Paper 32: Is there a fair allocation of healthcare research funds by the European Union?
Reference
Kalo Z, van den Akker LHM, Voko Z, Csana di M, Pitter JG (2019) Is there a fair allocation of healthcare research funds by the European Union? PLoS ONE 14(4): e0207046. https://doi.org/10.1371/journal.pone.0207046
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.
Results from the reproduction of the Kalo et al. (2019) paper are presented below. An overall summary of results is presented first, followed by model-specific results organised within tab panels. Within each panel, the Original results tab displays the linear regression outputs extracted from the published paper. The Reproduced results tab presents estimates derived from the authors’ shared data, along with a comprehensive assessment of linear regression assumptions. The Differences tab compares the original and reproduced models to assess computational reproducibility. Finally, the Sensitivity analysis tab evaluates inferential reproducibility by examining whether identified assumption violations meaningfully affected the results.
Summary from statistical review
This paper investigated factors associated with grant allocation in the European Union. The outcome in the linear regression analyses was country-level grant funding. The Multivariable model appears consistent with a backward selection approach, although this was not explicitly described as such. Assumptions of linear regression were assessed using residual diagnostics and graphical checks. Collinearity and outliers were examined; however, influential observations were retained in the final models without accompanying sensitivity analyses.
Data availability and software used
The authors provided the data in a Word (DOCX) file as supporting information, in a wide format. Importing the data was difficult and required additional cleaning due to the file format. The authors used Stata for the regression analyses.
Regression sample
There were two multivariable models examining health research funding per 100,000 people, which where related to the main research question, with initial variable model which had predictors of (1) average gross domestic product per capita (GDP per capita), (2) average population size, (3) disease burden in disability-adjusted life years (DALY) per 100,000 inhabitants , and (4) excellence of research capabilities (citations). The second and final multivariable model, had DALY removed. There were also four univariate analysis, of which citations was selected randomly for reproduction.
Computational reproducibility results
This paper was not computationally reproducible, as one of the three models could not be reproduced. The univariate analysis for citations was reproducible, and the final multivariable model was mostly reproducible, with only minor rounding differences. However, the initial multivariable model was not reproducible.
To investigate this further, the univariate association for DALYs was examined. The authors reported that “disease burden showed a statistically significant negative association of −97,410 EUR per 100,000 inhabitants, and per 1,000 additional DALYs per 100,000 inhabitants (p = 0.003; R² = 0.30).” While this presentation is confusing due to the simultaneous use of per 1,000 and per 100,000 scaling, rescaling the reproduced coefficient by 1,000 yields −97,727, matching the reported scale but not the exact value (paper: −97,410). This suggests that the discrepancy is not due solely to scaling; however, the reported p-value and R² were reproducible. In the initial multivariable model, the DALY coefficient was −30.15, whereas the reproduced estimate was −29.85. Although this difference was small and on the correct scale, all other coefficients and their associated statistics differed, suggesting that the data provided by the authors may differ from that used in the analyses.
Inferential reproducibility results
This paper was not inferentially reproducible. The univariate model for citations was successfully reproduced, with standardized coefficients and confidence interval bounds below 0.10, and with consistent coefficient directions and statistical significance. However, the final multivariable model contained a highly influential observation (Cook’s distance = 3.9). Although the authors acknowledged this outlier, no sensitivity analysis was conducted to assess its impact. Sensitivity analyses conducted here indicated substantial changes in effect sizes and linearity conclusions (as described below).
To mitigate the influence of an extreme observation, funding and GDP per capita were log-transformed, while citations were retained on the original scale. Each additional citation was associated with an 8.2% increase in funding (95% CI: 3.7% to 12.9%, p < 0.001). A 10% increase in GDP per capita was associated with an approximately 12% increase in funding. As the model was fitted on the log scale, fit statistics (e.g. R2, AIC, BIC) are not directly comparable with those from models on the original scale. The focus was therefore on obtaining a valid inferential model, assessed through residual diagnostics to ensure that the log transformation improved adherence to model assumptions and mitigated the impact of outliers. Although the influential observation continued to have some impact, its influence was substantially reduced, with Cook’s distance below 0.5. On the log scale, residual diagnostics did not indicate evidence of non-linearity in the association between GDP per capita and funding. Mild heteroscedasticity was observed, robust standard errors were used as a sensitivity analysis.
