Data Quality in Epidemiological Research


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Documentation for package ‘dataquieR’ version 2.5.0

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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

-- A --

acc_cat_distributions Plots and checks for distributions for categorical variables
acc_distributions Plots and checks for distributions
acc_distributions_ecdf ECDF plots for distribution checks
acc_distributions_loc Plots and checks for distributions - Location
acc_distributions_only Plots and checks for distributions - only
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 and longitudinal trends from logistic regression models
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 Utility function to compute model-based ICC depending on the (statistical) data type
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'
as.list.dataquieR_resultset2 inefficient way to convert a report to a list. try 'prep_set_backend()'
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 --

cash-.dataquieR_resultset2 Access single results from a dataquieR_resultset2 report
cash-set-.dataquieR_resultset2.Rd Write single results from a dataquieR_resultset2 report
cause_label_df Data frame with labels for missing- and jump-codes #' Metadata about value and missing 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 #' Metadata about value and missing codes
CODE_CLASSES types of value codes
CODE_INTERPRET Data frame with labels for missing- and jump-codes #' Metadata about value and missing codes
CODE_LABEL Data frame with labels for missing- and jump-codes #' Metadata about value and missing codes
CODE_LIST_TABLE Default Name of the Table featuring Code Lists
CODE_ORDER Only existence is checked, order not yet used
CODE_VALUE Data frame with labels for missing- and jump-codes #' Metadata about value and missing 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_inadmissible_vocabulary Detects variable levels not specified in standardized vocabulary
con_limit_deviations Detects variable values exceeding limits defined in metadata
CO_VARS Well-known metadata column names, names of metadata columns

-- D --

DATAFRAMES Well-known metadata column names, names of metadata columns
dataquieR.acc_loess.exclude_constant_subgroups Exclude subgroups with constant values from LOESS figure
dataquieR.acc_loess.mark_time_points Display time-points in LOESS plots
dataquieR.acc_loess.plot_format default for Plot-Format in 'acc_loess()'
dataquieR.acc_loess.plot_observations Display observations in LOESS plots
dataquieR.acc_margins_num Include number of observations for each level of the grouping variable in the 'margins' figure
dataquieR.acc_margins_sort Sort levels of the grouping variable in the 'margins' figures
dataquieR.acc_multivariate_outlier.scale Apply min-max scaling in parallel coordinates figure to inspect multivariate outliers
dataquieR.col_con_con_empirical Color for empirical contradictions
dataquieR.col_con_con_logical Color for logical contradictions
dataquieR.CONDITIONS_LEVEL_TRHESHOLD Log Level
dataquieR.CONDITIONS_WITH_STACKTRACE Add stack-trace in condition messages (to be deprecated)
dataquieR.debug Call 'browser()' on errors
dataquieR.des_summary_hard_lim_remove Removal of hard limits from data before calculating descriptive statistics.
dataquieR.dontwrapresults Disable automatic post-processing of 'dataquieR' function results
dataquieR.ELEMENT_MISSMATCH_CHECKTYPE Metadata describes more than the current study data
dataquieR.ERRORS_WITH_CALLER Set caller for error conditions (to be deprecated)
dataquieR.fix_column_type_on_read Try to avoid fallback to string columns when reading files
dataquieR.flip_mode Flip-Mode to Use for figures
dataquieR.force_item_specific_missing_codes Converting MISSING_LIST/JUMP_LIST to a MISSING_LIST_TABLE create on list per item
dataquieR.force_label_col Control, how the 'label_col' argument is used.
dataquieR.GAM_for_LOESS Enable to switch to a general additive model instead of LOESS
dataquieR.grading_formats Name of the data.frame featuring a format for grading-values
dataquieR.grading_rulesets Name of the data.frame featuring GRADING_RULESET
dataquieR.guess_missing_codes Control, if 'dataquieR' tries to guess missing-codes from the study data in absence of metadata
dataquieR.lang Language-Suffix for metadata Label-Columns
dataquieR.max_group_var_levels_in_plot Maximum number of levels of the grouping variable shown individually in figures
dataquieR.max_group_var_levels_with_violins Maximum number of levels of the grouping variable shown with individual histograms ('violins') in 'margins' figures
dataquieR.MAX_LABEL_LEN Maximum length for variable labels
dataquieR.MAX_VALUE_LABEL_LEN Maximum length for value labels
dataquieR.MESSAGES_WITH_CALLER Set caller for message conditions (to be deprecated)
dataquieR.min_obs_per_group_var_in_plot Minimum number of observations per grouping variable that is required to include an individual level of the grouping variable in a figure
dataquieR.MULTIVARIATE_OUTLIER_CHECK Default availability of multivariate outlier checks in reports
dataquieR.non_disclosure Remove all observation-level-real-data from reports
dataquieR.progress_fkt function to call on progress increase
dataquieR.progress_msg_fkt function to call on progress message update
dataquieR.scale_level_heuristics_control_binaryrecodelimit Number of levels to consider a variable ordinal in absence of SCALE_LEVEL
dataquieR.scale_level_heuristics_control_metriclevels Number of levels to consider a variable metric in absence of SCALE_LEVEL
dataquieR.testdebug Disable all interactively used metadata-based function argument provision
dataquieR.VALUE_LABELS_htmlescaped Assume, all VALUE_LABELS are HTML escaped
dataquieR.WARNINGS_WITH_CALLER Set caller for warning conditions (to be deprecated)
dataquieR_result Print a dataquieR result returned by dq_report2
dataquieR_resultset Internal constructor for the internal class dataquieR_resultset.
dataquieR_resultset2 Class dataquieR_resultset2.
dataquieR_resultset2-class 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_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
des_summary_categorical Compute Descriptive Statistics - categorical variables
des_summary_continuous Compute Descriptive Statistics - continuous variables
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_CODE Data frame level metadata attribute name
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 --

