version 2.0.0

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: dataquieR
 Title: Data Quality in Epidemiological Research
-Version: 1.0.13
+Version: 2.0.0
 Authors@R: 
     c(person(given = "University Medicine Greifswald",
              role = "cph"),
@@ -29,7 +29,9 @@ Authors@R:
              role = c("aut", "cre"),
              comment = c(ORCID = "0000-0002-8565-7962"),
              email = "stephan.struckmann@uni-greifswald.de"),
-      person(given = "German Research Foundation (DFG SCHM 2744/3-1)",
+      person(given = "German Research Foundation (DFG SCHM 2744/3-1, SCHM 2744/9-1, SCHM 2744/3-4)",
+             role = "fnd"),
+      person(given = "National Research Data Infrastructure for Personal Health Data: (NFDI 13/1)",
              role = "fnd"),
       person(given = "European Union’s Horizon 2020 programme (euCanSHare, grant agreement No. 825903)",
              role = "fnd"))
@@ -48,28 +50,34 @@ License: BSD_2_clause + file LICENSE
 URL: https://dataquality.ship-med.uni-greifswald.de/
 BugReports: https://gitlab.com/libreumg/dataquier/-/issues
 Depends: R (>= 3.6.0)
-Imports: patchwork, dplyr (>= 1.0.2), emmeans, ggplot2 (>= 3.4.0),
-        ggpubr, lme4, lubridate, MASS, MultinomialCI, parallelMap,
-        R.devices, reshape, rlang, robustbase, utils
-Suggests: cowplot (>= 0.9.4), anytime, digest, DT (>= 0.15),
-        flexdashboard, htmltools, knitr, rmarkdown, rstudioapi,
-        testthat (>= 2.3.2), tibble, markdown, vdiffr, parallel
+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,
+        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
 VignetteBuilder: knitr
 Encoding: UTF-8
 KeepSource: TRUE
 Language: en-US
-RoxygenNote: 7.2.1
+RoxygenNote: 7.2.3
 NeedsCompilation: no
-Packaged: 2022-11-16 08:28:59 UTC; struckmanns
+Packaged: 2023-03-01 16:10:20 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>),
   Adrian Richter [aut] (<https://orcid.org/0000-0002-3372-2021>),
   Carsten Oliver Schmidt [aut] (<https://orcid.org/0000-0001-5266-9396>),
   Stephan Struckmann [aut, cre] (<https://orcid.org/0000-0002-8565-7962>),
-  German Research Foundation (DFG SCHM 2744/3-1) [fnd],
+  German Research Foundation (DFG SCHM 2744/3-1, SCHM 2744/9-1, SCHM
+    2744/3-4) [fnd],
+  National Research Data Infrastructure for Personal Health Data: (NFDI
+    13/1) [fnd],
   European Union’s Horizon 2020 programme (euCanSHare, grant agreement
     No. 825903) [fnd]
 Maintainer: Stephan Struckmann <stephan.struckmann@uni-greifswald.de>
 Repository: CRAN
-Date/Publication: 2022-11-16 14:40:22 UTC
+Date/Publication: 2023-03-01 16:30:02 UTC

LICENSE

@@ -1,2 +1,2 @@
-YEAR: 2017-2021
+YEAR: 2017-2022
 COPYRIGHT HOLDER: University Medicine Greifswald, Greifswald, GERMANY.

