In retodomax/FunRZ: Useful functions

knitr::opts_chunk$set(comment = "##",
                      tidy = FALSE,
                      fig.align = "center",
                      out.width = "80%",
                      fig.width = 7,
                      fig.height = 5,
                      echo = TRUE,
                      warning = FALSE,
                      message = FALSE,
                      error = FALSE)

# automatically create a bib database for R packages
knitr::write_bib(c(
  .packages(), 'bookdown', 'knitr', 'rmarkdown', "mgcv"
), 'bib_packages.bib')

Overall {-}

DiagrammeR::mermaid('
flowchart TD
l([l: input list]) --update--> l
l --> column_rename_fun["column_rename_fun()"]
l --> create_rename_table["create_rename_table()"]
create_rename_table --> column_headers.xlsx
column_headers.xlsx --previous version--> create_rename_table
column_headers.xlsx --fill by hand--> column_header_filled.xlsx
column_header_filled.xlsx --> column_rename_fun
convention_table([convention_table]) --> column_rename_fun
column_rename_fun --> l_renamed
l_renamed --> l_final
l_final --> data_archive_RDS[(data_archive_XXX.RDS)]
l_final --> create_excel_archive["create_excel_archive()"]
column_header_filled.xlsx --> create_excel_archive
convention_table --> create_excel_archive
create_excel_archive --> data_archive_excel[(data_archive_XXX.xlsx)]
data_archive_excel --previous version --> create_excel_archive
data_archive_excel --fill by hand--> data_archive_excel

classDef myfun fill:#f9f
class column_rename_fun myfun
class create_rename_table myfun
class create_excel_archive myfun

linkStyle 0 stroke:green,stroke-width:4px,color:green;
linkStyle 4 stroke:green,stroke-width:4px,color:green;
linkStyle 15 stroke:green,stroke-width:4px,color:green;
linkStyle 16 stroke:green,stroke-width:4px,color:green;
', height = 1000)

`create_rename_table()` {-}

DiagrammeR::mermaid('
flowchart TD
l([l: input list]) --> column_headers
subgraph create_rename_table
column_headers --> file.exists{"file.exists()"}
file.exists --No--> wchs["write_column_headers_sheet()"]
file.exists --Yes--> opened{"opended?"}
opened --No--> archive_necessary{"table & orig_name
combo disappeard?"}
opened --Yes--> error([Error])
archive_necessary --No--> update_column_headers[update column_headers]
update_column_headers --> wchs
archive_necessary --Yes--> save_archive[save archive]
save_archive --> update_column_headers
wchs --> saveWorkbook["saveWorkbook()"]
end
saveWorkbook --> column_headers2(["column_headers.xlsx"])

style wchs fill:#f96
', height = 1200)

DiagrammeR::mermaid('
flowchart TD
column_headers([column_headers])
column_headers --> create_wb["create workbook"]
subgraph wchs["write_column_headers_sheet()"]
create_wb --> style1["Style column `table` & `data_type`"]
style1 --> for_readme_table{for_readme_table}
for_readme_table --No--> column_width[Set column width]
for_readme_table --Yes--> style2["Style column `has_convention`, `current_data_type` & `keep`"]
style2 --> column_width
end
column_width --return--> workbook([workbook])

classDef red fill:#f96
class wchs red
', height = 800)

`column_rename_fun()` {-}

DiagrammeR::mermaid('
flowchart TD

l([l: input list]) --> src[select, rename, change data type]
column_headers([column_headers]) --> column_headers2["column_headers"]
convention_table([convention_table]) --patch--> column_headers2
column_headers2 --> src
l --> checks{"checks
* individual (data type, col, row)
* combined"}
column_headers --> checks
convention_table --> checks
checks --Issue--> Error([Error])
src --> sfl[set factor levels]
sfl --> l2([l])
', height = 800)

`create_excel_archive()` {-}

DiagrammeR::mermaid('
flowchart TD

l([l: input list]) --> checks{"checks
* individual (data type, col, row)
* combined"}
column_headers --> checks
convention_table --> checks

l --> readme
convention_table --> patch_consistent
column_headers --patch--> readme2

subgraph check and join
checks --> Error
readme --> consitent_var_def{"inconsistent variable
definition within dataset"}
consitent_var_def --Yes--> patch_consistent{"patch consistent?"}
consitent_var_def --No--> Error1([Error])
patch_consistent --Yes--> readme2[readme]
patch_consistent --No--> Error2([Error])
end

subgraph write excel
readme2 --> wchs["write_column_headers_sheet()"]
wchs --> write_ERD[write ERD]
write_ERD --> write_data[write data]
write_data --> save_xlsx[save xlsx]
end

save_xlsx --> data_archive_excel[(data_archive_XXX.xlsx)]

style wchs fill:#f96
', height = 800)