version 2.0.1

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: dataquieR
 Title: Data Quality in Epidemiological Research
-Version: 2.0.0
+Version: 2.0.1
 Authors@R: 
     c(person(given = "University Medicine Greifswald",
              role = "cph"),
@@ -45,27 +45,28 @@ Description: Data quality assessments guided by a
     individually tailored reports can be generated. For an introduction
     into the specification of corresponding metadata, please refer to the
     'package website'
-    <https://dataquality.ship-med.uni-greifswald.de/Annotation_of_Metadata.html>.
+    <https://dataquality.qihs.uni-greifswald.de/Annotation_of_Metadata.html>.
 License: BSD_2_clause + file LICENSE
-URL: https://dataquality.ship-med.uni-greifswald.de/
+URL: https://dataquality.qihs.uni-greifswald.de/
 BugReports: https://gitlab.com/libreumg/dataquier/-/issues
 Depends: R (>= 3.6.0)
 Imports: dplyr (>= 1.0.2), emmeans, ggplot2 (>= 3.4.0), lme4,
         lubridate, MASS, MultinomialCI, parallelMap, patchwork,
         R.devices, reshape, rlang, robustbase, qmrparser, utils, rio,
         scales
-Suggests: cli, whoami, lifecycle, anytime, cowplot (>= 0.9.4), digest,
+Suggests: lifecycle, cli, whoami, anytime, cowplot (>= 0.9.4), digest,
         DT (>= 0.23), flexdashboard, flexsiteboard, htmltools, knitr,
-        markdown, parallel, rmarkdown, rstudioapi, testthat (>= 3.0.0),
-        tibble, vdiffr, pkgload, Rdpack, callr, colorspace, withr,
-        plotly, ggvenn, htmlwidgets
+        markdown, parallel, parallelly, rJava, rmarkdown, rstudioapi,
+        testthat (>= 3.1.9), tibble, vdiffr, pkgload, Rdpack, callr,
+        colorspace, withr, plotly, ggvenn, htmlwidgets, future,
+        processx, R6, shiny, summarytools
 VignetteBuilder: knitr
 Encoding: UTF-8
 KeepSource: TRUE
 Language: en-US
 RoxygenNote: 7.2.3
 NeedsCompilation: no
-Packaged: 2023-03-01 16:10:20 UTC; struckmanns
+Packaged: 2023-07-19 15:58:59 UTC; struckmanns
 Author: University Medicine Greifswald [cph],
   Elisa Kasbohm [aut] (<https://orcid.org/0000-0001-5261-538X>),
   Joany Marino [aut] (<https://orcid.org/0000-0002-4657-3758>),
@@ -80,4 +81,4 @@ Author: University Medicine Greifswald [cph],
     No. 825903) [fnd]
 Maintainer: Stephan Struckmann <stephan.struckmann@uni-greifswald.de>
 Repository: CRAN
-Date/Publication: 2023-03-01 16:30:02 UTC
+Date/Publication: 2023-07-19 16:20:10 UTC

LICENSE

@@ -1,2 +1,2 @@
-YEAR: 2017-2022
+YEAR: 2017-2023
 COPYRIGHT HOLDER: University Medicine Greifswald, Greifswald, GERMANY.

