R: Data Quality in Epidemiological Research

# Data Quality in Epidemiological Research

## Documentation for package ‘dataquieR’ version 2.1.0

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

## Help Pages

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

## -- 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_only | Plots and checks for distributions - only
acc_distributions_only_ecdf | Plots and checks for distributions - only, but with ecdf
acc_distributions_prop | Plots and checks for distributions - Proportion
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'
ASSOCIATION_DIRECTION | Cross-item level metadata attribute name
ASSOCIATION_FORM | Cross-item level metadata attribute name
ASSOCIATION_METRIC | Cross-item level metadata attribute name
ASSOCIATION_RANGE | Cross-item level metadata attribute name

## -- C --

cause_label_df | Data frame with labels for missing- and jump-codes
CHECK_ID | Cross-item level metadata attribute name
CHECK_LABEL | Cross-item level metadata attribute name
check_table | Data frame with contradiction rules
CODE_CLASS | Data frame with labels for missing- and jump-codes
CODE_INTERPRET | Data frame with labels for missing- and jump-codes
CODE_LABEL | Data frame with labels for missing- and jump-codes
CODE_VALUE | Data frame with labels for missing- and jump-codes
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_descriptions | description of the contradiction functions
CONTRADICTION_TERM | Cross-item level metadata attribute name
CONTRADICTION_TYPE | Cross-item level metadata attribute name
con_contradictions | Checks user-defined contradictions in study data
con_contradictions_redcap | Checks user-defined contradictions in study data
con_inadmissible_categorical | Detects variable levels not specified in metadata
con_limit_deviations | Detects variable values exceeding limits defined in metadata
CO_VARS | Well-known metadata column names, names of metadata columns

## -- D --

dataquieR_result | Print a dataquieR result returned by dq_report2
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_PREPARATION | Cross-item level metadata attribute name
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
des_scatterplot_matrix | Compute Pairwise Correlations
des_summary | Compute Descriptive Statistics
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)
dims | Dimension Titles for Prefixes
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 --

END_DIGIT_CHECK | Well-known metadata column names, names of metadata columns
enum | Data Types

## -- F --

FLOAT | Data Types
float | Data Types

## -- G --

GOLDSTANDARD | Cross-item level metadata attribute name
GRADING_RULESET | Well-known metadata column names, names of metadata columns
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_clipboard | HTML Dependency for report headers in 'clipboard'
html_dependency_dataquieR | HTML Dependency for 'dataquieR'
html_dependency_report_dt | HTML Dependency for report headers in 'DT::datatable'
html_dependency_tippy | HTML Dependency for 'tippy'
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 --

meta_data | Data frame with metadata about the study data on variable level
meta_data_cross | Well known columns on the 'meta_data_cross-item' sheet
meta_data_dataframe | Well known columns on the 'meta_data_dataframe' sheet
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
MULTIVARIATE_OUTLIER_CHECKTYPE | Cross-item level metadata attribute name

## -- N --

nres | return the number of result slots in a report
numeric | Data Types
N_RULES | Cross-item and item level metadata attribute name

## -- 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
plot.dataquieR_summary | Plot a 'dataquieR' summary
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_for_dataquieR_updates | Check for package updates
prep_check_meta_data_dataframe | Verify and normalize metadata on data frame level
prep_check_meta_data_segment | Verify and normalize metadata on segment level
prep_check_meta_names | Checks the validity of metadata w.r.t. the provided column names
prep_clean_labels | Support function to scan variable labels for applicability
prep_combine_report_summaries | Combine two report summaries
prep_create_meta | Support function to create data.frames of metadata
prep_create_meta_data_file | Instantiate a new metadata file
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_extract_classes_by_functions | Extract old function based summary from data quality results
prep_extract_summary | Extract summary from data quality results
prep_extract_summary.dataquieR_result | Extract report summary from reports
prep_extract_summary.dataquieR_resultset2 | Extract report summary from reports
prep_get_data_frame | Read data from files/URLs
prep_get_labels | Fetch a label for a variable based on its purpose
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_folder_with_metadata | Pre-load a folder with named (usually more than) one table(s)
prep_load_report | Load a 'dq_report2'
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 | Clear data frame cache
prep_render_pie_chart_from_summaryclasses_ggplot2 | Create a 'ggplot2' pie chart
prep_render_pie_chart_from_summaryclasses_plotly | Create a 'plotly' pie chart
prep_save_report | Save a 'dq_report2'
prep_scalelevel_from_data_and_metadata | Heuristics to amend a SCALE_LEVEL column and a UNIT column in the metadata
prep_study2meta | Guess a metadata data frame from study data.
prep_summary_to_classes | Classify metrics from a report summary table
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 dq_report2
print.dataquieR_resultset | Generate a RMarkdown-based report from a dataquieR report
print.dataquieR_resultset2 | Generate a HTML-based report from a dataquieR report
print.dataquieR_summary | Print a 'dataquieR' summary
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
REL_VAL | Cross-item level metadata attribute name
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 --

SCALE_LEVEL | Well-known metadata column names, names of metadata columns
SCALE_LEVELS | Scale Levels
SEGMENT_ID_REF_TABLE | Segment level metadata attribute name
SEGMENT_ID_TABLE | Deprecated segment level metadata attribute name
SEGMENT_ID_VARS | Segment level metadata attribute name
SEGMENT_MISS | 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 metadata 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 --

UNIT | Well-known metadata column names, names of metadata columns
UNITS | Valid unit symbols according to 'units::valid_udunits()'
UNIT_IS_COUNT | Is a unit a count according to 'units::valid_udunits()'
UNIT_PREFIXES | Valid unit prefixes according to 'units::valid_udunits_prefixes()'
UNIT_SOURCES | Maturity stage of a unit according to 'units::valid_udunits()'
UNIVARIATE_OUTLIER_CHECKTYPE | Item level metadata attribute name
UNKNOWN | Requirement levels of certain metadata columns
util_compute_kurtosis | Compute Kurtosis
util_compute_SE_skewness | Compute SE.Skewness
util_compute_skewness | Compute the Skewness
util_first_row_to_colnames | Move the first row of a data frame to its column names

## -- 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_LIST | Cross-item level metadata attribute name
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_resultset2 | Get a subset of a 'dataquieR' 'dq_report2' report