extract_data_raw: Import Raw PERCH Data 'extract_data_raw' imports and converts...
In oslerinhealth-releases/baker: Bayesian Analysis Kit for Etiology Research

Import Raw PERCH Data

extract_data_raw imports and converts the raw data to analyzable format

1 2	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.