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.
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 withidentical(X_strat,X_strat_val)==TRUE
. To perform analysis on a single site, say"02GAM"
, useX_strat="newSITE"
andX_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()
); Seeassign_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 inextract_data_raw()
.Y
1 for case; 0 for control;X
Data frame of covariates for cases and controls. The covariate names are specified inX_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.