ENCODING Well-known metadata column names, names of metadata columns
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_encoding_errors Encoding Errors
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 #' Metadata about value and missing codes
MULTIVARIATE_OUTLIER_CHECK Cross-item level metadata attribute name
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_acc_distributions_with_ecdf Utility function to plot a combined figure for distribution checks
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_computed_variables Insert missing codes for 'NA's based on rules
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_compare_meta_with_study Verify item-level metadata
prep_create_meta Support function to create data.frames of metadata
prep_create_meta_data_file Instantiate a new metadata file
prep_create_storr_factory Create a factory function for 'storr' objects for backing a dataquieR_resultset2
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_study_data_segment Get data frame for a given segment
prep_get_user_name Return the logged-in User's Full Name
prep_guess_encoding Guess encoding of text or text files
prep_link_escape Prepare a label as part of a link for 'RMD' files
prep_list_dataframes List Loaded Data Frames
prep_list_voc All valid voc: vocabularies
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_report_from_backend Load a report from a back-end
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_open_in_excel Open a data frame in Excel
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_remove_from_cache Remove a specified element from the 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_robust_guess_data_type Guess the data type of a vector
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_set_backend Change the back-end of a report
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_undisclose Remove data disclosing details
prep_unsplit_val_tabs Combine all missing and value lists to one big table
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.DataSlot Print a 'DataSlot' object
print.interval print implementation for the class 'interval'
print.list print a list of 'dataquieR_result' objects
print.master_result Print a 'master_result' object
print.ReportSummaryTable print implementation for the class 'ReportSummaryTable'
print.Slot Print a 'Slot' object
print.StudyDataSlot Print a 'StudyDataSlot' object
print.TableSlot Print a 'TableSlot' object
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_CASES Well-known metadata column names, names of metadata columns
RECODE_CONTROL 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)
RULE Cross-item level metadata attribute name

-- 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_ID 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
STANDARDIZED_VOCABULARY_TABLE Well-known metadata column names, names of metadata columns
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_bar_plot Utility function to create bar plots
util_combine_list_report_summaries Create a data frame containing all the results from summaries of reports
util_compute_kurtosis Compute Kurtosis
util_compute_SE_skewness Compute SE.Skewness
util_compute_skewness Compute the Skewness
util_create_report_by_overview Create an overview of the reports created with 'dq_report_by'
util_first_row_to_colnames Move the first row of a data frame to its column names
util_get_encoding Get encoding from metadata or guess it from data
util_has_no_group_vars Utility function to check whether a variable has no grouping variable assigned
util_histogram Utility function to create histograms
util_margins_bin Utility function to create a margins plot for binary variables
util_margins_lm Utility function to create a margins plot from linear regression models
util_margins_nom Utility function to create a plot similar to the margins plots for nominal variables
util_margins_ord Utility function to create a plot similar to the margins plots for ordinal variables
util_margins_poi Utility function to create a margins plot from Poisson regression models
util_plot_categorical_vars Utility function to create plots for categorical variables
util_varcomp_robust Utility function to compute the rank intraclass correlation

-- V --

value/missing-lists Data frame with labels for missing- and jump-codes #' Metadata about value and missing codes
VALUE_LABELS Well-known metadata column names, names of metadata columns
VALUE_LABEL_TABLE Well-known metadata column names, names of metadata columns
value_label_table Data frame with labels for missing- and jump-codes #' Metadata about value and missing codes
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 Access single results from a dataquieR_resultset2 report
$<-.dataquieR_resultset2 Write single results from a dataquieR_resultset2 report
.dataquieR_resultset2 Class dataquieR_resultset2.
[.dataquieR_resultset2 Get a subset of a 'dataquieR' 'dq_report2' report
[<-.dataquieR_resultset2 Write to a report
[[.dataquieR_resultset2 Get a single result from a dataquieR 2 report
[[<-.dataquieR_resultset2 Set a single result from a dataquieR 2 report