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Facilitating harmonized data quality assessments. A data quality framework for observational health research data collections with software implementations in R

Abstract

Background

No standards exist for the handling and reporting of data quality in health research. This work introduces a data quality framework for observational health research data collections with supporting software implementations to facilitate harmonized data quality assessments.

Methods

Developments were guided by the evaluation of an existing data quality framework and literature reviews. Functions for the computation of data quality indicators were written in R. The concept and implementations are illustrated based on data from the population-based Study of Health in Pomerania (SHIP).

Results

The data quality framework comprises 34 data quality indicators. These target four aspects of data quality: compliance with pre-specified structural and technical requirements (integrity); presence of data values (completeness); inadmissible or uncertain data values and contradictions (consistency); unexpected distributions and associations (accuracy). R functions calculate data quality metrics based on the provided study data and metadata and R Markdown reports are generated. Guidance on the concept and tools is available through a dedicated website.

Conclusions

The presented data quality framework is the first of its kind for observational health research data collections that links a formal concept to implementations in R. The framework and tools facilitate harmonized data quality assessments in pursue of transparent and reproducible research. Application scenarios comprise data quality monitoring while a study is carried out as well as performing an initial data analysis before starting substantive scientific analyses but the developments are also of relevance beyond research.

Peer Review reports

Background

Achieving a high data quality is a precondition for valid research results in all empirical sciences. Informative data quality indicators should inform data analysts about the “degree to which a set of inherent characteristics of data fulfils requirements” (ISO 8000). Data quality indicators thus describe actual and potential deviations from defined requirements such as formal compliance with pre-specified data structures, completeness, and the correctness of data values. Appropriately designing, assessing and quantifying data quality is of relevance during the entire research data life cycle. Already before the start of a data collection, having a clear understanding of data quality and its assessment should influence study design and data management. During study conduct, results of data quality assessments inform about the successful implementation of examinations, thereby triggering quality control and quality assurance activities such as data cleaning or training measures [1]. Data quality assessments after the end of a data collection influence decisions about data pooling and data harmonization [2], they can be used to benchmark studies and are necessary to safeguard responsible statistical analysis [3, 4].

While many data quality frameworks exist in the medical sciences [5,6,7,8,9,10,11,12,13,14,15,16], most of them target registries and electronic health records (EHR). These use data that have been generated outside of a research context, e.g. from administrative data. Yet, there is insufficient guidance on conducting data quality assessments for data that have specifically been generated for observational health research.

This lack of guidance is problematic as data quality frameworks for EHR data and registries are not directly applicable to designed research data collections [17]. For example, accessibility and interpretability have been defined as major quality criteria for EHR data [16]. Both are less relevant in research data collections where related issues are commonly solved by an appropriate study design, the standardisation of procedures, the training of examiners, and the implementation of a supporting infrastructure. Furthermore, preconditions for the computation of indicators may differ. Calculating the exact proportion of missing data in a population-based cohort study is based on a known sampling frame with a precisely defined number of study variables for each participant. In contrast, if, for example, information on a defined cardiovascular comorbidity in a patient with diabetes is missing in an EHR data set it is commonly unclear whether this comorbidity has not been diagnosed, examined, or simply not recorded. Therefore, a data quality framework must take specifics of the targeted data body into account.

A data quality framework must also guide the use of metadata and process variables for data quality assessments. Metadata in this context refers foremost to attributes that describe variables and expected data properties such as admissible values or distributional properties. Process variables describe aspects of the data generating process such as time stamps, observers or devices. Process variables are used to detect unexpected associations with study outcomes of interest. Ideally, each data quality indicator is accompanied by a description of the metadata and process variables that are required for its computation.

While a growing number of statistical routines address data quality issues [18,19,20,21], particularly in the programming language R [22,23,24], these routines are mostly not founded in data quality frameworks. Exceptions for EHR data are the approaches of Kahn et al. [10] within OHDSI [25] and Kapsner et al. [26].

The objectives of this work are twofold: (1) to provide a data quality framework tailored for designed data collections in observational health research, (2) to ease the application of the framework by providing openly available software implementations. All developments were integrated in a web-page to facilitate their successful application.

