Man pages for dataquieR
Data Quality in Epidemiological Research

acc_distributionsPlots and checks for distributions
acc_distributions_locPlots and checks for distributions - Location
acc_distributions_loc_ecdfPlots and checks for distributions - Location, ECDF
acc_distributions_onlyPlots and checks for distributions - only
acc_distributions_only_ecdfPlots and checks for distributions - only, but with ecdf
acc_distributions_propPlots and checks for distributions - Proportion
acc_end_digitsExtension of acc_shape_or_scale to examine uniform...
acc_loessSmoothes and plots adjusted longitudinal measurements
acc_marginsEstimate marginal means, see emmeans::emmeans
acc_multivariate_outlierCalculate and plot Mahalanobis distances
acc_robust_univariate_outlierIdentify univariate outliers by four different approaches
acc_shape_or_scaleCompare observed versus expected distributions
acc_univariate_outlierIdentify univariate outliers by four different approaches
acc_varcompEstimates variance components
API_VERSIONVersion of the API a full 'dataquieR' report to a 'data.frame'
as.list.dataquieR_resultsetConvert a full 'dataquieR' report to a 'list'
ASSOCIATION_DIRECTIONCross-item level metadata attribute name
ASSOCIATION_FORMCross-item level metadata attribute name
ASSOCIATION_METRICCross-item level metadata attribute name
ASSOCIATION_RANGECross-item level metadata attribute name
cash-.dataquieR_resultExtract elements of a 'dataquieR' Result Object
cause_label_dfData frame with labels for missing- and jump-codes
CHECK_IDCross-item level metadata attribute name
CHECK_LABELCross-item level metadata attribute name
check_tableData frame with contradiction rules
com_item_missingnessSummarize missingness columnwise (in variable)
com_qualified_item_missingnessCompute Indicators for Qualified Item Missingness
com_qualified_segment_missingnessCompute Indicators for Qualified Segment Missingness
com_segment_missingnessSummarizes missingness for individuals in specific segments
com_unit_missingnessCounts all individuals with no measurements at all
con_contradictionsChecks user-defined contradictions in study data
con_contradictions_redcapChecks user-defined contradictions in study data
con_detection_limitsDetects variable values exceeding detection limits
con_hard_limitsDetects variable values exceeding hard limits
con_inadmissible_categoricalDetects variable levels not specified in metadata
con_limit_deviationsDetects variable values exceeding limits defined in metadata
con_soft_limitsDetects variable values exceeding soft limits
contradiction_functions_descriptionsdescription of the contradiction functions
CONTRADICTION_TERMCross-item level metadata attribute name
CONTRADICTION_TYPECross-item level metadata attribute name
DATA_PREPARATIONCross-item level metadata attribute name
dataquieRThe 'dataquieR' package about Data Quality in Epidemiological...
dataquieR_resultsetInternal constructor for the internal class...
dataquieR_resultset2Internal constructor for the internal class...
dataquieR_resultset_verifyVerify an object of class dataquieR_resultset
DATA_TYPES_OF_R_TYPEAll available data types, mapped from their respective R...
DF_ELEMENT_COUNTData frame level metadata attribute name
DF_ID_REF_TABLEData frame level metadata attribute name
DF_ID_VARSData frame level metadata attribute name
DF_NAMEData frame level metadata attribute name
DF_RECORD_CHECKData frame level metadata attribute name
DF_RECORD_COUNTData frame level metadata attribute name
DF_UNIQUE_IDData frame level metadata attribute name
DF_UNIQUE_ROWSData frame level metadata attribute name
dim.dataquieR_resultset2Get the dimensions of a 'dq_report2' result
dimensionsNames of DQ dimensions
dimnames.dataquieR_resultset2Names of a 'dataquieR' report object (v2.0)
dimsDimension Titles for Prefixes
DISTRIBUTIONSAll available probability distributions for...
dot-get_internal_apiGet Access to Utility Functions
dot-.manualHolds parts of the manual at run-time
dot-util_internal_normalize_meta_dataMake normalizations of v2.0 item_level metadata.
