Import Raw PERCH Data extract_data_raw imports and converts the raw data to analyzable format

Import Raw PERCH Data

extract_data_raw imports and converts the raw data to analyzable format

Usage

extract_data_raw(
  dat_prepared,
  strat_nm,
  strat_val,
  meas_object,
  extra_covariates = NULL
)

dat_prepared: The data set prepared in clean_perch_data.
strat_nm: The vector of covariate names to separately extract data. For example, in PERCH data cleaning, X = c("newSITE","CASECONT").
strat_val: The list of covariate values to stratify data. Each element corresponds to elements in X. For example, in PERCH data cleaning, Xval = list("02GAM","1").
meas_object: A list of bronze-standard or silver-standard measurement objects made by function make_meas_object().
extra_covariates: The vector of covariate name for regression purposes. The default is NULL, which means not reading in any covariate.

A list of data.

Mobs

MBS: A list of Bronze-Standard (BrS) measurements. The names of the list take the form of specimen_test. Each element of the list is a data frame. The rows of the data frame are for subjects; the columns are for measured pathogens.
MSS: A list of Silver-Standard (SS) measurements. The formats are the same as MBS above.
MGS: A list of Gold-Standard (GS) measurements. It equals NULL if no GS data exist.

X

A data frame with columns specified by extra_covariates.