clean_perch_data {baker} | R Documentation |
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.
[Package
baker version 1.0.3
Index]