Data Quality in Epidemiological Research
Plots and checks for distributions for categorical variables
ECDF plots for distribution checks
Plots and checks for distributions -- Location
Plots and checks for distributions -- only
Plots and checks for distributions -- Proportion
Plots and checks for distributions
Extension of acc_shape_or_scale to examine uniform distributions of en...
Smoothes and plots adjusted longitudinal measurements and longitudinal...
Calculate and plot Mahalanobis distances for social science indices
Estimate marginal means, see emmeans::emmeans
Calculate and plot Mahalanobis distances
Identify univariate outliers by four different approaches
Compare observed versus expected distributions
Identify univariate outliers by four different approaches
Utility function to compute model-based ICC depending on the (statisti...
Version of the API
as.character implementation for the class interval
Convert a full dataquieR report to a data.frame
Convert a full dataquieR report to a list
inefficient way to convert a report to a list. try `prep_set_backend()...
Cross-item level metadata attribute name
Cross-item level metadata attribute name
Cross-item level metadata attribute name
Cross-item level metadata attribute name
Access single results from a dataquieR_resultset2 report
Write single results from a dataquieR_resultset2 report
Cross-item level metadata attribute name
Cross-item level metadata attribute name
Data frame with contradiction rules
types of value codes
Default Name of the Table featuring Code Lists
Only existence is checked, order not yet used
Summarize missingness columnwise (in variable)
Compute Indicators for Qualified Item Missingness
Compute Indicators for Qualified Segment Missingness
Summarizes missingness for individuals in specific segments
Counts all individuals with no measurements at all
Cross-item level metadata attribute name
SSI related Cross-item level metadata attribute names Computed Varia...
Checks user-defined contradictions in study data
Checks user-defined contradictions in study data
Detects variable levels not specified in metadata
Detects variable levels not specified in standardized vocabulary
Detects variable values exceeding limits defined in metadata
description of the contradiction functions
contradiction_functions
Cross-item level metadata attribute name
Cross-item level metadata attribute name
Cross-item level metadata attribute name
All available data types, mapped from their respective R types
Data Types
Verify an object of class dataquieR_resultset
Internal constructor for the internal class dataquieR_resultset .
Class dataquieR_resultset2 .
Exclude subgroups with constant values from LOESS figure
Display time-points in LOESS plots
Lower limit for the LOESS bandwidth
Lower limit for the proportion of cases or controls to create a smooth...
default for Plot-Format in acc_loess()
Display observations in LOESS plots
Include number of observations for each level of the grouping variable...
Sort levels of the grouping variable in the 'margins' figures
Apply min-max scaling in parallel coordinates figure to inspect multiv...
An exception class assigned for exceptions caused by trying to apply a...
Color for empirical contradictions
Color for logical contradictions
Log Level
Add stack-trace in condition messages (to be deprecated)
If report uses a storr back-end, do not convert to base-list
Call browser() on errors
Removal of hard limits from data before calculating descriptive statis...
Disable automatic post-processing of dataquieR function results
Show also unused levels in heatmaps
character Adjust data types according to metadata
Metadata describes more than the current study data
Set caller for error conditions (to be deprecated)
Try to avoid fallback to string columns when reading files
Flip-Mode to Use for figures
Converting MISSING_LIST /JUMP_LIST to a MISSING_LIST_TABLE create on l...
Control, how the label_col argument is used.
Enable to switch to a general additive model instead of LOESS
Name of the data.frame featuring a format for grading-values
Name of the data.frame featuring GRADING_RULESET
For metadata guessing, try to guess DATA_TYPE from the data values
Control, if dataquieR tries to guess missing-codes from the study da...
character remove variables with only empty values
An exception class assigned for exceptions caused by trying to apply a...
Language-Suffix for metadata Label-Columns
character cache realizations
character be as compatible with ggplot2 objects as possible
character plots realized lazy
character default language for type conversion
Default availability of Mahalanobis based multivariate outlier checks ...
Maximum number of levels of the categorical response variable shown in...
Maximum number of levels of the grouping variable shown individually i...
Maximum number of levels of the grouping variable shown with individua...
Maximum length for variable labels LABEL
Maximum length for long variable labels LONG_LABEL
Maximum length for value labels
Set caller for message conditions (to be deprecated)
Minimum number of observations per grouping variable that is required ...
Minimum number of data points to create a time course plot for an indi...
