Use redquack for REDCap API, add parameters to import_instruments(), add codebook functions, and update to 1.2.0

.Rbuildignore

@@ -9,3 +9,4 @@
 ^\.travis\.yml$
 ^doc$
 ^Meta$
+^\.claude$

.gitignore

@@ -44,3 +44,5 @@ inst/doc
 **/.DS_Store
 doc
 Meta
+/doc/
+/Meta/

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: tidyREDCap
 Title: Helper Functions for Working with 'REDCap' Data
-Version: 1.1.2
+Version: 1.2.0
 Authors@R: 
     c(person(
         given = "Raymond",
@@ -50,6 +50,13 @@ Authors@R:
         role = "aut",
         email = "kxg679@miami.edu",
         comment = c(ORCID = "0000-0002-9223-8854")
+      ),
+      person(
+        given = "Dylan",
+        family = "Pieper",
+        role = "aut",
+        email = "dylanpieper@gmail.com",
+        comment = c(ORCID = "0000-0002-2834-7351")
       )
     )
 Description:
@@ -62,11 +69,13 @@ RoxygenNote: 7.3.2
 Depends: R (>= 3.5.0)
 Imports: 
     cli,
+    DBI,
     dplyr,
+    duckdb,
     janitor,
-    labelVector,
-    magrittr,
+    labelled,
     purrr,
+    redquack,
     REDCapR,
     rlang,
     stringr,

NAMESPACE

@@ -1,5 +1,9 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(codebook,data.frame)
+S3method(codebook,default)
+S3method(codebook_convert,data.frame)
+S3method(codebook_convert,default)
 S3method(vec_cast,character.labelled)
 S3method(vec_cast,double.labelled)
 S3method(vec_cast,integer.labelled)
@@ -18,9 +22,11 @@ S3method(vec_ptype2,labelled.integer)
 S3method(vec_ptype2,labelled.labelled)
 S3method(vec_ptype2,labelled.logical)
 S3method(vec_ptype2,logical.labelled)
-export("%>%")
+export(codebook)
+export(codebook_convert)
 export(drop_label)
 export(drop_labels)
+export(has_redcap_values)
 export(import_instruments)
 export(make_binary_word)
 export(make_choose_all_table)
@@ -29,37 +35,52 @@ export(make_instrument)
 export(make_instrument_auto)
 export(make_yes_no)
 export(make_yes_no_unknown)
+importFrom(DBI,dbConnect)
+importFrom(DBI,dbDisconnect)
 importFrom(REDCapR,redcap_metadata_read)
 importFrom(REDCapR,redcap_read)
-importFrom(REDCapR,redcap_read_oneshot)
+importFrom(cli,cli_abort)
+importFrom(cli,cli_alert_info)
+importFrom(cli,cli_h1)
 importFrom(cli,cli_inform)
+importFrom(cli,cli_li)
+importFrom(cli,cli_text)
+importFrom(cli,cli_ul)
+importFrom(cli,cli_warn)
 importFrom(dplyr,across)
+importFrom(dplyr,all_of)
 importFrom(dplyr,bind_cols)
 importFrom(dplyr,case_when)
+importFrom(dplyr,collect)
+importFrom(dplyr,count)
+importFrom(dplyr,distinct)
+importFrom(dplyr,filter)
 importFrom(dplyr,if_else)
 importFrom(dplyr,mutate)
 importFrom(dplyr,pull)
 importFrom(dplyr,rename)
 importFrom(dplyr,select)
 importFrom(dplyr,starts_with)
 importFrom(dplyr,summarise_all)
+importFrom(dplyr,sym)
+importFrom(dplyr,tbl)
+importFrom(duckdb,duckdb)
 importFrom(janitor,adorn_pct_formatting)
 importFrom(janitor,tabyl)
-importFrom(labelVector,is_labelled)
-importFrom(labelVector,set_label)
-importFrom(magrittr,"%>%")
+importFrom(labelled,"var_label<-")
+importFrom(labelled,var_label)
 importFrom(purrr,map_chr)
 importFrom(purrr,map_df)
 importFrom(purrr,map_lgl)
+importFrom(redquack,redcap_to_db)
+importFrom(rlang,"!!")
 importFrom(rlang,.data)
-importFrom(stringr,fixed)
 importFrom(stringr,regex)
 importFrom(stringr,str_count)
 importFrom(stringr,str_detect)
 importFrom(stringr,str_extract)
 importFrom(stringr,str_locate)
-importFrom(stringr,str_remove)
-importFrom(stringr,str_remove_all)
+importFrom(stringr,str_replace)
 importFrom(stringr,str_replace_na)
 importFrom(stringr,str_sub)
 importFrom(tibble,enframe)
@@ -68,5 +89,6 @@ importFrom(tidyselect,ends_with)
 importFrom(tidyselect,everything)
 importFrom(tidyselect,starts_with)
 importFrom(tidyselect,vars_select_helpers)
+importFrom(utils,head)
 importFrom(vctrs,vec_cast)
 importFrom(vctrs,vec_ptype2)

