0046 assign datetime (#52)

* First mockup of `hardcode_no_ct()`

* Update `hardcode_no_ct()`

Update `hardcode_no_ct()` by allowing the rewriting of the `target_sdtm_variable` variable to preserve `NA`

* Align `hardcode_no_ct()` code style with Ramm's expectations

* Add `hardcode_*()` and `assign_*()` functions

* hardcode_no_ct algorithm code changes (#45)

* hardcode_no_ct algorithm code changes

* harcode_ct working as expected

* assign_ct and assign_no_ct works great.

* address review comments

* Add `oak_id_vars()`

* Fix typo in `recode()`

* Simplify `oak_id_vars()` docs

* Update `assign_*` and `hardcode_*` implementations

* Introduce memoisation of `ct_mappings()`

* Update of README introductory paragraph

* Update hardcode_* functions' interface

* Add `contains_oak_id_vars()` function

* Update `contains_oak_id_vars()` doc examples

* Update `sdtm_harcode()` and dependant functions

* Update `assign_*` and `hardcore_*` related functions

* Automatic renv profile update.

* Automatic renv profile update.

* Make `ct` and `cl` parameters mandatory for `assign_ct()`

* Add functions ct importing

- Adds three new user facing ct-related functions: `read_ct_example()`, `ct_example()` and `read_ct()`
- Provides a ct example file in inst/ct/

* Bring `hardcode*()` and `assign*()` related assertions closer to user calling functions

* Add lagging behind Rd for `ct_example()`

* Add `assert_ct()`

* Add ct assertions

* Remove R/.gitkeep

As it is no longer needed.

* Add unit tests for `ct_vars()`

* Update dependencies

* Export `ct_vars()`

Export `ct_vars()` such that we can cross-reference it from other functions' documentation.

* Update `assert_ct()` docs

* Clarify `assign_ct()`/`assign_no_ct()` doc

* Improve grammar in doc

* Remove last empty line from ct example file

* Add documentation to `sdtm_assign()` and ct-related unit tests

Although we had discussed to keep assertions only at the user facing functions, I am getting the feeling we would miss assertions also at the internal function... because of several reasons: firstly, the internal function is more flexible having more optional parameters, which requires extra assertion logic, and also because eventually we will be checking code coverage and we will regret not having done this now.

* Update hardcode-related fns

* Changes to meet linter issues

* Code reformatting

* Code reflow

* Improve `assert_cl()` docs

* Update `read_ct()` docs

* Automatic renv profile update.

* Automatic renv profile update.

* Add units tests for `recode()`

* Remove `are_to_recode()` function

Ended up not using this function.

* Add units tests for `assert_ct()`

* Add one more test for `assert_ct()`

* Add a basic unit test for `ct_mappings()`

* Fill in some doc details of ct-related functions

* Remove leftover doc text in `assign`

* Update website's reference

* Styling update

* Bump version and update NEWS

* Fix a few lintr issues

* Add examples to `ct_map()` doc

* Fix typo in `problems()` doc

* Fix typo

* Initial mockup of `assign_datetime()`

* Add `.warn` parameter to `create_iso8601()` internals

* Remove lint issues

* Replace `.data` usage in tidyselect expressions

See tidyverse/tidyverse.org#600 for more details.

* Variable renaming

- `ct` to `ct_spec` (ct specification)
- `cl` to `ct_cltc` (codelist code)

* Finish pending renaming of variables

* Rename code-list to codelist

* Fix style

* Fix style

* Add assertions to `assign_datetime()`

* Add merge example to `assign_datetime()` doc

* Style changes

* Style changes (.Rd)

* Bump version and update news

* Update `ct_map()` doc example

* Make tibbles more readable in doc examples

* Rename `ct_cltc` to `ct_clst`

As per @rammprasad's suggestion.

* Fix bug in `assign_datetime`

- This bug is related to the support of input is in two different variables (date and time).
- A unit test was also added

* Linting

* Update styling

* Add example with date and time to `assign_datetime()` docs

* Avoid backslash hell (մերսի)

Credit goes to @edgar-manukya for the expression

* Update `ct_spec_vars()` docs' examples

`ct_spec_vars()` used to be an internal function but not anymore: so no need for `:::`.

* Fix typo in `assign_datetime()` documentation

* Fix typo in `ct_map()` docs

---------

Co-authored-by: Ram Ganapathy <[email protected]>
Co-authored-by: ramiromagno <[email protected]>

R/assign_datetime.R

@@ -22,7 +22,7 @@
 #'   the variables indicated in `id_vars`. This parameter is optional, see
 #'   section Value for how the output changes depending on this argument value.
 #' @param id_vars Key variables to be used in the join between the raw dataset
-#'   (`raw_dat`) and the target data set (`raw_dat`).
+#'   (`raw_dat`) and the target data set (`tgt_dat`).
 #' @param .warn Whether to warn about parsing failures.
 #'
 #' @returns The returned data set depends on the value of `tgt_dat`:

R/ct.R

@@ -289,7 +289,7 @@ ct_mappings <- function(ct_spec, from = ct_spec_vars("from"), to = ct_spec_vars(
 #' # Note that if the controlled terminology mapping is restricted to a codelist
 #' # code, e.g. C71113, then only `"/day"` and `"Every 2 hours"` get mapped to
 #' # `"QD"` and `"Q2H"`, respectively; remaining terms won't match given the
-#' # codelist code # restriction, and will be mapped to an uppercase version of
+#' # codelist code restriction, and will be mapped to an uppercase version of
 #' # the original terms.
 #' ct_map(x = terms, ct_spec = ct_spec, ct_clst = "C71113")
 #'