

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.