# Data Quality in Epidemiological Research

## Documentation for package ‘dataquieR’ version 1.0.9

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

A C D E F H I J K L M N O P R S T U V W misc

dataquieR-package | The 'dataquieR' package about Data Quality in Epidemiological Research

## -- A --

acc_distributions | Function to plot histograms added by empirical cumulative distributions for subgroups
acc_end_digits | Extension of acc_shape_or_scale to examine uniform distributions of end digits
acc_loess | Smoothes and plots adjusted longitudinal measurements
acc_margins | Function to estimate marginal means, see emmeans::emmeans
acc_multivariate_outlier | Function to calculate and plot Mahalanobis distances
acc_robust_univariate_outlier | Function to identify univariate outliers by four different approaches
acc_shape_or_scale | Function to compare observed versus expected distributions
acc_univariate_outlier | Function to identify univariate outliers by four different approaches
acc_varcomp | Estimates variance components
as.data.frame.dataquieR_resultset | Convert a full 'dataquieR' report to a 'data.frame'
as.list.dataquieR_resultset | Convert a full 'dataquieR' report to a 'list'

## -- C --

COMPATIBILITY | Requirement levels of certain metadata columns
com_item_missingness | Summarize missingness columnwise (in variable)
com_segment_missingness | Summarizes missingness for individuals in specific segments
com_unit_missingness | Counts all individuals with no measurements at all
CONTRADICTIONS | Well-known metadata column names, names of metadata columns
contradiction_functions | contradiction_functions
contradiction_functions_descriptions | description of the contradiction functions
con_contradictions | Checks user-defined contradictions in study data
con_detection_limits | con_detection_limits
con_inadmissible_categorical | Detects variable levels not specified in metadata
con_limit_deviations | Detects variable values exceeding limits defined in metadata

## -- D --

dataquieR | The 'dataquieR' package about Data Quality in Epidemiological Research
dataquieR_result | Print a dataquieR result returned by pipeline_vectorized
dataquieR_resultset | Internal constructor for the internal class dataquieR_resultset.
dataquieR_resultset_verify | Verify an object of class dataquieR_resultset
DATA_ENTRY_TYPE | Well-known metadata column names, names of metadata columns
DATA_TYPE | Well-known metadata column names, names of metadata columns
DATA_TYPES | Data Types
DATA_TYPES_OF_R_TYPE | All available data types, mapped from their respective R types
DATETIME | Data Types
datetime | Data Types
DECIMALS | Well-known metadata column names, names of metadata columns
DETECTION_LIMITS | Well-known metadata column names, names of metadata columns
DETECTION_LIMIT_LOW | Well-known metadata column names, names of metadata columns
DETECTION_LIMIT_UP | Well-known metadata column names, names of metadata columns
dimensions | Names of DQ dimensions
DISTRIBUTION | Well-known metadata column names, names of metadata columns
DISTRIBUTIONS | All available probability distributions for acc_shape_or_scale
dq_report | Generate a full DQ report
dq_report_by | Generate a stratified full DQ report

## -- E --

enum | Data Types

## -- F --

FLOAT | Data Types
float | Data Types

## -- H --

HARD_LIMITS | Well-known metadata column names, names of metadata columns
HARD_LIMIT_LOW | Well-known metadata column names, names of metadata columns
HARD_LIMIT_UP | Well-known metadata column names, names of metadata columns
html_dependency_vert_dt | HTML Dependency for vertical headers in 'DT::datatable'

## -- I --

INCL_HARD_LIMIT_LOW | Well-known metadata column names, names of metadata columns
INCL_HARD_LIMIT_UP | Well-known metadata column names, names of metadata columns
INCL_SOFT_LIMIT_LOW | Well-known metadata column names, names of metadata columns
INCL_SOFT_LIMIT_UP | Well-known metadata column names, names of metadata columns
INTEGER | Data Types
integer | Data Types
int_datatype_matrix | Function to check declared data types of metadata in study data

## -- J --

JUMP_LIST | Well-known metadata column names, names of metadata columns

## -- K --

KEY_DATETIME | Well-known metadata column names, names of metadata columns
KEY_DEVICE | Well-known metadata column names, names of metadata columns
KEY_OBSERVER | Well-known metadata column names, names of metadata columns
KEY_STUDY_SEGMENT | Well-known metadata column names, names of metadata columns

## -- L --

LABEL | Well-known metadata column names, names of metadata columns
LONG_LABEL | Well-known metadata column names, names of metadata columns

## -- M --

MISSING_LIST | Well-known metadata column names, names of metadata columns

## -- N --

numeric | Data Types

## -- O --

OPTIONAL | Requirement levels of certain metadata columns

## -- P --

pipeline_recursive_result | Function to convert a pipeline result data frame to named encapsulated lists
pipeline_vectorized | Call (nearly) one "Accuracy" function with many parameterizations at once automatically
prep_add_to_meta | Support function to augment metadata during data quality reporting
prep_check_meta_names | Checks the validity of meta data w.r.t. the provided column names
prep_clean_labels | Support function to scan variable labels for applicability
prep_create_meta | Support function to create data.frames of metadata
prep_datatype_from_data | Get data types from data
prep_map_labels | Support function to allocate labels to variables
prep_min_obs_level | Support function to identify the levels of a process variable with minimum number of observations
prep_pmap | Support function for a parallel 'pmap'
prep_prepare_dataframes | Prepare and verify study data with metadata
prep_study2meta | Guess a meta data frame from study data.
prep_valuelabels_from_data | Get value labels from data
print.dataquieR_result | Print a dataquieR result returned by pipeline_vectorized
print.dataquieR_resultset | Generate a RMarkdown-based report from a dataquieR report
print.ReportSummaryTable | print implementation for the class 'ReportSummaryTable'
pro_applicability_matrix | Function to check applicability of DQ functions on study data