NAMESPACE

@@ -17,6 +17,17 @@ S3method(rbind,ReportSummaryTable)
 S3method(resnames,dataquieR_resultset2)
 S3method(summary,dataquieR_resultset)
 S3method(summary,dataquieR_resultset2)
+export(.get_internal_api)
+export(API_VERSION)
+export(ASSOCIATION_DIRECTION)
+export(ASSOCIATION_FORM)
+export(ASSOCIATION_METRIC)
+export(ASSOCIATION_RANGE)
+export(CHECK_ID)
+export(CHECK_LABEL)
+export(CONTRADICTION_TERM)
+export(CONTRADICTION_TYPE)
+export(DATA_PREPARATION)
 export(DATA_TYPES)
 export(DATA_TYPES_OF_R_TYPE)
 export(DF_ELEMENT_COUNT)
@@ -28,21 +39,29 @@ export(DF_RECORD_COUNT)
 export(DF_UNIQUE_ID)
 export(DF_UNIQUE_ROWS)
 export(DISTRIBUTIONS)
+export(GOLDSTANDARD)
+export(MULTIVARIATE_OUTLIER_CHECKTYPE)
+export(N_RULES)
+export(REL_VAL)
 export(SEGMENT_ID_TABLE)
 export(SEGMENT_ID_VARS)
+export(SEGMENT_MISS)
 export(SEGMENT_PART_VARS)
 export(SEGMENT_RECORD_CHECK)
 export(SEGMENT_RECORD_COUNT)
 export(SEGMENT_UNIQUE_ROWS)
 export(SPLIT_CHAR)
+export(UNIVARIATE_OUTLIER_CHECKTYPE)
 export(VARATT_REQUIRE_LEVELS)
+export(VARIABLE_LIST)
 export(VARIABLE_ROLES)
 export(WELL_KNOWN_META_VARIABLE_NAMES)
 export(acc_distributions)
 export(acc_distributions_loc)
 export(acc_distributions_loc_ecdf)
+export(acc_distributions_only)
+export(acc_distributions_only_ecdf)
 export(acc_distributions_prop)
-export(acc_distributions_prop_ecdf)
 export(acc_end_digits)
 export(acc_loess)
 export(acc_margins)
@@ -88,6 +107,7 @@ export(prep_add_data_frames)
 export(prep_add_missing_codes)
 export(prep_add_to_meta)
 export(prep_apply_coding)
+export(prep_check_for_dataquieR_updates)
 export(prep_check_meta_data_dataframe)
 export(prep_check_meta_data_segment)
 export(prep_check_meta_names)
@@ -102,6 +122,7 @@ export(prep_get_data_frame)
 export(prep_get_user_name)
 export(prep_link_escape)
 export(prep_list_dataframes)
+export(prep_load_report)
 export(prep_load_workbook_like_file)
 export(prep_map_labels)
 export(prep_merge_study_data)
@@ -110,6 +131,7 @@ export(prep_min_obs_level)
 export(prep_pmap)
 export(prep_prepare_dataframes)
 export(prep_purge_data_frame_cache)
+export(prep_save_report)
 export(prep_study2meta)
 export(prep_title_escape)
 export(prep_valuelabels_from_data)