NEWS.md

@@ -1,149 +1,182 @@
+---
+editor_options: 
+  markdown: 
+    wrap: 72
+---
+
+# tidyREDCap 1.2 (CRAN release)
+
+-   Change import package to redquack
+    (<https://github.com/dylanpieper/redquack/tree/main/R>)
+-   Add parameters to function `import_instruments()`:
+    -   `filter_instrument` and `filter_function` for lazy data
+        filtering
+    -   `return_list` for returning a list of instrument data.frames
+    -   `labels` for adding/removing column labels
+-   Add `codebook()` function for generating structured metadata
+    documentation
+-   Add `codebook_convert()` function for converting coded values to
+    labeled equivalents using stored metadata
+-   Add `has_redcap_values()` helper function for identifying columns
+    with REDCap value labels
+
 # tidyREDCap 1.1.2 (CRAN release)
 
-* Fix issues reported by CRAN with Linux and old R Windows (4.3.3) saying 
+-   Fix issues reported by CRAN with Linux and old R Windows (4.3.3)
+    saying
 
-```
+```         
 ✖ These names are duplicated:
     * "record_id" at locations 1 and 2.
 ```
 
-+ Update roxygen2 version (Thank you for Will Beasley)
-+ Fix .data$ was depreciated in `tidyselect` (https://github.com/r-lib/tidyselect/issues/169)
-+ Fixed missing global bindings caused by `tidyselect` fix.
+-   Update roxygen2 version (Thank you for Will Beasley)
+-   Fix .data\$ was depreciated in `tidyselect`
+    (<https://github.com/r-lib/tidyselect/issues/169>)
+-   Fixed missing global bindings caused by `tidyselect` fix.
 
 # tidyREDCap 1.1.1 (CRAN release)
 
 ## New features
 
-* Add `make_yes_no()` function to convert "checked" or "yes"-like answers to 
-  "Yes" and other answers to "No or Unknown".
-* Add `make_yes_no_unknown()` function to convert "checked" or "yes"-like 
-  answers to "Yes", unchecked or "no"-like answers to "No" and other answers to
-  "Unknown".
-  
+-   Add `make_yes_no()` function to convert "checked" or "yes"-like
+    answers to "Yes" and other answers to "No or Unknown".
+-   Add `make_yes_no_unknown()` function to convert "checked" or
+    "yes"-like answers to "Yes", unchecked or "no"-like answers to "No"
+    and other answers to "Unknown".
+
 ## Fixes/Changes
-* `make_choose_all_table()` now works with api or manual/point-and-click 
-  exports.
-## Added S3 methods so dplyr (and friends) can work with labelled objects
 
-# tidyREDCap 1.1.0  (CRAN release)
+-   `make_choose_all_table()` now works with api or
+    manual/point-and-click exports. \## Added S3 methods so dplyr (and
+    friends) can work with labelled objects
+
+# tidyREDCap 1.1.0 (CRAN release)
 
 ## New features
 
-* Add `drop_labels()` function for datasets. Used to deal with packages/functions 
-  that don't want labeled variables (i.e. `dplyr::pivot_longer()` and `skimr::skim()`
-* Added options (`record_id =` and `first_record_id =` for custom record_id fields in `import_instruments()`
-* Added repeat instance numbers for repeated instruments in `import_instruments()`
+-   Add `drop_labels()` function for datasets. Used to deal with
+    packages/functions that don't want labeled variables (i.e.
+    `dplyr::pivot_longer()` and `skimr::skim()`
+-   Added options (`record_id =` and `first_record_id =` for custom
+    record_id fields in `import_instruments()`
+-   Added repeat instance numbers for repeated instruments in
+    `import_instruments()`
 
 ## Fixes/Changes
 
-* Documentation fixes
-  + Suppress warning caused by dplyr 1.1
-  + fix wrong function in api vignette
+-   Documentation fixes
+    -   Suppress warning caused by dplyr 1.1
+    -   fix wrong function in api vignette
 
 ## Minor improvements and fixes
 
-* Add unit test on import_instruments() function call.
-
+-   Add unit test on import_instruments() function call.
 
-# tidyREDCap 1.0.1.9001  (dev version)
+# tidyREDCap 1.0.1.9001 (dev version)
 
 ## Fixes/Changes
 
-* Fixed bug that caused labels to be missing if they contained parentheses
+-   Fixed bug that caused labels to be missing if they contained
+    parentheses
 
-# tidyREDCap 1.0.1.9000  (dev version)
+# tidyREDCap 1.0.1.9000 (dev version)
 
 ## New features
 
-* Add drop label function
+-   Add drop label function
 
 ## Fixes/Changes
 
-* Fix message display bug while `import_instruments()` runs
-* Fix bug with `import_instruments()` loading repeated instruments (the first instrument in a project was badly messed up)
-* Row names no longer reflect the row number of the exported data