dot-variable_arg_rolesVariable-argument roles
dq_reportGenerate a full DQ report
dq_report2Generate a full DQ report, v2
dq_report_byGenerate a stratified full DQ report
GOLDSTANDARDCross-item level metadata attribute name
html_dependency_report_dtHTML Dependency for report headers in 'DT::datatable'
html_dependency_vert_dtHTML Dependency for vertical headers in 'DT::datatable'
int_all_datastructure_dataframeWrapper function to check for studies data structure
int_all_datastructure_segmentWrapper function to check for segment data structure
int_datatype_matrixCheck declared data types of metadata in study data
int_duplicate_contentCheck for duplicated content
int_duplicate_idsCheck for duplicated IDs
int_part_vars_structureDetect Expected Observations
int_sts_element_dataframeDetermine missing and/or superfluous data elements
int_sts_element_segmentChecks for element set
int_unexp_elementsCheck for unexpected data element count
int_unexp_records_dataframeCheck for unexpected data record count at the data frame...
int_unexp_records_segmentCheck for unexpected data record count within segments
int_unexp_records_setCheck for unexpected data record set
menu_env'.menu_env' - an environment for HTML menu creation
menu_env_drop_downCreates a drop-down menu
menu_env-menuGenerate the menu for a report
menu_env_menu_entryCreate a single menu entry
meta_dataData frame with metadata about the study data on variable...
meta_data_crossWell known columns on the 'meta_data_cross-item' sheet
meta_data_dataframeWell known columns on the 'meta_data_dataframe' sheet
meta_data_env'.meta_data_env' - an environment for easy metadata access
meta_data_env_co_varsExtract co-variables for a given item
meta_data_env_criteriaExtract selected outlier criteria for a given item or...
meta_data_env_group_varsExtract group variables for a given item
meta_data_env_id_varsExtract id variables for a given item or variable group
meta_data_env_n_rulesExtract outlier rules-number-threshold for a given item or...
meta_data_env_time_varsExtract measurement time variable for a given item
meta_data_segmentWell known columns on the 'meta_data_segment' sheet
MULTIVARIATE_OUTLIER_CHECKTYPECross-item level metadata attribute name
nresreturn the number of result slots in a report
N_RULESCross-item and item level metadata attribute name
pipeline_recursive_resultConvert a pipeline result data frame to named encapsulated...
pipeline_vectorizedCall (nearly) one "Accuracy" function with many...
prep_add_cause_label_dfConvert missing codes in metadata format v1.0 and a...
prep_add_data_framesAdd data frames to the pre-loaded / cache data frame...
prep_add_missing_codesInsert missing codes for 'NA's based on rules
prep_add_to_metaSupport function to augment metadata during data quality...
prep_apply_codingRe-Code labels with their respective codes according to the...
prep_check_for_dataquieR_updatesCheck for package updates
prep_check_meta_data_dataframeVerify and normalize metadata on data frame level
prep_check_meta_data_segmentVerify and normalize metadata on segment level
prep_check_meta_namesChecks the validity of metadata w.r.t. the provided column...
prep_clean_labelsSupport function to scan variable labels for applicability
prep_create_metaSupport function to create data.frames of metadata
prep_datatype_from_dataGet data types from data
prep_deparse_assignmentsConvert two vectors from a code-value-table to a key-value...
prep_dq_data_type_ofGet the dataquieR 'DATA_TYPE' of 'x'
prep_expand_codesExpand code labels across variables
prep_extract_cause_label_dfExtract all missing/jump codes from metadata and export a...
prep_get_data_frameRead data from files/URLs
prep_get_user_nameReturn the logged-in User's Full Name
prep_link_escapePrepare a label as part of a link for 'RMD' files
prep_list_dataframesList Loaded Data Frames
prep_load_reportLoad a 'dq_report2'
prep_load_workbook_like_filePre-load a file with named (usually more than) one table(s)
prep_map_labelsSupport function to allocate labels to variables
prep_merge_study_dataMerge a list of study data frames to one (sparse) study data...
prep_meta_data_v1_to_item_level_meta_dataConvert item-level metadata from v1.0 to v2.0
prep_min_obs_levelSupport function to identify the levels of a process variable...
