Data Quality in Epidemiological Research


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Documentation for package ‘dataquieR’ version 2.0.0

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A C D E F G 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 Plots and checks for distributions
acc_distributions_loc Plots and checks for distributions - Location
acc_distributions_loc_ecdf Plots and checks for distributions - Location, ECDF
acc_distributions_prop Plots and checks for distributions - Proportion
acc_distributions_prop_ecdf Plots and checks for distributions - Proportion, ECDF
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 Estimate marginal means, see emmeans::emmeans
acc_multivariate_outlier Calculate and plot Mahalanobis distances
acc_robust_univariate_outlier Identify univariate outliers by four different approaches
acc_shape_or_scale Compare observed versus expected distributions
acc_univariate_outlier 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 --

cause_label_df Data frame with labels for missing- and jump-codes
check_table Data frame with contradiction rules
COMPATIBILITY Requirement levels of certain metadata columns
com_item_missingness Summarize missingness columnwise (in variable)
com_qualified_item_missingness Compute Indicators for Qualified Item Missingness
com_qualified_segment_missingness Compute Indicators for Qualified Segment Missingness
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_contradictions_redcap Checks user-defined contradictions in study data
con_detection_limits Detects variable values exceeding detection limits
con_hard_limits Detects variable values exceeding hard limits
con_inadmissible_categorical Detects variable levels not specified in metadata
con_limit_deviations Detects variable values exceeding limits defined in metadata
con_soft_limits Detects variable values exceeding soft limits
CO_VARS Well-known metadata column names, names of metadata columns

-- 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_resultset2 Internal constructor for the internal class dataquieR_resultset2.
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
DF_ELEMENT_COUNT Data frame level metadata attribute name
DF_ID_REF_TABLE Data frame level metadata attribute name
DF_ID_VARS Data frame level metadata attribute name
DF_NAME Data frame level metadata attribute name
DF_RECORD_CHECK Data frame level metadata attribute name
DF_RECORD_COUNT Data frame level metadata attribute name
DF_UNIQUE_ID Data frame level metadata attribute name
DF_UNIQUE_ROWS Data frame level metadata attribute name
dim.dataquieR_resultset2 Get the dimensions of a 'dq_report2' result
dimensions Names of DQ dimensions
dimnames.dataquieR_resultset2 Names of a 'dataquieR' report object (v2.0)
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_report2 Generate a full DQ report, v2
dq_report_by Generate a stratified full DQ report

-- E --

enum Data Types

-- F --

FLOAT Data Types
float Data Types

-- G --

GROUP_VAR_DEVICE Well-known metadata column names, names of metadata columns
GROUP_VAR_OBSERVER Well-known metadata column names, names of metadata columns

-- 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_report_dt HTML Dependency for report headers in 'DT::datatable'
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_LOCATION_LIMIT_LOW Well-known metadata column names, names of metadata columns
INCL_LOCATION_LIMIT_UP Well-known metadata column names, names of metadata columns
INCL_PROPORTION_LIMIT_LOW Well-known metadata column names, names of metadata columns
INCL_PROPORTION_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_all_datastructure_dataframe Wrapper function to check for studies data structure
int_all_datastructure_segment Wrapper function to check for segment data structure
int_datatype_matrix Check declared data types of metadata in study data
int_duplicate_content Check for duplicated content
int_duplicate_ids Check for duplicated IDs
int_part_vars_structure Detect Expected Observations
int_sts_element_dataframe Determine missing and/or superfluous data elements
int_sts_element_segment Checks for element set
int_unexp_elements Check for unexpected data element count
int_unexp_records_dataframe Check for unexpected data record count at the data frame level
int_unexp_records_segment Check for unexpected data record count within segments
int_unexp_records_set Check for unexpected data record set

-- 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
LOCATION_LIMIT_LOW Well-known metadata column names, names of metadata columns
LOCATION_LIMIT_UP Well-known metadata column names, names of metadata columns
LOCATION_METRIC Well-known metadata column names, names of metadata columns
LOCATION_RANGE Well-known metadata column names, names of metadata columns
LONG_LABEL Well-known metadata column names, names of metadata columns

