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 |
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' |
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 |
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 |
enum | Data Types |
FLOAT | Data Types |
float | Data Types |
GROUP_VAR_DEVICE | Well-known metadata column names, names of metadata columns |
GROUP_VAR_OBSERVER | Well-known metadata column names, names of metadata columns |
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' |
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 |
JUMP_LIST | Well-known metadata column names, names of metadata columns |
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 |
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 |
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 |
nres | return the number of result slots in a report |
numeric | Data Types |
OPTIONAL | Requirement levels of certain metadata columns |
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 |
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) |
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 |
TECHNICAL | Requirement levels of certain metadata columns |
TIME_VAR | Well-known metadata column names, names of metadata columns |
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 |
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 |
WELL_KNOWN_META_VARIABLE_NAMES | Well-known metadata column names, names of metadata columns |
$.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 |