Recommended Changes
- Data underlying statistical analyses should be provided in a standard data format (e.g., CSV, XLSX, or similar) so it is machine readable.
- When influential outliers are identified, a sensitivity analysis is warranted. Appropriate approaches include refitting models with and without the influential observation.
- There were nonlinear relationships observed in the data as well as large outliers, this can be appropriately modelled by log transforming data.
- Adjusted R2 should be reported for multivariable models.
- Include a data dictionary.
- Consider creating a reproducible analysis workflow and sharing the code.
Model 1
Model results for Health research funding per 100,000
Term | B | SE | Lower | Upper | t | p-value |
|---|---|---|---|---|---|---|
Intercept | ||||||
Citations | 139046 | <0.001 | ||||
SE = Standard error; Lower = lower confidence interval; Upper = upper confidence interval. | ||||||
Fit statistics for Health research funding per 100,000
R | R2 | R2Adj | AIC | RMSE | F | DF1 | DF2 | p-value |
|---|---|---|---|---|---|---|---|---|
0.64 | ||||||||
R2 Adj = Adjusted R2; AIC = Akaike Information Criterion; RMSE = The Root Mean Squared Error; DF1 = Degrees of freedom for the model; DF2 = Degrees of freedom for the residuals. | ||||||||
ANOVA table for Health research funding per 100,000
Term | SS | DF | MS | F | p-value |
|---|---|---|---|---|---|
Citations | |||||
Residuals | |||||
SS = Sum of Squares; DF = Degrees of freedom; MS = Mean Square. | |||||
Model results for Health research funding per 100,000
Term | B | SE | Lower | Upper | t | p-value |
|---|---|---|---|---|---|---|
Intercept | −1,521,547.155 | 418,253.860 | −2,381,280.277 | −661,814.032 | −3.638 | 0.0012 |
Citations | 139,046.123 | 20,511.914 | 96,883.280 | 181,208.966 | 6.779 | <0.001 |
SE = Standard error; Lower = lower confidence interval; Upper = upper confidence interval. | ||||||
Fit statistics for Health research funding per 100,000
R | R2 | R2Adj | AIC | RMSE | F | DF1 | DF2 | p-value |
|---|---|---|---|---|---|---|---|---|
0.799 | 0.639 | 0.625 | 837.129 | 675,118.574 | 45.952 | 1 | 26 | <0.001 |
R2 Adj = Adjusted R2; AIC = Akaike Information Criterion; RMSE = The Root Mean Squared Error; DF1 = Degrees of freedom for the model; DF2 = Degrees of freedom for the residuals. | ||||||||
ANOVA table for Health research funding per 100,000
Term | SS | DF | MS | F | p-value |
|---|---|---|---|---|---|
Citations | 22,555,382,202,358.328 | 1 | 22,555,382,202,358.328 | 45.952 | <0.001 |
Residuals | 12,761,982,493,625.779 | 26 | 490,845,480,524.068 | ||
SS = Sum of Squares; DF = Degrees of freedom; MS = Mean Square; Calculated using type III SS. | |||||
Visualisation of regression model
The blue line shows the best line of fit with shading representing 95% confidence intervals, while holding all other covariates constant. The dots show partial residuals, which reflect the observed data adjusted for all other predictors except the one being plotted.
Checking residuals plots for patterns
Blue line showing quadratic fit for residuals
Testing residuals for non linear relationships
Term | Statistic | p-value | Results |
|---|---|---|---|
Citations | 1.366 | 0.1841 | No linearity violation |
Tukey test | 1.366 | 0.1719 | No linearity violation |
Specification test for predictors using quadratic tests, for fitted values curvature is tested through Tukey's one-degree-of-freedom test for nonadditivity. | |||
Checking univariate relationships with the dependent variable using scatterplots
Blue line shows linear relationship, red line indicates relationship inferred by GAM modelling
Linearity results
The residual and univariate plots show some signs of mild curvature but it was not significant therefore found to be linear.
Testing for homoscedasticity
Statistic | p-value | Parameter | Method |
|---|---|---|---|
6.071 | 0.0137 | 1 | studentized Breusch-Pagan test |
Homoscedasticity results
- The studentized Breusch-Pagan test indicates heteroscedasticity.