-- M --

menu_env '.menu_env' - an environment for HTML menu creation
menu_env-menu Generate the menu for a report
menu_env_drop_down Creates a drop-down menu
menu_env_menu_entry Create a single menu entry
meta_data Data frame with metadata about the study data on variable level
meta_data_cross_item Data frame with contradiction rules
meta_data_dataframe Well known columns on the 'meta_data_dataframe' sheet
meta_data_env '.meta_data_env' - an environment for easy metadata access
meta_data_env_co_vars Extract co-variables for a given item
meta_data_env_group_vars Extract group variables for a given item
meta_data_env_id_vars Extract id variables for a given item or variable group
meta_data_env_time_vars Extract measurement time variable for a given item
meta_data_segment Well known columns on the 'meta_data_segment' sheet
MISSING_LIST Well-known metadata column names, names of metadata columns
MISSING_LIST_TABLE Well-known metadata column names, names of metadata columns
missing_matchtable Data frame with labels for missing- and jump-codes

-- N --

nres return the number of result slots in a report
numeric Data Types

-- O --

OPTIONAL Requirement levels of certain metadata columns

-- P --

PART_VAR Well-known metadata column names, names of metadata columns
pipeline_recursive_result 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_cause_label_df Convert missing codes in metadata format v1.0 and a missing-cause-table to v2.0 missing list / jump list assignments
prep_add_data_frames Add data frames to the pre-loaded / cache data frame environment
prep_add_missing_codes Insert missing codes for 'NA's based on rules
prep_add_to_meta Support function to augment metadata during data quality reporting
prep_apply_coding Re-Code labels with their respective codes according to the 'meta_data'
prep_check_meta_data_dataframe Verify and normalize meta data on data frame level
prep_check_meta_data_segment Verify and normalize meta data on segment level
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_deparse_assignments Convert two vectors from a code-value-table to a key-value list
prep_dq_data_type_of Get the dataquieR 'DATA_TYPE' of 'x'
prep_expand_codes Expand code labels across variables
prep_extract_cause_label_df Extract all missing/jump codes from metadata and export a cause-label-data-frame
prep_get_data_frame Read data from files/URLs
prep_get_user_name Return the logged-in User's Full Name
prep_link_escape Prepare a label as part of a link for 'RMD' files
prep_list_dataframes List Loaded Data Frames
prep_load_workbook_like_file Pre-load a file with named (usually more than) one table(s)
prep_map_labels Support function to allocate labels to variables
prep_merge_study_data Merge a list of study data frames to one (sparse) study data frame
prep_meta_data_v1_to_item_level_meta_data Convert item-level metadata from v1.0 to v2.0
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_purge_data_frame_cache Title
prep_study2meta Guess a meta data frame from study data.
prep_title_escape Prepare a label as part of a title text for 'RMD' files
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.dataquieR_resultset2 Generate a RMarkdown-based report from a dataquieR report
print.interval print implementation for the class 'interval'
print.ReportSummaryTable print implementation for the class 'ReportSummaryTable'
PROPORTION_LIMIT_LOW Well-known metadata column names, names of metadata columns
PROPORTION_LIMIT_UP Well-known metadata column names, names of metadata columns
PROPORTION_RANGE Well-known metadata column names, names of metadata columns
pro_applicability_matrix 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
resnames Return names of result slots (e.g., 3rd dimension of dataquieR results)
resnames.dataquieR_resultset2 Return names of result slots (e.g., 3rd dimension of dataquieR results)

-- S --

SEGMENT_ID_TABLE Segment level metadata attribute name
SEGMENT_ID_VARS Segment level metadata attribute name
SEGMENT_PART_VARS Segment level metadata attribute name
SEGMENT_RECORD_CHECK Segment level metadata attribute name
SEGMENT_RECORD_COUNT Segment level metadata attribute name
SEGMENT_UNIQUE_ROWS Segment level metadata attribute name
set Data Types
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
study_data Data frame with the study data whose quality is being assessed
STUDY_SEGMENT Well-known metadata column names, names of metadata columns
summary.dataquieR_resultset Summarize a dataquieR report
summary.dataquieR_resultset2 Generate a report summary table

