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...
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
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
Extract elements of a dataquieR Result Object
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
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...
Color for empirical contradictions
Color for logical contradictions
Log Level
Add stack-trace in condition messages (to be deprecated)
Call browser() on errors
Removal of hard limits from data before calculating descriptive statis...
Disable automatic post-processing of dataquieR function results
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
Control, if dataquieR tries to guess missing-codes from the study da...
Language-Suffix for metadata Label-Columns
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
Maximum length for value labels
Set caller for message conditions (to be deprecated)
Minimum number of observations per grouping variable that is required ...
Default availability of multivariate outlier checks in reports
Remove all observation-level-real-data from reports
function to call on progress increase
function to call on progress message update
The dataquieR package about Data Quality in Epidemiological Research
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...
Disable all interactively used metadata-based function argument provis...
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
Holds Indicator .// Descriptor assignments from the manual at run-time
Holds parts of the manual at run-time
Write elements from a dataquieR_resultset2
Access elements from a dataquieR_resultset2
Get Access to Utility Functions
Roxygen-Template for indicator functions
Make normalizations of v2.0 item_level metadata.
Variable-argument roles
Generate a stratified full DQ report
Generate a full DQ report
Generate a full DQ report, v2
Cross-item level metadata attribute name
HTML Dependency for report headers in clipboard
HTML Dependency for dataquieR
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
An exception class assigned for exceptions caused by long variable lab...
Creates a drop-down menu
Create a single menu entry
Generate the menu for a report
.menu_env -- an environment for HTML menu creation
Well known columns on the meta_data_cross-item sheet
Well known columns on the meta_data_dataframe sheet
Extract co-variables for a given item
Extract MULTIVARIATE_OUTLIER_CHECK for variable group
Extract group variables for a given item
Extract id variables for a given item or variable group
Extract outlier rules-number-threshold for a given item or variable gr...
Extract measurement time variable 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 and 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
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
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
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 implementation for the class ReportSummaryTable
Print a Slot object
Print a StudyDataSlot object
Print a TableSlot object
Check applicability of DQ functions on study data
Combine ReportSummaryTable outputs
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...
Scale Levels
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
Character used by default as a separator in metadata such as missing c...
Data frame with the study data whose quality is being assessed
Extract Parts of a dataquieR Result Object
Get a subset of a dataquieR dq_report2 report
Extract Elements of a dataquieR Result Object
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
Is a unit a count according to units::valid_udunits()
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()
Item level metadata attribute name
Utility function for 3SD deviations rule
Abbreviate a vector of strings
Abbreviate snake_case function names to shortened CamelCase
Utility function for smoothed longitudinal trends from logistic regres...
Utility function for smoothes and plots adjusted longitudinal measurem...
Estimates variance components
Adjust the data types of study data, if needed
Place all geom_texts also in plotly right from the x position
Create a caption from an alias name of a dq_report2 result
All indicator functions of dataquieR
Get all PART_VARS for a response variable (from item-level metadata)
convenience function to abbreviate all(util_is_integer(...))
Test, if package anytime is installed
utility function for the applicability of contradiction checks
utility function for the applicability of contradiction checks
utility function for the applicability of of distribution plots
utility function to test for applicability of detection limits checks
utility function for the applicability of of end digits preferences ch...
utility function to test for applicability of hard limits checks
utility function for the applicability of categorical admissibility
utility function for the applicability of numeric admissibility
utility function applicability of item missingness
utility function for applicability of LOESS smoothed time course plots
utility function to test for applicability of marginal means plots
utility function applicability of multivariate outlier detection
utility function for the applicability of outlier detection
utility function to test for applicability of soft limits checks
utility function applicability of segment missingness
utility function applicability of distribution function's shape or sca...
utility applicability variance components
Convert a category to an ordered factor (1:5)
Convert a category to a number (1:5)
Convert factors to label-corresponding numeric values
Return the pre-computed plotly from a dataquieR result
Convert x to valid missing codes
utility function to assign labels to levels
Attach attributes to an object and return it
utility function to set string in backticks
Utility function to create bar plots
Put in back-ticks
Data frame leaves haven
Verify the data type of a value
Check data for observer levels
Check for one value only
Get Function called for a Call Name
Get description for a call
Return hex code colors from color names or STATAReporter syntax
Collect all errors, warnings, or messages so that they are combined fo...
Create a data frame containing all the results from summaries of repor...
Combine results for Single Variables
Combine two value lists
Compares study data data types with the ones expected according to the...
Remove specific classes from a ggplot plot_env environment
Compute Kurtosis
Compute SE.Skewness
Compute the Skewness
Produce a condition function
Extract condition from try error
Can a vector be converted to a defined DATA_TYPE
return a flip term for ggplot2 plots, if desired.
Copy default dependencies to the report's lib directory
Check referred variables
Count Expected Observations
Create an HTML file for the dq_report2
Create an overview of the reports created with dq_report_by
Create a dashboard-table from a report summary
Data type conversion
Expression De-Parsing
Detect cores
Escape characters for HTML in a data frame
Utility function to dichotomize variables
Utility function to characterize study variables
Create an environment with several alias names for the study data vari...
Test, if values of x are empty, i.e. NA or whitespace characters
convert a value to character
similar to match.arg
Utility function ensuring valid labels and variable names
Support function to stop, if an optional package is not installed
Produce an error message with a useful short stack trace. Then it stop...
Evaluate a parsed redcap rule for given study data
Evaluate an expression and create a dataquieR_result object from it'...