prep_pmapSupport function for a parallel 'pmap'
prep_prepare_dataframesPrepare and verify study data with metadata
prep_purge_data_frame_cacheClear data frame cache
prep_save_reportSave a 'dq_report2'
prep_study2metaGuess a metadata data frame from study data.
prep_title_escapePrepare a label as part of a title text for 'RMD' files
prep_valuelabels_from_dataGet value labels from data
print.dataquieR_resultPrint a dataquieR result returned by pipeline_vectorized
print.dataquieR_resultsetGenerate a RMarkdown-based report from a dataquieR report
print.dataquieR_resultset2Generate a HTML-based report from a dataquieR report
print.intervalprint implementation for the class 'interval'
print.ReportSummaryTableprint implementation for the class 'ReportSummaryTable'
pro_applicability_matrixCheck applicability of DQ functions on study data
rbind.ReportSummaryTableCombine 'ReportSummaryTable' outputs
REL_VALCross-item level metadata attribute name
resnamesReturn names of result slots (e.g., 3rd dimension of...
resnames.dataquieR_resultset2Return names of result slots (e.g., 3rd dimension of...
SEGMENT_ID_TABLESegment level metadata attribute name
SEGMENT_ID_VARSSegment level metadata attribute name
SEGMENT_MISSSegment level metadata attribute name
SEGMENT_PART_VARSSegment level metadata attribute name
SEGMENT_RECORD_CHECKSegment level metadata attribute name
SEGMENT_RECORD_COUNTSegment level metadata attribute name
SEGMENT_UNIQUE_ROWSSegment level metadata attribute name
SPLIT_CHARCharacter used by default as a separator in metadata such as...
study_dataData frame with the study data whose quality is being...
sub-.dataquieR_resultExtract Parts of a 'dataquieR' Result Object
sub-.dataquieR_resultset2Get a subset of a 'dataquieR' 'dq_report2' report
sub-sub-.dataquieR_resultExtract Elements of a 'dataquieR' Result Object
summary.dataquieR_resultsetSummarize a dataquieR report
summary.dataquieR_resultset2Generate a report summary table
UNIVARIATE_OUTLIER_CHECKTYPEItem level metadata attribute name
util_abbreviateAbbreviate snake_case function names to shortened 'CamelCase'
util_adjust_geom_text_for_plotlyPlace all geom_texts also in 'plotly' right from the x...
util_alias2captionCreate a caption from an alias name of a 'dq_report2' result
util_all_ind_functionsAll indicator functions of 'dataquieR'
util_all_intro_vars_for_rvGet all 'PART_VARS' for a response variable (from item-level...
util_all_is_integerconvenience function to abbreviate all(util_is_integer(...))
util_anytime_installedTest, if package 'anytime' is installed
util_app_cdutility function for the applicability of contradiction...
util_app_con_contradictions_redcaputility function for the applicability of contradiction...
util_app_dcutility function for the applicability of of distribution...
util_app_dlutility function to test for applicability of detection...
util_app_edutility function for the applicability of of end digits...
util_app_hlutility function to test for applicability of hard limits...
util_app_iacutility function for the applicability of categorical...
util_app_iavutility function for the applicability of numeric...
util_app_imutility function applicability of item missingness
util_app_loessutility function for applicability of LOESS smoothed time...
util_app_marutility function to test for applicability of marginal means...
util_app_molutility function applicability of multivariate outlier...
util_app_olutility function for the applicability of outlier detection
util_app_slutility function to test for applicability of soft limits...
util_app_smutility function applicability of segment missingness
util_app_sosutility function applicability of distribution function's...
util_app_vcutility applicability variance components
util_as_colorconvert a character to a specific ordered factor
util_as_numericConvert factors to label-corresponding numeric values
util_assign_levlabsutility function to assign labels to levels
util_attach_attrAttach attributes to an object and return it
util_backtickQuoteutility function to set string in backticks
util_bQuotePut in back-ticks
util_cast_offData frame leaves 'haven'
util_check_data_typeVerify the data type of a value
util_check_group_levelsCheck data for observer levels
util_check_one_unique_valueCheck for one value only
util_cll_nm2fkt_nmGet Function called for a Call Name
util_col_descriptionGet description for a call
util_combine_missing_listsCombine missing-lists for a set of variables to be displayed...