Default availability of multivariate outlier checks in reports
Remove all observation-level-real-data from reports
character use the old handling of study data already featuring factors
character use the old type conversion code (slower)
Pre-compute different curation levels of study data
numeric
function to call on progress increase
function to call on progress message update
The dataquieR package about Data Quality in Epidemiological Research
If result already exists in a storr back-end, re-use it
If output folder is not empty, try to resume stopped print()
Number of levels to consider a variable ordinal in absence of SCALE_LE...
Number of levels to consider a variable metric in absence of SCALE_LEV...
Maximum size of cache for curated study data
Default space for some metrics during report computation
environment for storing metrics on the study data cache
Collect metrics on cache usage of study data cache
Control the pre-computation of curation levels of study data
character Are column names in study data considered case-sensitive for...
Disable all interactively used metadata-based function argument provis...
Include full trace-back in captured conditions
character try to do type adjustments in parallel only, if `dq_report2(...
Assume, all VALUE_LABELS are [HTML escaped](https://www.w3.org/Interna...
Set caller for warning conditions (to be deprecated)
Compute Pairwise Correlations
Compute Descriptive Statistics - categorical variables
Compute Descriptive Statistics - continuous variables
Compute Descriptive Statistics
Descriptor Function
Data frame level metadata attribute name
Data frame level metadata attribute name
Data frame level metadata attribute name
Data frame level metadata attribute name
Data frame level metadata attribute name
Data frame level metadata attribute name
Data frame level metadata attribute name
Data frame level metadata attribute name
Data frame level metadata attribute name
Get the dimensions of a dq_report2 result
Names of DQ dimensions
Names of a dataquieR report object (v2.0)
Dimension Titles for Prefixes
All available probability distributions for acc_shape_or_scale
Get Access to Utility Functions
Operator caring for units
Roxygen-Template for indicator functions
Variable-argument roles
S3/S7 methods for lazy ggplot objects
Generate a stratified full DQ report
Generate a full DQ report
Generate a full DQ report, v2
Remove unused levels from ReportSummaryTable
Cross-item level metadata attribute name
Operator caring for units
Operator caring for units
grid.draw method for util_pairs_ggplot_panels objects
HTML Dependency for report headers in clipboard
HTML Dependency for dataquieR
HTML dependency for jsPDF
HTML Dependency for report headers in DT::datatable
HTML Dependency for tippy
HTML Dependency for vertical headers in DT::datatable
Indicator Function
Wrapper function to check for studies data structure
Wrapper function to check for segment data structure
Check declared data types of metadata in study data
Check for duplicated content
Check for duplicated IDs
Encoding Errors
Detect Expected Observations
Determine missing and/or superfluous data elements
Checks for element set
Check for unexpected data element count
Check for unexpected data record count at the data frame level
Check for unexpected data record count within segments
Check for unexpected data record set
Cross-item level metadata attribute name
Cross-item level metadata attribute name
Cross-item level metadata attribute name
Creates a drop-down menu
Create a single menu entry
Generate the menu for a report
Well known columns on the item_computation_level sheet
Well known columns on the cross-item_level sheet
Well known columns on the meta_data_dataframe sheet
Extract co-variables for a given item
.meta_data_env -- an environment for easy metadata access
Well known columns on the meta_data_segment sheet
Data frame with metadata about the study data on variable level
Cross-item level metadata attribute name
Cross-item level metadata attribute name
Cross-item level metadata attribute name
return the number of result slots in a report
Convert a pipeline result data frame to named encapsulated lists
Call (nearly) one "Accuracy" function with many parameterizations at o...
Plot a dataquieR summary
Operator caring for units
Operator caring for units
Utility function to plot a combined figure for distribution checks
Convert missing codes in metadata format v1.0 and a missing-cause-tabl...
Insert missing codes for NAs based on rules
Add data frames to the pre-loaded / cache data frame environment
Insert missing codes for NAs based on rules
Support function to augment metadata during data quality reporting
Re-Code labels with their respective codes according to the `meta_data...
Check for package updates
Verify and normalize metadata on data frame level
Verify and normalize metadata on segment level
Checks the validity of metadata w.r.t. the provided column names
Support function to scan variable labels for applicability
Combine two report summaries
Verify item-level metadata
Instantiate a new metadata file
Support function to create data.frame s of metadata
Create a factory function for storr objects for backing a dataquieR_...
Get data types from data
Convert two vectors from a code-value-table to a key-value list
Get the dataquieR DATA_TYPE of x
Expand code labels across variables
Extract all missing/jump codes from metadata and export a cause-label-...