NEWS.md

@@ -1,3 +1,53 @@
+# dataquieR 2.0.1
+
+## Reporting 
+  * New functions `prep_save_report` and `prep_load_report`
+  * Update and simplification of summary overview, empty columns/rows omitted from the matrices. Also, better classification of errors
+  * Many small updates in the usability of the report
+  * Fixes in `HTML/JS` output for `Firefox`
+  * Bug fixes of report outputs that were not looking as expected (in contradiction checks and limit violations)
+  * Fixed mixed distribution plots called several times
+  * Enable auto-resizing of `plot.ly`-plots
+  * Fixed rendering problems for the new, automatically size-reduced plots causing the report rendering to fail if having `gginnards` installed; removed dependency from `gginnards`.
+  * Do not show superfluous axis labels (e.g., variables, if variable names are on an axis because these usually overlap without improving the output)
+  * Prevent a warning of `robustbase` about `doScale`
+  * Less noisy display of conditions (e.g., warnings, errors, messages) with the results in `dq_report2` reports
+  * `summarytools` are included in `dq_report2` reports, if installed.
+  * New report rendering code polished, parallel execution of `HTML` generation prepared
+  * New parallel mode for `dq_report2` using a queue improves speed
+  * Full support for `VARIABLE_ROLES` in `dq_report2` and suppressing helper variable outputs in `dq_report_by`
+  * Do not show conditions (e.g., warnings, messages, errors) in reports if they address the call of the function (e.g., "using default for argument...") by `dq_report2` and not directly by the user
+  * No unit-missingness in `dq_report2` because it is not so useful in its current implementation
+  * More robust `dq_report_by` for large reports (can write and optionally render results to disk rather than returning them)
+  * Bug fix in `dq_report_by` causing `DATA_PROCESS` not to work
+  * Fixed some errors and `TODO`'s in `dq_report_by` and add dependent variables on the fly but with `VARIABLE_ROLE` suppress:
+     - If no role is given, add "primary" by default for single reports as well as for `dq_report_by`
+     - Support meta_data_v2 in `dq_report_by`
+     - FIXED: referred variables did not correctly resolve co_vars and labels instead of variable names
+  * Several bug fixes:
+     - Addressed most parts of https://gitlab.com/libreumg/dataquier/-/issues/242    
+     - Addressed https://gitlab.com/libreumg/dataquier/-/issues/244 and https://gitlab.com/libreumg/dataquier/-/issues/212
+     - Default for result-slot-filter was not set (`filter_result_slots` in `dq_report2`)
+     - Sometimes, long labels in the first columns of a `JS`-table prevented controlling the table
+
+## (Indicator) Functions related 
+  * Fixed missed check for missing cross-item level metadata and earlier check for valid item-level metadata
+  * Control crude segment missingness output, so that we see it only if there is more than one segment on the item-level after the removal of `VARIABLE_ROLES` filtered items
+  * Outliers should work with empty metadata in `UNIVARIATE_OUTLIER_CHECKTYPE` and `MULTIVARIATE_OUTLIER_CHECKTYPE`
+  * Fixed successive dates to ignore empty dates
+  * New functions in `REDCap` syntax: `strictly_successive_dates` and `successive_dates`
+  * Bug fixes for `REDCap` rules and `NA` handling and `DATA_PROCESS`.
+  * Checked, that code is in line with https://gitlab.com/libreumg/dataquier/-/issues/243#note_1419465360
+  * Default for contradictions with the new syntax is now that hard limits and missing codes are not removed. The argument `use_value_labels` is not supported anymore. You can specify the behavior on the rules level in the new cross-item-level metadata column `DATA_PREPARATION`
+  * Compute end digit preferences only if explicitly requested by a new item-level metadata column `END_DIGIT_CHECK` in `dq_report2`, (`DATA_ENTRY_TYPE` is still supported and auto-converted). If missing, `END_DIGIT_CHECK` defaults to `FALSE`
+  * Bug fix: Contradiction rules failed in specific cases if `NA` were in the data
+  * Bug fix: cross-item_level normalization crashed, causing rules to fail, e.g., `JUMP_LIST` could be added to the item-level metadata if missing, but causing this type of failing rules
+  * Bug fixes for `Windows` and uncommon variable names
+
+## General 
+  * Workbooks can now be loaded from the internet (using `prep_load_workbook_like_file` and `meta_data_v2 = ` formal in `dq_report2`) supporting `http` and `https` URLs (e.g., `Excel` or `OpenOffice` workbooks)
+  * Documentation updates
+
 # dataquieR 2.0.0
   * `dq_report2` replaces `dq_report`. Please use `dq_report2` from now on.
   * Full new reporting engine (needs `htmtools` and supports `plotly`)
@@ -23,8 +73,6 @@
   * fixed a left-over `~` from the `ggplot2` updates causing `acc_margins` to
     fail for categorical variables
 
-# dataquieR 1.0.12
-
 # dataquieR 1.0.12
   * Addressed a problem with the markdown template underlying the
   `dq_report` reports with wrong brackets
@@ -68,7 +116,7 @@
     for those.
 
 # dataquieR 1.0.6
-  * Robustness: Ensure `DT JS` is always loaded when a dq_report report is 
+  * Robustness: Ensure `DT JS` is always loaded when a `dq_report` report is 
     rendered
   * Bug fix: More robust handling of DECIMALS variable attribute, if
     this is delivered as a character.
@@ -95,7 +143,7 @@
   * Added a classification system for warnings and error messages to
     distinguish errors based on mismatching variables for a function from
     other error messages.
-  * https://github.com/openjournals/joss-reviews/issues/3093#issuecomment-840695360
+  * [JOSS](https://github.com/openjournals/joss-reviews/issues/3093#issuecomment-840695360)
   * Some tidy up and more tests.
 
 # dataquieR 1.0.5