-* Remove labels from a few automatically created REDCap variables ("record_id", "redcap_event_name", "redcap_repeat_instrument", "redcap_repeat_instance")
-
+-   Fix message display bug while `import_instruments()` runs
+-   Fix bug with `import_instruments()` loading repeated instruments
+    (the first instrument in a project was badly messed up)
+-   Row names no longer reflect the row number of the exported data
+-   Remove labels from a few automatically created REDCap variables
+    ("record_id", "redcap_event_name", "redcap_repeat_instrument",
+    "redcap_repeat_instance")
 
-# tidyREDCap 1.0.1  (CRAN release)
+# tidyREDCap 1.0.1 (CRAN release)
 
 ## New features
 
-* Added support for REDCapR API
-  - `import_instruments()` function imports all instruments with a single command
-  - Added targeted status messaging during the import
-
-## Minor improvements and fixes
+-   Added support for REDCapR API
+    -   `import_instruments()` function imports all instruments with a
+        single command
+    -   Added targeted status messaging during the import
 
-* `make_choose_one_table()` no longer requires factors
-* `make_choose_all_table()` now works with "1" vs "0" indicator variables
-* Greatly improved vignettes
+## Minor improvements and fixes
 
-# tidyREDCap 1.0.0.9002  (dev version)
+-   `make_choose_one_table()` no longer requires factors
+-   `make_choose_all_table()` now works with "1" vs "0" indicator
+    variables
+-   Greatly improved vignettes
 
-* Add {REDCapR} support
-* Added `import_instruments()` function to import all instruments; currently uses the `REDCapR` package as the API
+# tidyREDCap 1.0.0.9002 (dev version)
 
+-   Add {REDCapR} support
+-   Added `import_instruments()` function to import all instruments;
+    currently uses the `REDCapR` package as the API
 
-# tidyREDCap 1.0.0.9001  (dev version)
+# tidyREDCap 1.0.0.9001 (dev version)
 
-* Fix bug in `make_choose_all_table()` with repeating instruments showing NA counts
-* Removes superseded `summarise_all()` function
+-   Fix bug in `make_choose_all_table()` with repeating instruments
+    showing NA counts
+-   Removes superseded `summarise_all()` function
 
-# tidyREDCap 1.0.0.9000  (dev version)
+# tidyREDCap 1.0.0.9000 (dev version)
 
-* Removes superseded `mutate_if` and `mutate_all` from `make_choose_all_table()`
-* Added `import_instruments()` function
-* Added `make_instrument_auto()` function
-* Adds checks on arguments
+-   Removes superseded `mutate_if` and `mutate_all` from
+    `make_choose_all_table()`
+-   Added `import_instruments()` function
+-   Added `make_instrument_auto()` function
+-   Adds checks on arguments
 
-# tidyREDCap 0.2.2  (CRAN patch)
+# tidyREDCap 0.2.2 (CRAN patch)
 
-* Fix `rlang` bug in `make_choose_all_table()`; see <https://github.com/RaymondBalise/tidyREDCap/pull/13>
+-   Fix `rlang` bug in `make_choose_all_table()`; see
+    <https://github.com/RaymondBalise/tidyREDCap/pull/13>
 
-# tidyREDCap 0.2.1  (CRAN release)
+# tidyREDCap 0.2.1 (CRAN release)
 
-* Fix bug with "" character stings with make_instrument()
+-   Fix bug with "" character stings with make_instrument()
 
 # tidyREDCap 0.2.0 (CRAN release)
 
-* Cleaned up vignettes, docs
+-   Cleaned up vignettes, docs
 
-# tidyREDCap 0.1.3.1 
+# tidyREDCap 0.1.3.1
 
-* Cleaned up vignettes, docs
+-   Cleaned up vignettes, docs
 
-# tidyREDCap 0.1.3.0 
+# tidyREDCap 0.1.3.0
 
-* Added `make_choose_all_table()` function
+-   Added `make_choose_all_table()` function
 
-# tidyREDCap 0.1.2.1 
+# tidyREDCap 0.1.2.1
 
-* Cleaned up vignettes
+-   Cleaned up vignettes
 
-# tidyREDCap 0.1.2 
+# tidyREDCap 0.1.2
 
-* Added `make_instrument()` function
+-   Added `make_instrument()` function
 
 # tidyREDCap 0.1.1
 
-* Added `make_choose_one_table()` function
+-   Added `make_choose_one_table()` function
 
 # tidyREDCap 0.1.0 (CRAN release)
 
-* Fixed title capitalization.
-* Added reference to REDCap website.
-* Updated the release year in the license.
-* Updated hyperlinks to vignettes and example instrument description.
-* Added references to financial support in the ReadMe.
+-   Fixed title capitalization.
+-   Added reference to REDCap website.
+-   Updated the release year in the license.
+-   Updated hyperlinks to vignettes and example instrument description.
+-   Added references to financial support in the ReadMe.
 
 # tidyREDCap 0.0.0.9005
 
-* Added check on number of arguments
+-   Added check on number of arguments
 
 # tidyREDCap 0.0.0.9004
 
-* Added a `NEWS.md` file to track changes to the package.
-
-
+-   Added a `NEWS.md` file to track changes to the package.