Methods

Background

We built on an existing data quality framework, the 2nd edition of the TMF (Technology, Methods, and Infrastructure for Networked Medical Research) guideline for data quality [11, 14]. TMF is a major umbrella organization for networked medical research in Germany. The guideline was chosen because, unlike other frameworks, it includes data quality indicators, which are of specific relevance for cohort studies. Literature reviews and overviews of data quality concepts in health research [5,6,7,8,9,10, 27, 28] informed the development of our framework.

The focus of the presented framework is “intrinsic data quality” [16] which means that “data have quality in their own right”. Evaluating intrinsic data quality rests primarily on knowledge about the data generating process. This is in contrast to “contextual data quality” which means that data quality is considered within the context of a particular task, e.g. the analysis of a defined scientific research question. We currently exclude such task- and situation-specific indicators.

Evaluation of the TMF guideline for data quality

The TMF guideline for data quality was subject to an evaluation by representatives of German general-population cohort studies to assess its suitability for this study type. Details of the evaluation process and results are available elsewhere [29]. In total, 43 out of the 51 quality indicators in the guideline have been assessed as being potentially relevant for cohort studies. In total 29 were classified as essential or important (mean evaluation score < =2; out of: 1 = essential, 2 = important, 3 = less important, and 4 = not important) and have been included in the current framework. Metrics of data quality indicators in the TMF guideline are restricted to counts and percentages, yet a broader scope of statistical metrics related to distributions, associations and measures of agreement were considered important for the quantification of aspects of data quality, as was a more specific handling of metadata compared to the TMF guideline. Therefore, novel indicators that cover aspects of descriptive statistics and initial data analysis [3] were added.

Computing data quality with R

Functions were developed as part of this project in the dataquieR package, available at CRAN [30], to compute data quality indicators, using R as the programming language because of its widespread use and free access [31]. We followed the style guide first published by Hadley Wickham [32]. R scripts were tested on simulated data and on data from several cohort studies, e.g. Study of Health in Pomerania [33], LIFE-Adult-Study [34], and the IDEFICS study [35]. An R Markdown generated website provides access to the concept, dataquieR functions, sample data, metadata descriptions, references, and tutorials [36].

Application example

The framework and implementations are illustrated using data from the Study of Health in Pomerania (SHIP), a population-based cohort study [33]. We used data from the baseline assessment of SHIP-0 from 1997 to 2001 (N = 4308). The data set comprises variables on: height, weight, and waist circumference from the somatometric examination, systolic and diastolic blood pressure from a blood pressure measurement, and information on smoking, marital status and intake of contraceptives from the computer assisted medical interview. An anonymized dataset was created based on a 50% random subset of the original sample (N = 2154). It is publicly available at [36].

R Markdown reports were rendered to HTML documents. These provide an overview of the results of the data quality assessment, including tables, and graphs. Modified study data sets are automatically generated to highlight unexpected findings at the level of individual observations with the purpose of simplifying subsequent data management steps.

Results

Structure of the data quality framework

In accordance with existing data quality concepts [6, 7, 9], completeness and correctness are the two core aspects of data quality (Table 1). Completeness is represented as a single dimension while correctness is subdivided into the two dimensions consistency and accuracy. The reason for this separation is introduced in the paragraph correctness. A precondition for successfully conducting any data quality assessment is the correct technical setup of study data and metadata. Related aspects are targeted within the integrity dimension.

Table 1 Data Quality Dimensions and Domains

Each dimension is subdivided into different data quality domains, an overview on dimensions and domains is provided in Table 1. The domains differ mainly in terms of the methodology used to assess data quality. The next level defines data quality indicators (Table 2). Currently, 34 indicators are distinguished. They describe quality attributes of the data at the level of single data fields, data records, data elements, and data sets [37]. Figure 1 displays the hierarchical structure. Figure 2 illustrates the used nomenclature of terms for data structures within the framework.

Table 2 Overview on Data Quality Indicators with Definitions
Fig. 1
figure1

Data Quality Concept Overview

Fig. 2
figure2

Key terms related to data structures

Integrity

Integrity related analyses are guided by the question: Do all data comply with pre-specified structural and technical requirements? Addressing this as an independent step is necessary in any data quality assessment, because study data and metadata are often deficient. The three domains within this dimension address:

  1. 1)

    the structurally correct representation of data elements or data records within data sets (structural data set error), e.g. a mismatch of observed and expected number of data records;

  2. 2)

    the correspondence between multiple data sets (relational data set error), e.g. the appropriate integration of multiple study data sets; and

  3. 3)

    the correct representation of data values within data sets (value format error), e.g. a mismatch between the expected and observed data type.

