Abstract
R language has gained traction in laboratory medicine for its statistical power and dynamic tools like RMarkdown and RShiny. However, there is limited literature summarizing R packages and functions tailored for laboratory medicine, making it difficult for clinical laboratory workers to access these tools. Additionally, varying algorithms across R packages can lead to inconsistencies in published reports. This review addresses these challenges by providing an overview of R’s evolution and its key features, followed by a summary of statistical methods implemented in R, including platform comparisons, precision verification, factor analysis, and the establishment of reference intervals (RIs). We also highlight the development and validation of predictive models using techniques such as linear and logistic regression, decision trees, random forests, support vector machines, naive Bayes, K-Nearest Neighbors, k-means clustering, and backpropagation neural networks – all implemented in R. To ensure transparency and reproducibility in research, a checklist is provided for authors publishing papers using R for data analysis in laboratory medicine. In the final section, the potential of R in big data analytics is explored, focusing on standardized reporting through RMarkdown and the creation of user-friendly data visualization platforms with RShiny. Moreover, the integration of large language models (LLMs), such as ChatGPT, is discussed for their benefits in enhancing R programming, automating reporting, and offering insights from data analysis, thus improving the efficiency and accuracy of laboratory data analysis.
Acknowledgments
The code in this article was written using R language (version 4.3.1). The manuscript was edited using Rmarkdown (source code available upon request from the corresponding author). Images were edited using WPS Office software (version 6.7.1). Additionally, this research utilized Chat GPT-4 for coding assistance and language improvement.
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Research ethics: Not applicable.
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Informed consent: Not applicable.
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Author contributions: Chaochao Ma wrote and revised this manuscript. Ling Qiu made suggestions for the revision of the manuscript. The authors have accepted responsibility for the entire content of this manuscript and approved its submission.
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Use of Large Language Models, AI and Machine Learning Tools: Chat GPT-4 for coding assistance and language improvement.
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Conflict of interest: The authors state no conflict of interest.
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Research funding: The study was supported by the National Natural Science Foundation of China (72274218).
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Data availability: Not applicable.
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Supplementary Material
This article contains supplementary material (https://doi.org/10.1515/cclm-2024-1193).
© 2025 Walter de Gruyter GmbH, Berlin/Boston
Articles in the same Issue
- Frontmatter
- Editorial
- Setting analytical performance specification by simulation (Milan model 1b)
- Reviews
- Unveiling the power of R: a comprehensive perspective for laboratory medicine data analysis
- Clostebol detection after transdermal and transmucosal contact. A systematic review
- Opinion Papers
- A value-based score for clinical laboratories: promoting the work of the new EFLM committee
- Digital metrology in laboratory medicine: a call for bringing order to chaos to facilitate precision diagnostics
- Perspectives
- Supporting prioritization efforts of higher-order reference providers using evidence from the Joint Committee for Traceability in Laboratory Medicine database
- Clinical vs. statistical significance: considerations for clinical laboratories
- Genetics and Molecular Diagnostics
- Reliable detection of sex chromosome abnormalities by quantitative fluorescence polymerase chain reaction
- Targeted proteomics of serum IGF-I, -II, IGFBP-2, -3, -4, -5, -6 and ALS
- Candidate Reference Measurement Procedures and Materials
- Liquid chromatography tandem mass spectrometry (LC-MS/MS) candidate reference measurement procedure for urine albumin
- General Clinical Chemistry and Laboratory Medicine
- Patient risk management in laboratory medicine: an international survey to assess the severity of harm associated with erroneous reported results
- Exploring the extent of post-analytical errors, with a focus on transcription errors – an intervention within the VIPVIZA study
- A survey on measurement and reporting of total testosterone, sex hormone-binding globulin and free testosterone in clinical laboratories in Europe
- Quality indicators in laboratory medicine: a 2020–2023 experience in a Chinese province
- Impact of delayed centrifugation on the stability of 32 biochemical analytes in blood samples collected in serum gel tubes and stored at room temperature
