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)
• Better report layout and improved functionality
• Support for reading and referring to data in files/URLs
• Support for the integrity dimension in data quality report
• Included distribution and multivariate outlier (provide cross-item level metadata for the latter) plots in data quality report
• Metadata scheme update (segment, data.frame, and cross-item levels). No required action by user, previous version still supported
• REDCap rules for contradictions (cross-item level metadata), previous contradictions function still supported
• Support metadata describing segment data and study data tables (segment and data.frame-level metadata)
• New item-level metadata version (backwards compatible)
• Support for computation of qualified missingness based on labels from the AAPOR concept
• acc_univariate_outlier and acc_multivariate_outlier now allow selecting the methods used to flag outliers
• Included distributional checks in the accuracy dimension for location and proportion
• Rotation of plots can now be controlled
• Improved many figures
• Better control over warnings
• If whoami is installed, reports now show a more suitable user name
• Many minor improvements
• Updated citations

dataquieR 1.0.13

• fixed a left-over ~ from the ggplot2 updates causing acc_margins to fail for categorical variables

dataquieR 1.0.12

• Addressed a problem with the markdown template underlying the dq_report reports with wrong brackets
• Addressed deprecations from ggplot2 3.4.0
• Added ORCIDs for two authors
• Updated the CITATION file
• Updated the README.md file adding the funding sources.

dataquieR 1.0.11

• Addressed a problem with some test platforms
• Added funding agencies in the manual

dataquieR 1.0.10

• Fixed NEWS.md file
• Fixed documentation

dataquieR 1.0.9

• Fixed bug in sigmagap and made missing guessing more robust.
• Fixed checks on missing code detection failing for logical.
• Fixed a damaged check for numeric threshold values in acc_margins.
• Fixed wrongly named GRADING columns.
• Improved parallel execution by automatic detection of cores.
• Tidy html dependency

dataquieR 1.0.8

• Removed formal arguments from rbind.ReportSummaryTable since these are not needed anyways and the inherited documentation for those arguments rbind from base contains an invalid URL triggering a NOTE.

dataquieR 1.0.7

• Fixed bugs in example metadata.
• Figures now have size hints as attributes.
• Added simple type conversion check indicator function of dimension integrity, int_datatype_matrix.
• Corrected some error classifications
• prep_study2meta can now also convert factors to dataquieR compatible meta_data/study_data
• Slightly improved documentation.
• Bug fix in com_item_missingness for textual response variables.
• Added new output slot with heat-map like tables. Implemented some generics for those.

dataquieR 1.0.6

• 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.
• Bug Fix: com_segment_missingness with strata_vars / group_vars did not work
• Bug Fix: If label_col was set to something else than LABEL, strata_vars did not work for com_unit_missingness
• More precise documentation.
• Fixed a bug in a utility function for the univariate outliers indicator function, which caused many data points flagged as outliers by the sigma- gap criterion.
• Made outlier function aware of too many non-outlier points causing too complex graphics (e.g. pdf rendering crashes the PDF reader).
• Fixes and small improvements in dq_report.
• Switched from cowplot to patchwork in acc_margins yielding figures that can be easier manipulated. Please note, that this change could break existing output manipulations, since the structure of the margins plots has changed internally. However, output manipulations were hardly possible for margins plots before, so it is unlikely, that there are pipelines affected.
• More control about the output of the acc_loess function.
• More robust prep_create_meta handling length-0 arguments by ignoring these variable attributes at all.
• Added a classification system for warnings and error messages to distinguish errors based on mismatching variables for a function from other error messages.
• JOSS
• Some tidy up and more tests.

dataquieR 1.0.5

• Fixed two bugs in con_inadmissible_categorical (one resp_var only and value-limits all the same for all resp_vars)
• Changed LICENSE to BSD-2
• Slightly updated documentation
• Updated README-File

dataquieR 1.0.4

• Fixed CITATION, a broken reference in Rd and a problem with the vignette on pandoc-less systems
• Improved an inaccurate argument description for multivariate outliers
• Fixed a problem with error messages, if a dataquieR function was called by a generated function f that lives in an environment directly inheriting from the empty environment, e.g.  environment(f) <- new.env(parent = emptyenv()).
• Marked some examples as dontrun, because they sometimes caused NOTEs on rhub.

dataquieR 1.0.3

• Addressed all comments by the CRAN reviewers, thank you.

dataquieR 1.0.2

• Bug Fix: If an empty data frame was delivered in the SummaryTable entry of a result within a dq_report output, the summary and also print generic did not work on the report.

dataquieR 1.0.1

• Skipping some of the slower tests on CRAN now. On my local system, a full devtools::check(cran = TRUE, env_vars = c(NOT_CRAN = "false")) takes 2:22 minutes now.

dataquieR 1.0.0

• Initial CRAN release candidate