Deficits at the integrity level may invalidate any findings at subsequent stages of data quality assessments and for any substantial scientific analyses. Assessments of metadata are confined to the integrity domain.

Completeness

Completeness related assessments are guided by the question: Are the expected data values available? Results provide knowledge about the frequency and distribution of missing data. Two domains within completeness treat missing data differently. Within the “crude missingness” domain, any specific reasons that underlie missing data are ignored because missing data are often improperly coded and meaningful indicators must nevertheless be computable. A common example is the provision of system-indicated missing values only such as NA in R. This impedes inferences on why data values are not available without context information. In contrast, “Qualified missingness” makes use of coded reasons for missing data such as refusals, met exclusion criteria or any other reason. The use of such missing codes enables the valid computation of non-response or refusal rates [38].

Missing data occur at different stages of a data collection. Reasons for participants not entering a study (1: unit missingness) may be different from those prompting a participant to leave the study after initial participation (2: longitudinal missingness, e.g. drop-out). Further restraints may impede the conduct of a segment of the study, such as a specific examination (3: segment missingness, e.g. taking part in an ultrasound examination). Within segments, there may be a failure to fully collect information (4: item missingness, e.g. refusal to respond to a question). Different sets of actionable information may result at each of these stages, both at the level of data quality management and statistical analyses. Analysing missing data at the stages 1 to 3 should forego the assessment of item missingness.

Correctness: consistency and accuracy

Correctness related analyses are guided by the question: Are data values free of errors? The first dimension, consistency comprises indicators that use Boolean type checks to identify inadmissible, impossible, or uncertain data values or combinations of data values. The domain range and value violations targets single data values that do not comply with allowed data values or value ranges [39]. The second domain, contradictions examines impossible or improbable combinations of multiple data values.

In contrast, indicators within the accuracy dimension use diverse statistical methods to identify unexpected data properties. Its first domain, unexpected distributions targets discrepancies between observed and expected distributional characteristics, e.g. the violation of an expected normal distribution. The second domain, unexpected associations, assesses discrepancies between observed and expected associations. The third domain, disagreement of repeated measurements, targets the correspondence between repeated measurements of the same outcome, for example related to the precision of measurements, or the correspondence with gold standard measurements.

Implementations

Various methods exist to compute data quality indicators. For example, different approaches are available to calculate response rates [38] or to assess outliers [40, 41]. Implementations describe the actual computation of data quality indicators. They can be tailored to specific demands of data quality assessments and may summarize results from different indicators. Implementations may therefore be linked to any level of the data quality framework hierarchy, for example to provide overall estimates of data quality for some dimension. Changes of implementations do not constitute a modification of the data quality concept.

Descriptors

Results of data quality assessments should be available in machine-readable format. This is a necessary precondition for automated processing and subsequent aggregation of results. Yet, not all data-quality-related information may be expressed in a machine-readable format. For example, histograms or smoothed curves [42] may provide important insights in addition to a statistical test of some assumption about a distribution or association. However, the detection of a data quality issue based on graphs relies on the implicit knowledge of a person inspecting the results. Such output without a machine-readable metric is named a descriptor. All descriptive statistics are descriptors as well. To consider a sample mean as being problematic without an explicit rule-based assessment relies on implicit knowledge. A single descriptor may provide information for different indicators, as there are various possible interpretations. For example, a scatterplot may serve to identify outliers but also to detect unexpected associations and distributional properties.

Data quality and process variables

Data are collected over time, possibly at different sites, by different examiners using diverse methods. Ambient conditions may vary. Such sources of variability, coded as process variables [43], may affect measurements and result in data quality issues. Unexpected association of statistical parameters with process variables may constitute novel data quality problems and can be related to almost all data quality indicators. An example of high practical relevance are examiner effects (indicator: unexpected location, Table 2; implementation: examiner effects - margins, Table 3). Another example are time trends in the data. Such associations with process variables should routinely be targeted.

