Data Quality in Epidemiological Research
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Documentation for package ‘dataquieR’ version 2.1.0
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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_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 |