- Some heteroscedasticity is present in plots, and a sensitivity analysis using weighted or robust regression or wild bootstrapping is recommended.
Model descriptives including cook’s distance and leverage to understand outliers
Term | N | Mean | SD | Median | Min | Max | Skewness | Kurtosis |
|---|---|---|---|---|---|---|---|---|
Health research funding per 100,000 | 28 | 1,167,902.821 | 1,143,700.373 | 782,287.500 | 54,627.000 | 4,074,757.000 | 0.984 | −0.178 |
Citations | 28 | 19.342 | 6.573 | 18.230 | 8.600 | 32.250 | 0.144 | −1.090 |
.fitted | 28 | 1,167,902.821 | 913,993.723 | 1,013,263.669 | −325,750.496 | 2,962,690.314 | 0.144 | −1.090 |
.resid | 28 | 0.000 | 687,507.104 | 44,991.747 | −1,783,550.216 | 1,568,137.969 | −0.033 | 0.426 |
.leverage | 28 | 0.071 | 0.037 | 0.058 | 0.037 | 0.179 | 1.043 | 0.297 |
.sigma | 28 | 700,025.221 | 24,751.280 | 710,911.088 | 611,566.783 | 714,429.733 | −2.376 | 5.032 |
.cooksd | 28 | 0.046 | 0.085 | 0.007 | 0.000 | 0.368 | 2.435 | 5.624 |
.std.resid | 28 | 0.005 | 1.024 | 0.067 | −2.636 | 2.379 | −0.011 | 0.430 |
dfb.1_ | 28 | 0.001 | 0.193 | −0.006 | −0.582 | 0.386 | −0.431 | 1.765 |
dfb.Cttn | 28 | −0.000 | 0.249 | −0.012 | −0.558 | 0.791 | 0.623 | 2.572 |
dffit | 28 | 0.022 | 0.329 | 0.020 | −0.813 | 0.952 | 0.240 | 1.497 |
cov.r | 28 | 1.082 | 0.135 | 1.120 | 0.623 | 1.216 | −1.978 | 3.560 |
* categorical variable | ||||||||
Cooks threshold
Cook’s distance measures the overall change in fit, if the ith observation is removed. Potential influential observations are identified by \(\text{Cook's Distance}_i > \frac{4}{n}\), where n is the number of observations. In practice a threshold of 0.5 to 1 is often used to identify influential observations.
DFFIT threshold
DFFIT measures how many standard deviations the fitted values will change when the ith observation is removed. Potential influential observations \(\left| \text{DFFITS}_i \right| > \frac{2\sqrt{p}}{\sqrt{n}}\) where p is the number of predictors (including the intercept) and n is the number of observations. In practice this can result in a large number of points identified, a practical cut-off of 1 was used to flag observations with meaningful impact.
DFBETA threshold
DFBETAS quantify the influence of the ith observation on the jth regression coefficient as the change in that coefficient when the observation is omitted, expressed in units of the coefficient’s estimated standard error. There is a DFBETA for each parameter in the model. Potential influential observations \(|\text{DFBETA}_{ij}| > \frac{2}{\sqrt{n}}\), where n is the number of observations. In larger datasets, this threshold can flag a high number of observations with only minor influence on the model. A practical cut-off of 1 was used to flag observations with meaningful impact.
Influence plot
Observations with high leverage (horizontal) and large residuals (vertical, typically at ±2 or ±3 studentized residuals) are concerning, as they may disproportionately influence the model. This combination is reflected by large bubbles with high Cook’s distance indicated by darker shadings of blue.
COVRATIO plot
COVRATIO measures the overall change in the precision (covariance matrix) of the estimated regression coefficients when the ith observation is removed. Values close to 1 indicate little influence on the model’s precision. Values below 1 suggest that an observation inflates the variances and reduces precision, resulting in wider confidence intervals, whereas values above 1 suggest deflated variances and narrower confidence intervals. A commonly cited guideline is \(\left|\mathrm{COVRATIO}_i - 1\right| > \frac{3p}{n}\), where p is the number of parameters and n is the number of observations. A practical cut-off between 0.9 to 1.1 was used to flag observations with meaningful impact on precision, although there is no agreed universal alternative cut-off.
