Paper 18: Benefits of dietary supplements on the physical fitness of German Shepherd dogs during a drug detection training course
References
Menchetti L, Guelfi G, Speranza R, Carotenuto P, Moscati L, Diverio S (2019) Benefits of dietary supplements on the physical fitness of German Shepherd dogs during a drug detection training course. PLoS ONE 14(6): e0218275. https://doi.org/10.1371/journal.pone.0218275
Disclosure
This reproducibility project was conducted to the best of our ability, with careful attention to statistical methods and assumptions. The research team comprises four senior biostatisticians (three of whom are accredited), with 20 to 30 years of experience in statistical modelling and analysis of healthcare data. While statistical assumptions play a crucial role in analysis, their evaluation is inherently subjective, and contextual knowledge can influence judgements about the importance of assumption violations. Differences in interpretation may arise among statisticians and researchers, leading to reasonable disagreements about methodological choices.
Our approach aimed to reproduce published analyses as faithfully as possible, using the details provided in the original papers. We acknowledge that other statisticians may have differing success in reproducing results due to variations in data handling and implicit methodological choices not fully described in publications. However, we maintain that research articles should contain sufficient detail for any qualified statistician to reproduce the analyses independently.
Methods used in our reproducibility analyses
There were two parts to our study. First, 100 articles published in PLOS ONE were randomly selected from the health domain and sent for post-publication peer review by statisticians. Of these, 95 included linear regression analyses and were therefore assessed for reporting quality. The statisticians evaluated what was reported, including regression coefficients, 95% confidence intervals, and p-values, as well as whether model assumptions were described and how those assumptions were evaluated. This report provides a brief summary of the initial statistical review.
The second part of the study involved reproducing linear regression analyses for papers with available data to assess both computational and inferential reproducibility. All papers were initially assessed for data availability and the statistical software used. From those with accessible data, the first 20 papers (from the original random sample) were evaluated for computational reproducibility. Within each paper, individual linear regression models were identified and assigned a unique number. A maximum of three models per paper were selected for assessment. When more than three models were reported, priority was given to the final model or the primary models of interest as identified by the authors; any remaining models were selected at random.
To assess computational reproducibility, differences between the original and reproduced results were evaluated using absolute discrepancies and rounding error thresholds, tailored to the number of decimal places reported in each paper. Results for each reported statistic, e.g., regression coefficient, were categorised as Reproduced, Incorrect Rounding, or Not Reproduced, depending on how closely they matched the original values. Each paper was then classified as Reproduced, Mostly Reproduced, Partially Reproduced, or Not Reproduced. The mostly reproduced category included cases with minor rounding or typographical errors, whereas partially reproduced indicated substantial errors were observed, but some results were reproduced.
For models deemed at least partially computationally reproducible, inferential reproducibility was further assessed by examining whether statistical assumptions were met and by conducting sensitivity analyses, including bootstrapping where appropriate. We examined changes in standardized regression coefficients, which reflect the change in the outcome (in standard deviation units) for a one standard deviation increase in the predictor. Meaningful differences were defined as a relative change of 10% or more, or absolute differences of 0.1 (moderate) and 0.2 (substantial). When non-linear relationships were identified, inferential reproducibility was assessed by comparing model fit measures, including R², Akaike Information Criterion (AIC), and Bayesian Information Criterion (BIC). When the Gaussian distribution was not appropriate for the dependent variable, alternative distributions were considered, and model fit was evaluated using AIC and BIC.
Summary from statistical review
This study examines the effects of dietary supplements on the physical fitness of dogs (German Shepherds). Linear regression was a minor aspect of this paper, while it could be considered pre-processing, as regression was applied to each dog. The linear regression was presented in the main figures and the supplementary material; therefore, it was considered part of the main paper. Scatterplots were used to display the data, and third-order curvilinear regression was performed to assess linearity. However, no other assumptions were mentioned.
Data availability and software used
While the authors state that all relevant data are within the manuscript and its Supporting Information files, the data for the linear regression could not be located. Demographic data for the dogs were available in the paper as an image file. SPSS was used for analyses of linear regression models.
Regression sample
The data to reproduce the linear regression models were not available.
Computational reproducibility results
The data to reproduce the linear regression models were not available.
Inferential reproducibility results
The data to reproduce the linear regression models were not available.
Recommended changes
- Include data to reproduce all analyses in the paper and supplementary files.
- Update the data availability statement to reflect the status of the data.
- Evaluate the assumptions of the linear regression models by examining residuals, identifying influential outliers, and assessing multicollinearity among predictors. If any assumptions are violated, address them using appropriate methods.
- Consider creating a reproducible analysis workflow and sharing the code.