Table 3 Example R-Functions and their Links to The Data Quality Framework

Using R and the data quality workflow

Data quality can be assessed using the R package dataquieR. Table 3 provides an overview of the applied computational and statistical methods. The use of dataquieR can be twofold: (1) all-at-once without an in-depth specification of parameters using the function dq_report() to create complete default reports or (2) step-by-step allowing for a detailed data quality assessment in a sequential approach. The first option checks the availability of metadata and applies all appropriate functions to the specified study data. A flexdashboard [51] is then generated which summarizes the results by data quality dimensions and variables.

In contrast, the sequential approach allows for specific parameter settings, changes to the output, corrections and modification of the data, and stratification according to additional variables. Examples of the step-by-step approach are shown in Fig. 3 using SHIP data. For the sake of clarity, only five variables (data elements) have been selected for display. First, the applicability of implementations to each data element was checked. Apparently, the data type of “waist circumference” did not comply with the data type specified in the metadata (Fig. 3, panel 1 top-left). After resolving this issue further data quality checks were conducted. Item missingness has been tabulated to provide insights about different reasons for missing data at this level (Fig. 3, panel 2 bottom-left). Afterwards the consistency of the data was examined with respect to limit deviations (Fig. 3, panel 3 top-right). Among the different applications addressing accuracy, the adjusted margins function compares mean values across observers to address examiner effects while adjusting for a for a vector of covariates (Fig. 3, panel 4 bottom-right). A commented example is available in the tutorial section of the webpage.

Fig. 3
figure3

Example results using R dataquieR applied to SHIP data. 1: A heatmap-like plot to illustrate the applicability of data quality implementations based on an assessment of metadata and study data properties. 2: Histogram with illustrated range violations. 3: Illustration of missing values across different reasons for missing data. 4: Margins-plot to illustrate observer effects

Discussion

We provide a data quality framework for research data collections in observational health research, accompanied by software implementations in R. Data quality is addressed with regards to four core requirements: compliance with pre-specified structural and technical requirements (integrity), presence of data values (completeness), and absence of errors in the sense of, first, inadmissible data values, uncertain data values and contradictions (consistency) and second, unexpected distributions or associations (accuracy). To the best of our knowledge, this is the first data quality framework in the field that is accompanied by documented and freely available software code to compute indicators. A web page provides further guidance on all concepts and tools. The framework may promote harmonized data quality assessments and can be extended to accommodate other aspects of data quality and study types.

The framework was built from the perspective of “intrinsic data quality” [16] with requirements focussing on 1. processable data, 2. complete data, and 3. error-free data. The first dimension to target is integrity, as data quality assessments are a complex workflow where preconditions must be checked and reported first to safeguard the validity of subsequent results. Integrity in our framework resembles the conformance dimension in other approaches [8, 10], but focusses more narrowly structural requirements on data sets and data values. In practice, integrity checks often reveal recoverable issues. Additional data management processes may restore compliance with requirements, for example, by adding missing data structures.

In line with other approaches [6,7,8], completeness and correctness are the other main aspects of data quality. Both have been defined as core data quality constructs with regard to EHR data in the framework of Weiskopf et al. [9]. The stronger notion of correctness was preferred over plausibility [8, 10] because the data generation in observational health research data collections is largely under the control of the researchers. This implies strong options to address errors during data collections and thereafter. We did not include the third core dimension by Weiskopf et al. [9], currency, which denotes whether “a value is representative of the clinically relevant time”. This aspect is considered to be of lesser importance in a research data collection from an intrinsic perspective.

Despite overlap with the TMF guideline [11, 14], Table 4, our data quality framework differs in several regards. The TMF-guideline focuses on registries while our framework focuses data collected for research purposes. Our framework is organized hierarchically, whereas there is no comparable structure in the TMF-guideline. TMF indicators correspond to different elements of our approach, ranging from data quality dimensions to implementations (Table 4). We cover all of the indicators classified as important [29] in the evaluation of the TMF-guideline with two exceptions: Compliance with operating procedures (TMF-1047) has not been included because information in standard operating procedures or study protocols is not available in an appropriate format for automated assessments. Representativeness (TMF-1048) can be formally targeted using indicators within the unexpected distributions domain to check observed sample properties against known population characteristics. It is however a matter of context-knowledge to interpret findings as a result of selection bias instead of measurement error. As such, representativeness is a contextual rather than an intrinsic aspect of data quality.