## -- R --

rbind.ReportSummaryTable | Combine 'ReportSummaryTable' outputs
RECODE | Well-known metadata column names, names of metadata columns
RECOMMENDED | Requirement levels of certain metadata columns
REQUIRED | Requirement levels of certain metadata columns

## -- S --

SOFT_LIMITS | Well-known metadata column names, names of metadata columns
SOFT_LIMIT_LOW | Well-known metadata column names, names of metadata columns
SOFT_LIMIT_UP | Well-known metadata column names, names of metadata columns
SPLIT_CHAR | Character used by default as a separator in meta data such as missing codes
STRING | Data Types
string | Data Types
summary.dataquieR_resultset | Summarize a dataquieR report

## -- T --

TECHNICAL | Requirement levels of certain metadata columns

## -- U --

UNKNOWN | Requirement levels of certain metadata columns
util_anytime_installed | Test, if package 'anytime' is installed
util_app_cd | utility function for the applicability of contradiction checks
util_app_dc | utility function for the applicability of of distribution plots
util_app_dl | utility function to test for applicability of detection limits checks
util_app_ed | utility function for the applicability of of end digits preferences checks
util_app_iac | utility function for the applicability of categorical admissibility
util_app_iav | utility function for the applicability of numeric admissibility
util_app_im | utility function applicability of item missingness
util_app_loess | utility function for applicability of LOESS smoothed time course plots
util_app_mar | utility function to test for applicability of marginal means plots
util_app_mol | utility function applicability of multivariate outlier detection
util_app_ol | utility function for the applicability of outlier detection
util_app_sm | utility function applicability of segment missingness
util_app_sos | utility function applicability of distribution function's shape or scale check
util_app_vc | utility applicability variance components
util_assign_levlabs | utility function to assign labels to levels
util_as_numeric | Convert factors to label-corresponding numeric values
util_backtickQuote | utility function to set string in backticks
util_check_data_type | Support function to verify the data type of a value
util_check_one_unique_value | Check for one value only
util_compare_meta_with_study | Compares study data data types with the ones expected according to the metadata
util_correct_variable_use | Check referred variables
util_correct_variable_use2 | Check referred variables
util_count_codes | count realizations of missing codes of any class
util_count_code_classes | count distinct realizations of missing codes of a specific class
util_count_NA | Support function to count number of 'NA's
util_detect_cores | Detect cores
util_dichotomize | utility function to dichotomize variables
util_dist_selection | Utility function distribution-selection
util_empty | Test, if values of x are empty, i.e. NA or whitespace characters
util_ensure_suggested | Support function to stop, if an optional package is not installed
util_error | Produce an error message with a useful short stack trace. Then it stops the execution.
util_find_external_functions_in_stacktrace | Find externally called function in the stack trace
util_find_first_externally_called_functions_in_stacktrace | Find first externally called function in the stack trace
util_fix_rstudio_bugs | RStudio crashes on parallel calls in some versions on Darwin based operating systems with R 4
util_get_code_list | Fetch a missing code list from the metadata
util_get_var_att_names_of_level | Get variable attributes of a certain provision level
util_heatmap_1th | Utility Function Heatmap with 1 Threshold
util_hubert | utility function for the outliers rule of Huber et al.
util_interpret_limits | Utility function to interpret mathematical interval notation
util_is_integer | Check for integer values
util_looks_like_missing | Check for repetitive values using the digits 8 or 9 only
util_make_function | Make a function capturing errors and other conditions for parallelization
util_map_all | Maps label column meta data on study data variable names
util_map_labels | Support function to allocate labels to variables
util_no_value_labels | Select really numeric variables
util_observations_in_subgroups | Utility function observations in subgroups
util_only_NAs | identify 'NA'-only variables
util_parse_assignments | Utility function to parse assignments
util_par_pmap | Utility function parallel version of 'purrr::pmap'
util_prepare_dataframes | util_prepare_dataframes
util_replace_codes_by_NA | Utility function to replace missing codes by 'NA's
util_set_dQuoteString | Utility function to put strings in quotes
util_set_size | Attaches attributes about the recommended minimum absolute sizes to the plot p
util_set_sQuoteString | Utility function single quote string
util_sigmagap | Utility function outliers according to the rule of Huber et al.
util_sixsigma | Utility function for six sigma deviations rule
util_tukey | Utility function Tukey outlier rule
util_validate_known_meta | Utility function verifying syntax of known metadata columns
util_warning | Produce a warning message with a useful short stack trace.
util_warn_unordered | Warn about a problem in 'varname', if 'x' has no natural order

## -- V --

VALUE_LABELS | Well-known metadata column names, names of metadata columns
VARATT_REQUIRE_LEVELS | Requirement levels of certain metadata columns
variable | Data Types
variable attribute | Well-known metadata column names, names of metadata columns
variable list | Data Types
variable roles | Variable roles can be one of the following:
VARIABLE_ORDER | Well-known metadata column names, names of metadata columns
VARIABLE_ROLE | Well-known metadata column names, names of metadata columns
VARIABLE_ROLES | Variable roles can be one of the following:
VAR_NAMES | Well-known metadata column names, names of metadata columns

## -- W --

WELL_KNOWN_META_VARIABLE_NAMES | Well-known metadata column names, names of metadata columns

## -- misc --

.variable_arg_roles | Variable-argument roles