Learn R Programming

⚠️There's a newer version (2.1.0) of this package.Take me there.

`dataquieR`

The goal of dataquieR is to provide functions for assessing data quality issues in studies, that can be used alone or in a data quality pipeline. dataquieR also implements one generic pipeline producing flexdashboard based HTML5 reports.

See also

https://dataquality.ship-med.uni-greifswald.de

Installation

You can install the released version of dataquieR from CRAN with:

install.packages("dataquieR")

The developer version from GitLab.com can be installed using:

if (!requireNamespace("devtools")) {
  install.packages("devtools")
}
devtools::install_gitlab("libreumg/dataquier")

For examples and additional documentation, please refer to our website.

References

Funding

German Research Foundation (DFG: SCHM 2744/3–1)
European Union’s Horizon 2020 research and innovation program (grant agreement No 825903.

Copy Link

Version

Install

install.packages('dataquieR')

Monthly Downloads

708

Version

1.0.8

License

BSD_2_clause + file LICENSE

Maintainer

Stephan Struckmann

Last Published

August 12th, 2021

Functions in dataquieR (1.0.8)

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

Variable roles can be one of the following:

com_item_missingness

Summarize missingness columnwise (in variable)

Function to estimate marginal means, see emmeans::emmeans

com_segment_missingness

Summarizes missingness for individuals in specific segments

Smoothes and plots adjusted longitudinal measurements

Estimates variance components

acc_univariate_outlier

Function to identify univariate outliers by four different approaches

dataquieR_resultset

Internal constructor for the internal class dataquieR_resultset.

dataquieR_resultset_verify

Verify an object of class dataquieR_resultset

acc_robust_univariate_outlier

Function to identify univariate outliers by four different approaches

con_limit_deviations

Detects variable values exceeding limits defined in metadata

acc_multivariate_outlier

Function to calculate and plot Mahalanobis distances

contradiction_functions

contradiction_functions

com_unit_missingness

Counts all individuals with no measurements at all

acc_shape_or_scale

Function to compare observed versus expected distributions

pipeline_vectorized

Call (nearly) one "Accuracy" function with many parameterizations at once automatically

The dataquieR package about Data Quality in Epidemiological Research

contradiction_functions_descriptions

description of the contradiction functions

prep_add_to_meta

Support function to augment metadata during data quality reporting

prep_min_obs_level

Support function to identify the levels of a process variable with minimum number of observations

prep_map_labels

Support function to allocate labels to variables

utility function for the applicability of of distribution plots

Generate a stratified full DQ report

prep_study2meta

Guess a meta data frame from study data.

Generate a full DQ report

utility function to test for applicability of detection limits checks

Support function to count number of NAs

con_contradictions

Checks user-defined contradictions in study data

con_detection_limits

con_detection_limits

prep_valuelabels_from_data

Get value labels from data

util_count_code_classes

count distinct realizations of missing codes of a specific class

util_heatmap_1th

Utility Function Heatmap with 1 Threshold

util_looks_like_missing

Check for repetitive values using the digits 8 or 9 only

util_get_var_att_names_of_level

Get variable attributes of a certain provision level

util_is_integer

Check for integer values

Attaches attributes about the recommended minimum absolute sizes to the plot p

Utility function outliers according to the rule of Huber et al.

prep_datatype_from_data

Get data types from data

prep_create_meta

Support function to create data.frames of metadata

utility function for the applicability of categorical admissibility

utility function applicability of item missingness

utility function for the applicability of of end digits preferences checks

utility function for the applicability of numeric admissibility

util_anytime_installed

Test, if package anytime is installed

utility function for the applicability of contradiction checks

Names of DQ dimensions

util_assign_levlabs

utility function to assign labels to levels

utility function to test for applicability of marginal means plots

utility function for applicability of LOESS smoothed time course plots

util_correct_variable_use

Check referred variables

utility function for the outliers rule of Huber et al.

util_compare_meta_with_study

Compares study data data types with the ones expected according to the metadata

util_interpret_limits

Utility function to interpret mathematical interval notation

util_set_dQuoteString

Utility function to put strings in quotes

.variable_arg_roles

Variable-argument roles

utility applicability variance components

util_backtickQuote

utility function to set string in backticks

util_as_numeric

Convert factors to label-corresponding numeric values

con_inadmissible_categorical

Detects variable levels not specified in metadata

util_ensure_suggested

Support function to stop, if an optional package is not installed

pipeline_recursive_result

Function to convert a pipeline result data frame to named encapsulated lists

int_datatype_matrix

Function to check declared data types of metadata in study data

Support function for a parallel pmap

util_set_sQuoteString

Utility function single quote string

Produce an error message with a useful short stack trace. Then it stops the execution.

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

util_check_data_type

Support function to verify the data type of a value

prep_prepare_dataframes

Prepare and verify study data with metadata

util_map_labels

Support function to allocate labels to variables

print.ReportSummaryTable

print implementation for the class ReportSummaryTable

util_no_value_labels

Select really numeric variables

util_check_one_unique_value

Check for one value only

rbind.ReportSummaryTable

Combine ReportSummaryTable outputs

summary.dataquieR_resultset

Summarize a dataquieR report

utility function applicability of distribution function's shape or scale check

utility function applicability of segment missingness

util_count_codes

count realizations of missing codes of any class

pro_applicability_matrix

Function to check applicability of DQ functions on study data

print.dataquieR_resultset

Generate a RMarkdown-based report from a dataquieR report

print.dataquieR_result

Print a dataquieR result returned by pipeline_vectorized

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_make_function

Make a function capturing errors and other conditions for parallelization

Utility function parallel version of purrr::pmap

Produce a warning message with a useful short stack trace.

Maps label column meta data on study data variable names

util_parse_assignments

Utility function to parse assignments

util_dichotomize

utility function to dichotomize variables

util_fix_rstudio_bugs

RStudio crashes on parallel calls in some versions on Darwin based operating systems with R 4

utility function applicability of multivariate outlier detection

utility function for the applicability of outlier detection

util_get_code_list

Fetch a missing code list from the metadata

util_prepare_dataframes

util_prepare_dataframes

util_validate_known_meta

Utility function verifying syntax of known metadata columns

util_replace_codes_by_NA

Utility function to replace missing codes by NAs

util_warn_unordered

Warn about a problem in varname, if x has no natural order

util_dist_selection

Utility function distribution-selection

Test, if values of x are empty, i.e. NA or whitespace characters

Utility function Tukey outlier rule

identify NA-only variables

Utility function for six sigma deviations rule

util_observations_in_subgroups

Utility function observations in subgroups

Extension of acc_shape_or_scale to examine uniform distributions of end digits

VARATT_REQUIRE_LEVELS

Requirement levels of certain metadata columns

All available probability distributions for acc_shape_or_scale

acc_distributions

Function to plot histograms added by empirical cumulative distributions for subgroups

Character used by default as a separator in meta data such as missing codes

DATA_TYPES_OF_R_TYPE

All available data types, mapped from their respective R types

WELL_KNOWN_META_VARIABLE_NAMES

Well-known metadata column names, names of metadata columns