util_combine_resCombine results for Single Variables
util_compare_meta_with_studyCompares study data data types with the ones expected...
util_compress_ggplots_in_resRemove specific classes from a ggplot 'plot_env' environment
util_condition_constructor_factoryProduce a condition function
util_coord_flipreturn a flip term for 'ggplot2' plots, if desired.
util_copy_all_depsCopy default dependencies to the report's lib directory
util_correct_variable_useCheck referred variables
util_count_expected_observationsCount Expected Observations
util_count_NASupport function to count number of 'NA's
util_create_page_fileCreate an HTML file for the dq_report2
util_deparse1Expression De-Parsing
util_deprecate_softDeprecate functions and arguments
util_detect_coresDetect cores
util_dichotomizeutility function to dichotomize variables
util_dist_selectionUtility function distribution-selection
util_ds1_eval_envCreate an environment with several alias names for the study...
util_emptyTest, if values of x are empty, i.e. NA or whitespace...
util_ensure_characterconvert a value to character
util_ensure_data_typeEnsure matching data types
util_ensure_insimilar to match.arg
util_ensure_labelUtility function ensuring valid labels
util_ensure_suggestedSupport function to stop, if an optional package is not...
util_errorProduce an error message with a useful short stack trace....
util_eval_ruleEvaluate a parsed redcap rule for given study data
util_eval_to_dataquieR_resultEvaluate an expression and create a 'dataquieR_result' object...
util_evaluate_callsGenerate a full DQ report, v2
util_expect_data_frameVerify, that argument is a data frame
util_expect_scalarcheck, if a scalar/vector function argument matches...
util_extract_matchesreturn all matches of an expression
util_filter_missing_list_table_for_rvFilter a 'MISSING_LIST_TABLE' for rows matching the variable...
util_filter_names_by_regexpsFilter collection based on its 'names()' using regular...
util_find_external_functions_in_stacktraceFind externally called function in the stack trace
util_find_first_externally_called_functions_in_stacktraceFind first externally called function in the stack trace
util_find_var_by_metaTry hard, to map a variable
util_fix_rstudio_bugsRStudio crashes on parallel calls in some versions on Darwin...
util_float_index_menureturn a single page navigation menu floating on the right
util_formattablePlots simple HTML tables with background color scale
util_function_descriptionGet description for an indicator function
util_generate_anchor_linkGenerate a link to a specific result
util_generate_anchor_tagGenerate a tag for a specific result
util_generate_callsGenerate an execution/calling plan for computing a report...
util_generate_calls_for_functionGenerate function calls for a given indicator function
util_generate_pages_from_reportConvert a dataquieR report v2 to a named list of web pages
util_get_code_listFetch a missing code list from the metadata
util_get_color_for_resultReturn the color for a result
util_get_concept_infoRead additional concept tables
util_get_html_cell_for_resultReturn the html summary table cell for a result
util_get_message_for_resultReturn messages/warnings/notes/error messages for a result
util_get_redcap_rule_envan environment with functions available for 'REDcap' rules
util_get_var_att_names_of_levelGet variable attributes of a certain provision level
util_get_vars_in_segmentReturn all variables in the segment 'segment'
util_gg_var_labelAdd labels to 'ggplot'
util_heatmap_1thUtility Function Heatmap with 1 Threshold
util_html_attr_quote_escapeescape "
util_html_for_dimsCreate a dynamic dimension related page for the report
util_html_for_varCreate a dynamic single variable page for the report
util_html_tableThe jack of all trades device for tables
util_hubertutility function for the outliers rule of Huber et al.
util_int_duplicate_content_dataframeCheck for duplicated content
util_int_duplicate_content_segmentCheck for duplicated content
util_int_duplicate_ids_dataframeCheck for duplicated IDs
util_int_duplicate_ids_segmentCheck for duplicated IDs
util_interpret_limitsUtility function to interpret mathematical interval notation
util_interpret_rangeUtility function to interpret mathematical interval notation...
