Merge pull request #136 from pharmaverse/supp-messaging

Enhance user experience and package feedback for various functions in R/supp and R/checks

Author: LiamHobby

DESCRIPTION

@@ -46,4 +46,4 @@ Encoding: UTF-8
 Language: en-US
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3

NEWS.md

@@ -1,41 +1,110 @@
+---
+editor_options: 
+  markdown: 
+    wrap: 72
+---
+
 # metatools 0.3.0
-* Bugfix issue in `create_var_from_codelist()` where supplied codelist contains negative numeric values. (#111)
+
+-   Enhancement: `verbose` Adds a verbose parameter to
+    `build_from_derived()`, `set_variable_labels()`, and `build_qnam()`
+    to allow users to suppress informational messages and warnings
+    during execution. Permissible values "message", "warn", "silent".
+
+-   Enhancement: `verbose` parameter also added to `check_ct_col` and
+    `check_ct_data`. Warnings cannot be suppressed for these functions
+    to prevent unnoticed data quality issues. Permissible values
+    "message", "warn". [#136](https://github.com/pharmaverse/metatools/pull/136)
+
+-   Enhancement: `add_labels()` now prints out variables that do not
+    exist in the dataset.
+    [#113](https://github.com/pharmaverse/metatools/pull/113)
+
+-   Bugfix issue where `create_var_from_codelist()` would throw an error
+    when `strict=TRUE` and `input_var` was numeric.
+    [#111](https://github.com/pharmaverse/metatools/pull/108)
+
+-   Bugfix issue in `create_var_from_codelist()` where supplied codelist
+    contains negative numeric
+    values.[#102](https://github.com/pharmaverse/metatools/pull/102)
+
+-   Bugfix logic for detecting variable mismatches in
+    `set_variable_labels()`.
+    [#112](https://github.com/pharmaverse/metatools/pull/112)
+
+-   Bugfix `combine_supp_join()` no longer throws an error when rows
+    exist in the supp that do not correspond to a record in the core
+    dataset. [#115](https://github.com/pharmaverse/metatools/pull/115)
+
+-   Various updates and refinements to documentation. - GitHub workflows
+    for package styling and spelling enabled.
+    [#128](https://github.com/pharmaverse/metatools/pull/128)
 
 # metatools 0.2.0
-* Functions now require a subsetted metacore object to be used i.e., created via `metacore::select_dataset()`.
-* `create_cat_var()` now allows the new variable to be create using the `decode` part of the codelist as a label.(#82)
-* `create_var_from_codelist()` now allows the user to specify a codelist to use to create the new variables. (#83)
-* `check_variables()` now provides a `strict` option that issues warnings rather than errors when `FALSE`. (#86)
-* `combine_supp()` now adds labels from the "QLABEL" (#71)
-* `combine_supp()` no longer creates an "IDVARVAL" column (#78)
-* Improved error reporting for `create_cat_var`, `create_var_from_codelist`, and `check_variables`.
-* The `dataset_name` argument has been deprecated in various functions.
-* The `make_lone_dataset` function has been deprecated. 
+
+-   Functions now require a subsetted metacore object to be used i.e.,
+    created via `metacore::select_dataset()`.
+-   `create_cat_var()` now allows the new variable to be create using
+    the `decode` part of the codelist as a label.(#82)
+-   `create_var_from_codelist()` now allows the user to specify a
+    codelist to use to create the new variables. (#83)
+-   `check_variables()` now provides a `strict` option that issues
+    warnings rather than errors when `FALSE`. (#86)
+-   `combine_supp()` now adds labels from the "QLABEL" (#71)
+-   `combine_supp()` no longer creates an "IDVARVAL" column (#78)
+-   Improved error reporting for `create_cat_var`,
+    `create_var_from_codelist`, and `check_variables`.
+-   The `dataset_name` argument has been deprecated in various
+    functions.
+-   The `make_lone_dataset` function has been deprecated.
 
 # metatools 0.1.6
-* Breaking change: `combine_supp()` requires that the QNAM columns are not in the source dataset (#64)
-* Breaking change: `build_from_derived()` no longer requires all datasets with predecessors, but can run on a single dataset or multiple. It will also now accept unnamed datasets. 
-* `combine_supp()` now allows multiple `QNAM` values to go to the same `IDVAR` (#63)
-* Allow supp data to be zero-row with `combine_supp()` (#45)
-* Enhance `check_ct_data()` so that `na_acceptable` can now accept a vector of variables. Also add new argument `omit_vars` to control if any variables should be skipped when doing controlled terminology checks (#57)
-* Add `check_unique_keys()` to check the uniqueness of records in the dataset by variable keys (#52)
-* Correct the description of `build_from_derived()` predecessor_only parameter
+
+-   Breaking change: `combine_supp()` requires that the QNAM columns are
+    not in the source dataset (#64)
+-   Breaking change: `build_from_derived()` no longer requires all
+    datasets with predecessors, but can run on a single dataset or
+    multiple. It will also now accept unnamed datasets.
+-   `combine_supp()` now allows multiple `QNAM` values to go to the same
+    `IDVAR` (#63)
+-   Allow supp data to be zero-row with `combine_supp()` (#45)
+-   Enhance `check_ct_data()` so that `na_acceptable` can now accept a
+    vector of variables. Also add new argument `omit_vars` to control if
+    any variables should be skipped when doing controlled terminology
+    checks (#57)
+-   Add `check_unique_keys()` to check the uniqueness of records in the
+    dataset by variable keys (#52)
+-   Correct the description of `build_from_derived()` predecessor_only
+    parameter
 
 # metatools 0.1.4
-* correct bug with `combine_supp()` when the data and the supp have white space. Now it will be trimmed before attempting to merge  
-* Updates made to work with the newest version of dplyr 
+
+-   correct bug with `combine_supp()` when the data and the supp have
+    white space. Now it will be trimmed before attempting to merge\
+-   Updates made to work with the newest version of dplyr
 
 # metatools 0.1.3
-* correct bug with `build_from_derived()` that prevented multiple from being combined 
-* removed library calls from tests 
-* remove `floating_pt_correction` from `combine_supp()` as it is best to never change the type of the main dataset 
-* Add a message to `drop_unspec_vars` to explain which variables are dropped 
-* Correct bug in `order_cols`, so it will still work when not all columns are present 
+
+-   correct bug with `build_from_derived()` that prevented multiple from
+    being combined
+-   removed library calls from tests
+-   remove `floating_pt_correction` from `combine_supp()` as it is best
+    to never change the type of the main dataset
+-   Add a message to `drop_unspec_vars` to explain which variables are
+    dropped
+-   Correct bug in `order_cols`, so it will still work when not all
+    columns are present
 
 # metatools 0.1.2
-* correct bug with `combine_supp()` when the data and the supp have different classes for the IDVARVAL
-* add error to `combine_supp()` to report when not all the rows in the supp have merged
-* add `floating_pt_correction` argument to `combine_supp()` used for when there are floating point errors with `IDVARVAL`
+
+-   correct bug with `combine_supp()` when the data and the supp have
+    different classes for the IDVARVAL
+-   add error to `combine_supp()` to report when not all the rows in the
+    supp have merged
+-   add `floating_pt_correction` argument to `combine_supp()` used for
+    when there are floating point errors with `IDVARVAL`
 
 # metatools 0.1.1
-* Based on tester feedback, remove any row in supplemental qualifiers that are empty and rearranged the columns
+
+-   Based on tester feedback, remove any row in supplemental qualifiers
+    that are empty and rearranged the columns