Data Quality in Epidemiological Research


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Documentation for package ‘dataquieR’ version 1.0.5

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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

-- 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

-- 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.
print.dataquieR_result Print a dataquieR result returned by pipeline_vectorized
print.dataquieR_resultset Generate a RMarkdown-based report from a dataquieR report
pro_applicability_matrix Function to check applicability of DQ functions on study data

-- R --

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_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_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_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