-- T --

TECHNICAL Requirement levels of certain metadata columns
TIME_VAR Well-known metadata column names, names of metadata columns

-- U --

UNKNOWN Requirement levels of certain metadata columns
util_abbreviate Abbreviate snake_case function names to shortened 'CamelCase'
util_adjust_geom_text_for_plotly Place all geom_texts also in 'plotly' right from the x position
util_alias2caption Create a caption from an alias name of a 'dq_report2' result
util_all_intro_vars_for_rv Get all 'PART_VARS' for a response variable (from item-level metadata)
util_all_is_integer convenience function to abbreviate all(util_is_integer(...))
util_anytime_installed Test, if package 'anytime' is installed
util_app_cd utility function for the applicability of contradiction checks
util_app_con_contradictions_redcap 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_hl utility function to test for applicability of hard limits 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_sl utility function to test for applicability of soft limits checks
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_color convert a character to a specific ordered factor
util_as_numeric Convert factors to label-corresponding numeric values
util_attach_attr Attach attributes to an object and return it
util_backtickQuote utility function to set string in backticks
util_bQuote Put in back-ticks
util_check_data_type Verify the data type of a value
util_check_group_levels Check data for observer levels
util_check_one_unique_value Check for one value only
util_combine_missing_lists Combine missing-lists for a set of variables to be displayed in the same heat-map
util_compare_meta_with_study Compares study data data types with the ones expected according to the metadata
util_condition_constructor_factory Produce a condition function
util_coord_flip return a flip term for 'ggplot2' plots, if desired.
util_copy_all_deps Copy default dependencies to the report's lib directory
util_correct_variable_use Check referred variables
util_correct_variable_use2 Check referred variables
util_count_expected_observations Count Expected Observations
util_count_NA Support function to count number of 'NA's
util_create_page_file Create an HTML file for the dq_report2
util_deparse1 Expression De-Parsing
util_deprecate_soft Deprecate functions and arguments
util_detect_cores Detect cores
util_dichotomize utility function to dichotomize variables
util_dist_selection Utility function distribution-selection
util_ds1_eval_env Create an environment with several alias names for the study data variables
util_empty Test, if values of x are empty, i.e. NA or whitespace characters
util_ensure_character convert a value to character
util_ensure_data_type Ensure matching data types
util_ensure_in similar to match.arg
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_evaluate_calls Generate a full DQ report, v2
util_eval_rule Evaluate a parsed redcap rule for given study data
util_eval_to_dataquieR_result Evaluate an expression and create a 'dataquieR_result' object from it's evaluated value
util_expect_data_frame Verify, that argument is a data frame
util_expect_scalar check, if a scalar/vector function argument matches expectations
util_extract_matches return all matches of an expression
util_filter_missing_list_table_for_rv Filter a 'MISSING_LIST_TABLE' for rows matching the variable 'rv'
util_filter_names_by_regexps Filter collection based on its 'names()' using regular expressions
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_find_var_by_meta Try hard, to map a variable
util_fix_rstudio_bugs RStudio crashes on parallel calls in some versions on Darwin based operating systems with R 4
util_float_index_menu return a single page navigation menu floating on the right
util_generate_anchor_link Generate a link to a specific result
util_generate_anchor_tag Generate a tag for a specific result
util_generate_calls Generate an execution/calling plan for computing a report from the metadata
util_generate_calls_for_function Generate function calls for a given indicator function
util_generate_pages_from_report Convert a dataquieR report v2 to a named list of web pages
util_get_code_list Fetch a missing code list from the metadata
util_get_color_for_result Return the color for a result
util_get_concept_info Read additional concept tables
util_get_html_cell_for_result Return the html summary table cell for a result
util_get_message_for_result Return messages/warnings/notes/error messages for a result
util_get_redcap_rule_env an environment with functions available for 'REDcap' rules
util_get_vars_in_segment Return all variables in the segment 'segment'