Extract old function based summary from data quality results
Extract report summary from reports
Extract report summary from reports
Extract summary from data quality results
Fix metadata duplicates
Read data from files/URLs
Fetch a label for a variable based on its purpose
Get data frame for a given segment
Return the logged-in User's Full Name
Get machine variant for snapshot tests
Guess encoding of text or text files
Prepare a label as part of a link for RMD files
List Loaded Data Frames
All valid voc: vocabularies
Pre-load a folder with named (usually more than) one table(s)
Load a report from a back-end
Load a dq_report2
Pre-load a file with named (usually more than) one table(s)
Support function to allocate labels to variables
Merge a list of study data frames to one (sparse) study data frame
Convert item-level metadata from v1.0 to v2.0
Support function to identify the levels of a process variable with min...
Open a data frame in Excel
Support function for a parallel pmap
Prepare and verify study data with metadata
Clear data frame cache
Materialize a lazy ggplot
Remove a specified element from the data frame cache
Create a ggplot2 pie chart
Create a plotly pie chart
Guess the data type of a vector
Save a dq_report2
Heuristics to amend a SCALE_LEVEL column and a UNIT column in the meta...
Change the back-end of a report
Guess a metadata data frame from study data.
Classify metrics from a report summary table
Prepare a label as part of a title text for RMD files
Remove data disclosing details
Combine all missing and value lists to one big table
Get value labels from data
Print a dataquieR result returned by dq_report2
Generate a RMarkdown-based report from a dataquieR report
Generate a HTML-based report from a dataquieR report
Print a dataquieR summary
Print a DataSlot object
print implementation for the class interval
print a list of dataquieR_result objects
Print a master_result object
Print a number with unit
print implementation for the class ReportSummaryTable
Print a Slot object
Print a StudyDataSlot object
Print a TableSlot object
Print method for util_pairs_ggplot_panels objects
Check applicability of DQ functions on study data
function to call on progress initialization
Combine ReportSummaryTable outputs
Cross-item level metadata attribute name
Cross-item level metadata attribute name
Return names of result slots (e.g., 3rd dimension of dataquieR results...
Return names of result slots (e.g., 3rd dimension of dataquieR results...
Cross-item level metadata attribute name
Cross-item level metadata attribute name TODO
Scale Levels
Cross-item level metadata attribute name TODO
Segment level metadata attribute name
Deprecated segment level metadata attribute name
Segment level metadata attribute name
Segment level metadata attribute name
Segment level metadata attribute name
Segment level metadata attribute name
Segment level metadata attribute name
Segment level metadata attribute name
Segment level metadata attribute name
Operator caring for units
Character used by default as a separator in metadata such as missing c...
Data frame with the study data whose quality is being assessed
Get a subset of a dataquieR dq_report2 report
Get a single result from a dataquieR 2 report
Set a single result from a dataquieR 2 report
Write to a report
Summarize a dataquieR report
Generate a report summary table
Operator caring for units
Cross-item level metadata attribute name
Is a unit a count according to units::valid_udunits()
Factors related to unit prefixes units::valid_udunits_prefixes()
Valid unit prefixes according to units::valid_udunits_prefixes()
Maturity stage of a unit according to units::valid_udunits()
Valid unit symbols according to units::valid_udunits()
Delete rows from summary table for SSI or non-SSI variables
Convert a dataquieR report v2 to a named list of web pages
Create a dynamic dimension related page for the report
Create a dynamic single variable page for the report
Check for duplicated content
Check for duplicated content
Check for duplicated IDs
Check for duplicated IDs
Check for unexpected data record set
Check for unexpected data record set
Operator caring for units
Translate standard column names to readable ones
Data frame with labels for missing- and jump-codes #' Metadata about v...
Requirement levels of certain metadata columns
Cross-item level metadata attribute name TODO internal use, only
Cross-item level metadata attribute name
Variable roles can be one of the following:
Well-known metadata column names, names of metadata columns
Data quality assessments guided by a 'data quality framework introduced by Schmidt and colleagues, 2021' <doi:10.1186/s12874-021-01252-7> target the data quality dimensions integrity, completeness, consistency, and accuracy. The scope of applicable functions rests on the availability of extensive metadata which can be provided in spreadsheet tables. Either standardized (e.g. as 'html5' reports) or individually tailored reports can be generated. For an introduction into the specification of corresponding metadata, please refer to the 'package website' <https://dataquality.qihs.uni-greifswald.de/VIN_Annotation_of_Metadata.html>.
Useful links