fixed preprocessing scripts #712

[thibaud-porphyre]

Some of the preprocessing script were not working due to various bugs. this pull request is solving some of the issues in #712.

[kzscisoft]

@thibaud-porphyre this still does not work for me I get the exact same error! Also do we need .Rhistory in the branch?

$ Rscript eeraModel_data_preprocessing.r

Error: Assigned data `values` must be compatible with existing data.
ℹ Error occurred for column `Ayrshire and Arran`.
✖ Can't convert <double> to <character>.
Backtrace:
     █
  1. ├─global::extend_epi_records(...)
  2. │ └─`%>%`(...)
  3. │   ├─base::withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
  4. │   └─base::eval(quote(`_fseq`(`_lhs`)), env, env)
  5. │     └─base::eval(quote(`_fseq`(`_lhs`)), env, env)
  6. │       └─`_fseq`(`_lhs`)
  7. │         └─magrittr::freduce(value, `_function_list`)
  8. │           ├─base::withVisible(function_list[[k]](value))
  9. │           └─function_list[[k]](value)
 10. │             └─base::replace(., is.na(.), -999)
 11. │               ├─base::`[<-`(`*tmp*`, list, value = -999)
 12. │               └─tibble:::`[<
Execution halted