Table 4 Correspondence of TMF data quality indicators with the current data quality framework

Computation of data quality indicators

The necessity to develop software for data quality assessments has previously been acknowledged [8, 9]. Providing not only a theoretical framework but also the code to analyse data quality is important to facilitate homogeneous and transparent assessments across studies. This is also of relevance for the implementation of harmonized data quality assessments within complex research data infrastructures such as euCanSHare [52] or NFDI4Health, a federated research data infrastructure for personal health data [53]. Our implementations differ from most other available program codes [18,19,20,21,22,23,24] in that they are attached to a formal framework. To ensure the robustness of implementation, dozens of utility functions support their appropriate application in the background. Standards for the setup of metadata were defined to enable automated data quality checks [43] as well as for the programmed R routines to avoid heterogeneous programming code. This will facilitate extensions by other scientists. Further software implementations within the program Stata and a Java web-application [54] are currently being programmed.

Data quality assessments in research

Data quality assessments must generate actionable information. While a study is carried out, the main aim is to detect and mitigate errors. After the end of a data collection, data quality assessments can be conceived as a specific aspect of initial data analysis [3], which aims “to provide reliable knowledge about the data to enable responsible statistical analyses and interpretation”. As such, the presented work also provides a framework for structuring initial data analysis.

Data quality assessments may be conducted locally at the sites of the respective data holders by using the software implementations above. Further transparency is possible if data quality related metadata is stored centrally in widely used metadata repositories. One example are the Opal and Mica [55] tools which are used, among others, in euCanSHare [52], Maelstrom [56], and NFDI4Health [53]. Another example is the Medical Data Models Portal, a meta-data registry for sharing and reusing medical forms [57]. Developments to host the necessary metadata in metadata repositories are currently ongoing.

Another aspect are intelligible metrics to communicate information about the achieved data quality, such as visual alerts. This has been implemented in the SHIP-project. Related standards could facilitate communication between scientists to leverage a common understanding of data quality. This goal is also pursued by the Data Nutrition Project [58]. Yet, the latter takes a different methodological approach and focusses primarily on the intended use of data, thus emphasizing contextual data quality [16], whereas we emphasize intrinsic data quality. Future extensions of our framework to cover contextual data quality may increase overlap. Vice versa, structural aspects of the framework and suggested workflow may be of relevance to guide other approaches.

Another goal is to improve the scientific reporting of studies and the further elaboration of guidance documents to cover aspects of data quality more extensively, such as for example by the EQUATOR (Enhancing the QUAlity and Transparency Of health Research) network [59] or the STRATOS (STRengthening Analytical Thinking for Observational Studies) initiative [60]. Furthermore, many funding bodies require data management plans but no system exists for the handling or reporting of data quality. Standardized data quality reports may accompany both, final reports and scientific papers to provide transparent insights into data properties and study success. As a necessary precondition for harmonized data quality assessments, the improved management of metadata would contribute to a better compliance with FAIR (Findable, Accessible, Interoperable and Reusable) data principles [61].

Limitations and outlook

The presented data quality framework does not cover all aspects of “fitness for use” (ISO 8000) as contextual aspects have not been taken into account. For example, a single missing data value due to a technical error may trigger corrective actions during data collection but may not affect statistical analyses. Thresholds for critical amounts of missing data depend on the methods and aims of a statistical analysis plan [62]. Even without data quality issues at the intrinsic level some data set may prove unfit for the study of a research question because of issues such as an insufficient number of events if the main outcome is a time-to-event variable.

While the defined set of indicators suffices to address a wide range of data quality issues further expansions will be necessary. For example, speaking of non-response rate in studies without a clearly defined sampling frame may not be appropriate and additional indicators need to be added [38]. The framework currently also does not address specific demands arising from special data sources such as omics or medical imaging.

Indicators make no assumptions about the underlying reasons for data quality issues. It is up to the scientist or data manager to make causal decisions, for example on the presence of some type of bias [63]. This in turn relies on the study design being well-documented and the study being conducted accordingly [64, 65].

We defined indicators that are statistically computable in an automated workflow, using a set of study data and metadata. Therefore, we did not address approaches of source data verification. To avoid lengthy computational times, in some cases heuristic statistical methods have been favoured over ones that are more sophisticated.

