extract_data_raw: Convert raw data sheet to analyzable format
In zhenkewu/nplcm: Nested Partially-Latent Class Models (nplcm)

Convert raw data sheet to analyzable format

1 2	extract_data_raw(Pathogen, Specimen, Test, X, Xval, meas_dir, extra_covariates = NULL, silent = TRUE, individual = NULL)

`Pathogen`	The vector of pathogen names. It will be reordered according according to pathogen_type (alphabetical order, "B"->"F"->"V")
`Specimen`	The vector of specimen names
`Test`	The vector of test names
`X`	The vector of covariate names to separately extract data. For example, in PERCH data cleaning, `X = c("newSITE","CASECONT")`
`Xval`	The list of covariate values to stratify data. Each element corresponds to that in `X`. For example, in PERCH data cleaning, `Xval = list("02GAM","1")`
`meas_dir`	The directory to the data set (.csv)
`extra_covariates`	The vector of covariate name for regression purposes. The default is NULL, which means no such covariate is necessary.
`silent`	Default is `TRUE`: the function will not print anything on the screen; otherwise specify as `FALSE`.
`individual`	index for an individual to print his/her measurements