util_get_var_att_names_of_level Get variable attributes of a certain provision level
util_gg_var_label Add labels to 'ggplot'
util_heatmap_1th Utility Function Heatmap with 1 Threshold
util_html_attr_quote_escape escape "
util_html_table The jack of all trades device for tables
util_hubert utility function for the outliers rule of Huber et al.
util_interpret_limits Utility function to interpret mathematical interval notation
util_interpret_range Utility function to interpret mathematical interval notation for numeric ranges
util_int_duplicate_content_dataframe Check for duplicated content
util_int_duplicate_content_segment Check for duplicated content
util_int_duplicate_ids_dataframe Check for duplicated IDs
util_int_duplicate_ids_segment Check for duplicated IDs
util_int_unexp_records_set_dataframe Check for unexpected data record set
util_int_unexp_records_set_segment Check for unexpected data record set
util_is_integer Check for integer values
util_is_na_0_empty_or_false Detect falsish values
util_is_numeric_in Create a predicate function to check for certain numeric properties
util_load_manual being called by the active binding function for .manual
util_looks_like_missing Check for repetitive values using the digits 8 or 9 only
util_make_data_slot_from_table_slot Rename columns of a 'SummaryTable' (or Segment, ...) to look nice
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_by_largest_prefix Map based on largest common prefix
util_map_labels Support function to allocate labels to variables
util_match_arg 'dataquieR' version of match.arg
util_merge_data_frame_list Combine data frames by merging
util_message Produce a condition message with a useful short stack trace.
util_no_value_labels Select really numeric variables
util_observations_in_subgroups Utility function observations in subgroups
util_observation_expected Detect Expected Observations
util_only_NAs identify 'NA'-only variables
util_optimize_histogram_bins Utility function to compute and optimize bin breaks for histograms
util_order_by_order Get the order of a vector with general order given in some other vector
util_parse_assignments Utility function to parse assignments
util_parse_interval Utility function to parse intervals
util_parse_redcap_rule Interpret a 'REDcap'-style rule and create an expression, that represents this rule
util_par_pmap Utility function parallel version of 'purrr::pmap'
util_prepare_dataframes util_prepare_dataframes
util_prep_location_check Utility function to prepare the metadata for location checks
util_prep_proportion_check Utility function to prepare the metadata for proportion checks
util_pretty_vector_string Prepare a vector four output
util_rbind Bind data frames row-based
util_recode Map a vector of values based on an assignment table
util_remove_empty_rows removes empty rows from 'x'
util_remove_na_records remove all records, that have at least one 'NA' in any of the given variables
util_replace_codes_by_NA Utility function to replace missing codes by 'NA's
util_replace_hard_limit_violations Replace limit violations (HARD_LIMITS) by NAs
util_setup_rstudio_job Set up an RStudio job
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_sort_by_order Sort a vector by order given in some other vector
util_stop_if_not Verify assumptions made by the code, that must be TRUE
util_study_var2factor Convert a study variable to a factor
util_sub_string_left_from_. Get sub-string left from first '.'
util_sub_string_right_from_. Get sub-string right from first '.'
util_table_of_vct Tabulate a vector
util_tukey Utility function Tukey outlier rule
util_validate_known_meta Utility function verifying syntax of known metadata columns
util_validate_missing_lists Validate code lists for missing and/or jump codes
util_variable_references Find all columns in item-level-metadata, that refer to some other variable
util_view_file View a file in most suitable viewer
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 --

$.dataquieR_result Extract elements of a 'dataquieR' Result Object
..manual Holds parts of the manual at run-time
.dataquieR_resultset2 Internal constructor for the internal class dataquieR_resultset2.
.menu_env '.menu_env' - an environment for HTML menu creation
.meta_data_env '.meta_data_env' - an environment for easy metadata access
.util_internal_normalize_meta_data Make normalizations of v2.0 item_level metadata.
.variable_arg_roles Variable-argument roles
[.dataquieR_result Extract Parts of a 'dataquieR' Result Object
[.dataquieR_resultset2 Get a subset of a 'dataquieR' 'dq_report2' report
[[.dataquieR_result Extract Elements of a 'dataquieR' Result Object