The functionality of R code is supported by versatile and numerous utility function to mitigate user errors. Nonetheless, this code relies on the existence of sufficient metadata and metadata itself may constitute a gateway for data quality issues. Any user must comprehend the framework and the conventions underlying the definition of metadata. Because the handling of study data varies greatly across studies, interoperability issues may arise, and the provision of interfaces to facilitate data transfer will be an important future extension of our work. Therefore, an alignment of data quality related metadata with standards for information exchange such as HL7 FHIR [66] and common data models to enable data quality assessments without additional efforts in a harmonized fashion across data sets is a main objective [53, 67].

We have sketched application scenarios of data quality assessments during the research data life cycle, yet quantitative approaches to data quality are also of relevance in other areas of life. For example, data quality monitoring during study conduct shares structural similarities with quality improvement related activities in a hospital setting. Benchmarking is of relevance for production processes in industrial settings. Sustainable decision-making and innovation rests on the availability of data with adequate quality properties. Aspects of the outlined framework may be useful whenever data is collected for such purposes in a designed and controlled fashion. Yet, each application scenario has its specific requirements that likely require adaptions and extensions of this framework as well as the related software implementations.

Conclusions

A data quality framework for research data collections in observational health research is provided with software implementations in the programming language R. The framework covers four core aspects of data quality: compliance with pre-specified formats and structures (integrity), the presence of data values (completeness), and errors in the data values in the sense of inadmissible or uncertain data values as well as contradictions (consistency) and unexpected distributions or associations (accuracy). R functions facilitate harmonized data quality assessments within and across studies in pursue of transparent and reproducible research. Applications of the framework and software implementations are not limited to research.

Availability of data and materials

The datasets generated and/or analyzed during the current study are available in the dataquieR repository on gitlab, https://gitlab.com/libreumg/dataquier/-/tree/master/inst/extdata

Abbreviations

ANOVA:

Analysis of variance

DQ:

Data quality

DQI:

Data quality indicator

ecdf:

Empirical cumulative distribution functions

EHR:

Electronic health records

EQUATOR:

Enhancing the QUAlity and Transparency Of health Research

exdat:

Examination date

FAIR:

Findable, Accessible, Interoperable and Reusable

FHIR:

Fast Healthcare Interoperability Resources

HL7:

Health Level 7

IDA:

Initial data analysis

ISO:

International standards organization

LOESS:

Locally estimated scatterplot smoothing

NA:

Not applicable

sbp:

Systolic blood pressure

SHIP:

Study of Health in Pomerania

STRATOS:

STRengthening Analytical Thinking for Observational Studies

TMF:

Technology, Methods, and Infrastructure for Networked Medical Research

TMFID:

TMF guideline identifier

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Acknowledgements

We thank the TMF e.V., an umbrella organization for networked medical research in Germany, for providing infrastructure to facilitate interdisciplinary exchange on our developments and participants of meetings for their comments.

Funding

This work was supported by the German Research Foundation (DFG: SCHM 2744/3–1, JO 170/10–1, KU 3111/2–1, LO 342/13–1, PI 345/11–1, STA 454/17–1, SCHM 2744/9–1, SA 580/10–1), by the TMF grant V114-01 M, and by the European Union’s Horizon 2020 research and innovation programme under grant agreement No 825903 (euCanSHare project). Open Access funding enabled and organized by Projekt DEAL.

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COS: design of the research project, manuscript drafting and concept development, support of software development / web design, evaluation of TMF guideline; AR: manuscript drafting, software development, concept development, web design; StS: software development; website design; manuscript revision; CE, ACR, JS, SD, BS: evaluation of TMF guideline, input regarding epi study data quality assessments; feedback/revision on concept and tools; critical revision of manuscript; WS, MH: feedback on concept and tools with a focus on statistics, initial data analysis; critical revision of manuscript. All authors have approved the manuscript.

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Schmidt, C.O., Struckmann, S., Enzenbach, C. et al. Facilitating harmonized data quality assessments. A data quality framework for observational health research data collections with software implementations in R. BMC Med Res Methodol 21, 63 (2021). https://0-doi-org.brum.beds.ac.uk/10.1186/s12874-021-01252-7

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Keywords

  • Data quality
  • Observational health studies
  • Data quality indicators
  • Data quality monitoring
  • Initial data analysis
  • R
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