- Concordance between the updated Elecsys cerebrospinal fluid immunoassays and amyloid positron emission tomography for Alzheimer’s disease assessment: findings from the Apollo study
- Novel protocol for metabolomics data normalization and biomarker discovery in human tears
- Use of the BIOGROUP® French laboratories database to conduct CKD observational studies: a pilot EPI-CKD1 study
- Reference Values and Biological Variations
- Consensus instability equations for routine coagulation tests
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- Flow-cytometric lymphocyte subsets enumeration: comparison of single/dual-platform method in clinical laboratory with dual-platform extended PanLeucogating method in reference laboratory
- Cardiovascular Diseases
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- Infectious Diseases
- Cell population data for early detection of sepsis in patients with suspected infection in the emergency department
- Letters to the Editor
- Lab Error Finder: A call for collaboration
- Cascading referencing of terms and definitions
- Strengthening international cooperation and confidence in the field of laboratory medicine by ISO standardization
- Determining the minimum blood volume required for laboratory testing in newborns
- Performance evaluation of large language models with chain-of-thought reasoning ability in clinical laboratory case interpretation
- Vancomycin assay interference: low-level IgM paraprotein disrupts Siemens Atellica® CH VANC assay
- Dr. Morley Donald Hollenberg. An extraordinary scientist, teacher and mentor
Articles in the same Issue
- Frontmatter
- Editorial
- Setting analytical performance specification by simulation (Milan model 1b)
- Reviews
- Unveiling the power of R: a comprehensive perspective for laboratory medicine data analysis
- Clostebol detection after transdermal and transmucosal contact. A systematic review
- Opinion Papers
- A value-based score for clinical laboratories: promoting the work of the new EFLM committee
- Digital metrology in laboratory medicine: a call for bringing order to chaos to facilitate precision diagnostics
- Perspectives
- Supporting prioritization efforts of higher-order reference providers using evidence from the Joint Committee for Traceability in Laboratory Medicine database
- Clinical vs. statistical significance: considerations for clinical laboratories
- Genetics and Molecular Diagnostics
- Reliable detection of sex chromosome abnormalities by quantitative fluorescence polymerase chain reaction
- Targeted proteomics of serum IGF-I, -II, IGFBP-2, -3, -4, -5, -6 and ALS
- Candidate Reference Measurement Procedures and Materials
- Liquid chromatography tandem mass spectrometry (LC-MS/MS) candidate reference measurement procedure for urine albumin
- General Clinical Chemistry and Laboratory Medicine
- Patient risk management in laboratory medicine: an international survey to assess the severity of harm associated with erroneous reported results
- Exploring the extent of post-analytical errors, with a focus on transcription errors – an intervention within the VIPVIZA study
- A survey on measurement and reporting of total testosterone, sex hormone-binding globulin and free testosterone in clinical laboratories in Europe
- Quality indicators in laboratory medicine: a 2020–2023 experience in a Chinese province
- Impact of delayed centrifugation on the stability of 32 biochemical analytes in blood samples collected in serum gel tubes and stored at room temperature
- Concordance between the updated Elecsys cerebrospinal fluid immunoassays and amyloid positron emission tomography for Alzheimer’s disease assessment: findings from the Apollo study
- Novel protocol for metabolomics data normalization and biomarker discovery in human tears
- Use of the BIOGROUP® French laboratories database to conduct CKD observational studies: a pilot EPI-CKD1 study
- Reference Values and Biological Variations
- Consensus instability equations for routine coagulation tests
- Hematology and Coagulation
- Flow-cytometric lymphocyte subsets enumeration: comparison of single/dual-platform method in clinical laboratory with dual-platform extended PanLeucogating method in reference laboratory
- Cardiovascular Diseases
- Novel Mindray high sensitivity cardiac troponin I assay for single sample and 0/2-hour rule out of myocardial infarction: MERITnI study
- Infectious Diseases
- Cell population data for early detection of sepsis in patients with suspected infection in the emergency department
- Letters to the Editor
- Lab Error Finder: A call for collaboration
- Cascading referencing of terms and definitions
- Strengthening international cooperation and confidence in the field of laboratory medicine by ISO standardization
- Determining the minimum blood volume required for laboratory testing in newborns
- Performance evaluation of large language models with chain-of-thought reasoning ability in clinical laboratory case interpretation
- Vancomycin assay interference: low-level IgM paraprotein disrupts Siemens Atellica® CH VANC assay
- Dr. Morley Donald Hollenberg. An extraordinary scientist, teacher and mentor