util_int_unexp_records_set_dataframeCheck for unexpected data record set
util_int_unexp_records_set_segmentCheck for unexpected data record set
util_is_integerCheck for integer values
util_is_na_0_empty_or_falseDetect falsish values
util_is_numeric_inCreate a predicate function to check for certain numeric...
util_load_manualbeing called by the active binding function for .manual
util_looks_like_missingCheck for repetitive values using the digits 8 or 9 only
util_make_data_slot_from_table_slotRename columns of a 'SummaryTable' (or Segment, ...) to look...
util_make_functionMake a function capturing errors and other conditions for...
util_map_allMaps label column metadata on study data variable names
util_map_by_largest_prefixMap based on largest common prefix
util_map_labelsSupport function to allocate labels to variables
util_match_arg'dataquieR' version of match.arg
util_merge_data_frame_listCombine data frames by merging
util_messageProduce a condition message with a useful short stack trace.
util_normalize_cross_itemNormalize and check cross-item-level metadata
util_no_value_labelsSelect really numeric variables
util_observation_expectedDetect Expected Observations
util_observations_in_subgroupsUtility function observations in subgroups
util_online_refCreates a Link to our Website
util_only_NAsidentify 'NA'-only variables
util_optimize_histogram_binsUtility function to compute and optimize bin breaks for...
util_order_by_orderGet the order of a vector with general order given in some...
util_par_pmapUtility function parallel version of 'purrr::pmap'
util_parse_assignmentsUtility function to parse assignments
util_parse_intervalUtility function to parse intervals
util_parse_redcap_ruleInterpret a 'REDcap'-style rule and create an expression,...
util_plot_figure_no_plotlyPlot a 'ggplot2' figure without 'plotly'
util_plot_figure_plotlyPlot a 'ggplot2' figure using 'plotly'
util_prep_location_checkUtility function to prepare the metadata for location checks
util_prep_proportion_checkUtility function to prepare the metadata for proportion...
util_pretty_printConvert single 'dataquieR' result to an 'htmltools'...
util_pretty_vector_stringPrepare a vector four output
util_rbindBind data frames row-based
util_recodeMap a vector of values based on an assignment table
util_remove_empty_rowsremoves empty rows from 'x'
util_remove_na_recordsremove all records, that have at least one 'NA' in any of the...
util_replace_codes_by_NAUtility function to replace missing codes by 'NA's
util_replace_hard_limit_violationsReplace limit violations (HARD_LIMITS) by NAs
util_set_dQuoteStringUtility function to put strings in quotes
util_set_sizeAttaches attributes about the recommended minimum absolute...
util_set_sQuoteStringUtility function single quote string
util_setup_rstudio_jobSet up an RStudio job
util_sigmagapUtility function outliers according to the rule of Huber et...
util_sixsigmaUtility function for six sigma deviations rule
util_sort_by_orderSort a vector by order given in some other vector
util_startsWith_prefix._or_equals_prefixString check for results/combined results
util_stop_if_notVerify assumptions made by the code, that must be TRUE
util_study_var2factorConvert 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_vctTabulate a vector
util_table_rotatorRotate 1-row data frames to key-value data frames
util_translate_indicator_metricsTranslate standard column names to readable ones
util_tukeyUtility function Tukey outlier rule
util_user_hintSave a hint to the user during package load
util_validate_known_metaUtility function verifying syntax of known metadata columns
util_validate_missing_listsValidate code lists for missing and/or jump codes
util_variable_referencesFind all columns in item-level-metadata, that refer to some...
util_view_fileView a file in most suitable viewer
util_warningProduce a warning message with a useful short stack trace.
util_warn_unorderedWarn about a problem in 'varname', if 'x' has no natural...
VARATT_REQUIRE_LEVELSRequirement levels of certain metadata columns
VARIABLE_LISTCross-item level metadata attribute name
VARIABLE_ROLESVariable roles can be one of the following:
WELL_KNOWN_META_VARIABLE_NAMESWell-known metadata column names, names of metadata columns
dataquieR documentation built on July 26, 2023, 6:10 p.m.