NAMESPACE

@@ -2,22 +2,47 @@
 
 S3method("$",dataquieR_result)
 S3method("[",dataquieR_result)
+S3method("[",dataquieR_resultset2)
 S3method("[[",dataquieR_result)
 S3method(as.data.frame,dataquieR_resultset)
 S3method(as.list,dataquieR_resultset)
+S3method(dim,dataquieR_resultset2)
+S3method(dimnames,dataquieR_resultset2)
 S3method(print,ReportSummaryTable)
 S3method(print,dataquieR_result)
 S3method(print,dataquieR_resultset)
+S3method(print,dataquieR_resultset2)
+S3method(print,interval)
 S3method(rbind,ReportSummaryTable)
+S3method(resnames,dataquieR_resultset2)
 S3method(summary,dataquieR_resultset)
+S3method(summary,dataquieR_resultset2)
 export(DATA_TYPES)
 export(DATA_TYPES_OF_R_TYPE)
+export(DF_ELEMENT_COUNT)
+export(DF_ID_REF_TABLE)
+export(DF_ID_VARS)
+export(DF_NAME)
+export(DF_RECORD_CHECK)
+export(DF_RECORD_COUNT)
+export(DF_UNIQUE_ID)
+export(DF_UNIQUE_ROWS)
 export(DISTRIBUTIONS)
+export(SEGMENT_ID_TABLE)
+export(SEGMENT_ID_VARS)
+export(SEGMENT_PART_VARS)
+export(SEGMENT_RECORD_CHECK)
+export(SEGMENT_RECORD_COUNT)
+export(SEGMENT_UNIQUE_ROWS)
 export(SPLIT_CHAR)
 export(VARATT_REQUIRE_LEVELS)
 export(VARIABLE_ROLES)
 export(WELL_KNOWN_META_VARIABLE_NAMES)
 export(acc_distributions)
+export(acc_distributions_loc)
+export(acc_distributions_loc_ecdf)
+export(acc_distributions_prop)
+export(acc_distributions_prop_ecdf)
 export(acc_end_digits)
 export(acc_loess)
 export(acc_margins)
@@ -27,42 +52,83 @@ export(acc_shape_or_scale)
 export(acc_univariate_outlier)
 export(acc_varcomp)
 export(com_item_missingness)
+export(com_qualified_item_missingness)
+export(com_qualified_segment_missingness)
 export(com_segment_missingness)
 export(com_unit_missingness)
 export(con_contradictions)
+export(con_contradictions_redcap)
 export(con_detection_limits)
+export(con_hard_limits)
 export(con_inadmissible_categorical)
 export(con_limit_deviations)
+export(con_soft_limits)
 export(contradiction_functions)
 export(contradiction_functions_descriptions)
 export(dq_report)
+export(dq_report2)
 export(dq_report_by)
+export(int_all_datastructure_dataframe)
+export(int_all_datastructure_segment)
 export(int_datatype_matrix)
+export(int_duplicate_content)
+export(int_duplicate_ids)
+export(int_part_vars_structure)
+export(int_sts_element_dataframe)
+export(int_sts_element_segment)
+export(int_unexp_elements)
+export(int_unexp_records_dataframe)
+export(int_unexp_records_segment)
+export(int_unexp_records_set)
+export(nres)
 export(pipeline_recursive_result)
 export(pipeline_vectorized)
+export(prep_add_cause_label_df)
+export(prep_add_data_frames)
+export(prep_add_missing_codes)
 export(prep_add_to_meta)
+export(prep_apply_coding)
+export(prep_check_meta_data_dataframe)
+export(prep_check_meta_data_segment)
 export(prep_check_meta_names)
 export(prep_clean_labels)
 export(prep_create_meta)
 export(prep_datatype_from_data)
+export(prep_deparse_assignments)
+export(prep_dq_data_type_of)
+export(prep_expand_codes)
+export(prep_extract_cause_label_df)
+export(prep_get_data_frame)
+export(prep_get_user_name)
+export(prep_link_escape)
+export(prep_list_dataframes)
+export(prep_load_workbook_like_file)
 export(prep_map_labels)
+export(prep_merge_study_data)
+export(prep_meta_data_v1_to_item_level_meta_data)
 export(prep_min_obs_level)
 export(prep_pmap)
 export(prep_prepare_dataframes)
+export(prep_purge_data_frame_cache)
 export(prep_study2meta)
+export(prep_title_escape)
 export(prep_valuelabels_from_data)
 export(pro_applicability_matrix)
+export(resnames)
 import(patchwork)
+import(qmrparser)
 importFrom(MASS,fitdistr)
 importFrom(MultinomialCI,multinomialCI)
 importFrom(dplyr,"%>%")
 importFrom(dplyr,recode)
 importFrom(ggplot2,aes)
 importFrom(ggplot2,annotate)
+importFrom(ggplot2,coord_cartesian)
 importFrom(ggplot2,coord_flip)
 importFrom(ggplot2,discrete_scale)
 importFrom(ggplot2,element_blank)
 importFrom(ggplot2,element_text)
+importFrom(ggplot2,expansion)
 importFrom(ggplot2,facet_grid)
 importFrom(ggplot2,facet_wrap)
 importFrom(ggplot2,geom_bar)
@@ -77,6 +143,7 @@ importFrom(ggplot2,geom_line)
 importFrom(ggplot2,geom_path)
 importFrom(ggplot2,geom_point)
 importFrom(ggplot2,geom_pointrange)
+importFrom(ggplot2,geom_segment)
 importFrom(ggplot2,geom_text)
 importFrom(ggplot2,geom_tile)
 importFrom(ggplot2,geom_violin)
@@ -90,6 +157,7 @@ importFrom(ggplot2,labs)
 importFrom(ggplot2,position_jitter)
 importFrom(ggplot2,scale_alpha)
 importFrom(ggplot2,scale_alpha_manual)
+importFrom(ggplot2,scale_color_gradientn)
 importFrom(ggplot2,scale_color_manual)
 importFrom(ggplot2,scale_colour_manual)
 importFrom(ggplot2,scale_fill_gradientn)
@@ -105,21 +173,23 @@ importFrom(ggplot2,theme)
 importFrom(ggplot2,theme_minimal)
 importFrom(ggplot2,theme_set)
 importFrom(ggplot2,vars)
+importFrom(ggplot2,waiver)
 importFrom(ggplot2,xlab)
 importFrom(ggplot2,ylab)
-importFrom(ggpubr,ggarrange)
-importFrom(ggpubr,ggballoonplot)
 importFrom(grDevices,col2rgb)
 importFrom(grDevices,colorRamp)
+importFrom(grDevices,hcl.colors)
 importFrom(grDevices,rgb)
 importFrom(reshape,melt)
 importFrom(rlang,":=")
 importFrom(rlang,.data)
 importFrom(rlang,caller_fn)
 importFrom(stats,IQR)
 importFrom(stats,aggregate)
+importFrom(stats,alias)
 importFrom(stats,as.formula)
 importFrom(stats,binomial)
+importFrom(stats,complete.cases)
 importFrom(stats,cov)
 importFrom(stats,dgamma)
 importFrom(stats,dnorm)
@@ -143,4 +213,7 @@ importFrom(utils,adist)
 importFrom(utils,browseURL)
 importFrom(utils,capture.output)
 importFrom(utils,head)
+importFrom(utils,osVersion)
+importFrom(utils,packageName)
+importFrom(utils,packageVersion)
 importFrom(utils,tail)

NEWS.md

@@ -1,19 +1,42 @@
+# 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
+
 # dataquieR 1.0.12
   * Addressed a problem with the markdown template underlying the
   `dq_report` reports with wrong brackets
-  * Addressed issue with `ggplot2`'s breaking changes for the release `3.4.0`
+  * 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