Generate a full DQ report, v2
Verify, that argument is a data frame
check, if a scalar/vector function argument matches expectations
Extract all ids from a list of htmltools objects
Extract columns of a SummaryTable (or Segment, ...)
return all matches of an expression
Filter a MISSING_LIST_TABLE for rows matching the variable rv
Filter collection based on its names() using regular expressions
Function that calculated height and width values for script_iframe
Find externally called function in the stack trace
Find first externally called function in the stack trace
Check, if x contains valid missing codes
Search for a formal in the stack trace
Try hard, to map a variable
Move the first row of a data frame to its column names
Fix results from merge
RStudio crashes on parallel calls in some versions on Darwin based ope...
Ensure, sizing hint sticks at the dqr, only
Fix a storr object, if it features the factory-attribute
return a single page navigation menu floating on the right
Plots simple HTML tables with background color scale
Get description for an indicator function
Generate a link to a specific result
Generate a tag for a specific result
Generate function calls for a given indicator function
Generate an execution/calling plan for computing a report from the met...
Convert a dataquieR report v2 to a named list of web pages
Create a table summarizing the number of indicators and descriptors in...
Return the category for a result
Fetch a missing code list from the metadata
Get colors for each russet DQ category
Read additional concept tables
Get encoding from metadata or guess it from data
Find a foreground color for a background
Import vector of hover text for tables in the report
Get labels for each russet DQ category
Return messages/warnings/notes/error messages for a result
an environment with functions available for REDcap rules
Get rule sets for DQ grading
Get formats for DQ categories
Get namespace for attributes
Get the storr object backing a report
Get namespace specifically for summary attributes for speed-up
Get the thresholds for grading
Get variable attributes of a certain provision level
Return all variables in the segment segment
Get the Table with Known Vocabularies
Add labels to ggplot
Utility function to check whether a variable has no grouping variable ...
Utility Function Heatmap with 1 Threshold
If on Windows, hide a file
Utility function to create histograms
escape "
Create a dynamic dimension related page for the report
Create a dynamic single variable page for the report
The jack of all trades device for tables
utility function for the outliers rule of Hubert and Vandervieren 2008
Make it scalable, if it is a figure
Extract all properties of a ReportSummaryTable
Integer breaks for ggplot2
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
Utility function to interpret mathematical interval notation
Check for integer values
Detect falsish values
Create a predicate function to check for certain numeric properties
Detect un-disclosed ggplot
Check, if x is a try-error
Check, if x contains valid missing codes
being called by the active binding function for .manual
Check for repetitive values using the digits 8 or 9 only
Rename columns of a SummaryTable (or Segment, ...) to look nice
Maps label column metadata on study data variable names
Map based on largest common prefix
Support function to allocate labels to variables
Utility function to create a margins plot for binary variables
Utility function to create a margins plot from linear regression model...
Utility function to create a plot similar to the margins plots for nom...
Utility function to create a plot similar to the margins plots for ord...
Utility function to create a margins plot from Poisson regression mode...
dataquieR version of match.arg
Combine data frames by merging
Produce a condition message with a useful short stack trace.
Select really numeric variables
Distribute CODE_LIST_TABLE in item level metadata
Normalize and check cross-item-level metadata
Convert VALUE_LABELS to separate tables
Detect Expected Observations
Utility function observations in subgroups
Creates a Link to our Website
Utility function to compute and optimize bin breaks for histograms
Utility function to distribute points across a time variable
Get the order of a vector with general order given in some other vecto...
Utility function parallel version of purrr::pmap
Utility function to parse assignments
Utility function to parse intervals
Interpret a REDcap-style rule and create an expression, that represe...
Paste strings but keep NA
Paste strings but keep NA (paste0)
Utility function to create plots for categorical variables
Plot a ggplot2 figure without plotly
Plot a ggplot2 figure using plotly
Replacement for htmltools::plotTag
Plot to un-disclosed ggplot object
Plotly to un-disclosed ggplot object
Utility function to prepare the metadata for location checks
Utility function to prepare the metadata for proportion checks
Convert single dataquieR result to an htmltools compatible object
Prepare a vector four output
Bind data frames row-based
Can we really be sure to run RStudio
Map a vector of values based on an assignment table
For a group of variables (original) the function provides all original...
removes empty rows from x
remove all records, that have at least one NA in any of the given va...
Render a table summarizing dataquieR results
Utility function to replace missing codes by NAs
Replace limit violations (HARD_LIMITS) by NAs
Import list of data frames
Import a data frame
Round number of decimal places to 3 if the values are between 0.001 an...
Utility function to put strings in quotes
Attaches attributes about the recommended minimum absolute sizes to th...
Utility function single quote string
Set up an RStudio job
Utility function outliers according to the rule of Huber et al.
Sort a vector by order given in some other vector
Split table with mixed code/missing lists to single tables
Compute something comparable from an ordered
String check for results/combined results
Verify assumptions made by the code, that must be TRUE
Create a storr object with a storr_factory attribute
Create a storr-object using the factory
Utility function for judging whether a character vector does not appea...
Convert a study variable to a factor
Get sub-string left from first .
Get sub-string right from first .
Suppress any output to stdout using sink()
Suppress warnings conditionally
Tabulate a vector
Rotate 1-row data frames to key-value data frames
Translate standard column names to readable ones
Get a translation
Utility function Tukey outlier rule
Remove tables referred to by metadata and use SVG for most figures
Detect base unit from composite units
Save a hint to the user during package load
Utility function verifying syntax of known metadata columns
Validate code lists for missing and/or jump codes
Verify the class ReportSummaryTable
Utility function to compute the rank intraclass correlation
Find all columns in item-level-metadata, that refer to some other vari...
Verify encoding
Test for likely misspelled data frame references
View a file in most suitable viewer
Warn about a problem in varname, if x has no natural order
Produce a warning message with a useful short stack trace.
Data frame with labels for missing- and jump-codes #' Metadata about v...
Requirement levels of certain metadata columns
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