Observations of interest identified by the influence plot
ID | StudRes | Leverage | CookD | dfb.1_ | dfb.Cttn | dffit | cov.r |
|---|---|---|---|---|---|---|---|
4 | 0.972 | 0.135 | 0.074 | 0.374 | −0.328 | 0.383 | 1.161 |
9 | −1.172 | 0.179 | 0.147 | 0.386 | −0.489 | −0.546 | 1.183 |
16 | −3.020 | 0.068 | 0.252 | 0.343 | −0.558 | −0.813 | 0.623 |
20 | 2.638 | 0.115 | 0.368 | −0.582 | 0.791 | 0.952 | 0.748 |
StudRes = studentized residuals; CookD = Cook's Distance a combined measure of leverage and influence. DFBETAS (dfb.*) measures how much a specific regression coefficient changes (in standard errors) when an observation is removed; DFFITS measures how much the fitted (predicted) value for an observation changes (in standard deviations) when that observation is removed; cov.r = coefficient covariance ratio which measures how much the overall variance (precision) of the coefficients changes when that observation is removed. | |||||||
Results for outliers and influential points
One observation had a studentized residual greater than 3, indicating a small outlier; however, this value remained within conventional thresholds for Cook’s distance, DFBETA and DFFit. The COVRATIO indicated observations that may affect confidence intervals widths.
Checking for normality of the residuals using a Q–Q plot
Normality of residuals using Shapiro-Wilk and Kolmogorov-Smirnov tests
Statistic | p-value | Method |
|---|---|---|
0.109 | 0.8568 | Exact one-sample Kolmogorov-Smirnov test |
Statistic | p-value | Method |
|---|---|---|
0.976 | 0.7493 | Shapiro-Wilk normality test |
Normality results
- The Kolmogorov-Smirnov supports residuals being normally distributed.
- The Shapiro-Wilk supports residuals being normally distributed.
- QQ-plot looks roughly normal.
Assessing independence with the Durbin–Watson test for autocorrelation
AutoCorrelation | Statistic | p-value |
|---|---|---|
0.015 | 1.967 | 0.8800 |
Independence results
- The Durbin–Watson test suggests there are no auto-correlation issues.
- The study design seems to be independent.
Assumption conclusions
No meaningful departures from the assumptions of linearity and independence were observed. The Breusch-Pagan test was statistically significant and the residuals vs. fitted plot showed a funnel shape, suggesting heteroscedasticity and a sensitivity analysis using weighted or robust regression is recommended. Normality tests and the Q-Q plot indicated the residuals were approximately normally distributed. Outlier diagnostics indicated that point estimates were unlikely to be substantially affected by influential points, but confidence-interval width could be affected and should be further investigated.
Forest plot showing original and reproduced coefficients and 95% confidence intervals for Health research funding per 100,000
Change in regression coefficients
term | O_B | R_B | Change.B | reproduce.B |
|---|---|---|---|---|
Intercept | −1,521,547.2 | |||
Citations | 139046 | 139,046.1 | 0.1231 | Reproduced |
O_B = original B; R_B = reproduced B; Change.B = change in R_B - O_B; Reproduce.B = B reproduced. | ||||
Change in R2
O_R2 | R_R2 | Change.R2 | Reproduce.R2 |
|---|---|---|---|
0.640 | 0.6386 | −0.0014 | Reproduced |
O_R2 = original R2; R_R2 = reproduced R2; Change.R2 = change in R_R2 - O_R2 | |||
Change in p-values
Term | O_p | R_p | Change.p | Reproduce.p | SigChangeDirection |
|---|---|---|---|---|---|
Intercept | 0.0012 | ||||
Citations | <0.001 | <0.001 | 0.0000 | Reproduced | Remains sig, B same direction |
O_p = original p-value; R_p = reproduced p-value; Changep = change in p-value R_p - O_p; Reproduce.p = p-values reproduced. SigChangeDirection = statistical significance and B change between original and reproduced models. Note, p-values that were <0.001 were set to 0.00099 for the purposes of comparison. | |||||
Results for p-values
The p-value was reproduced.
Conclusion computational reproducibility
This model was computationally reproducible, with all reported statistics that were assessed being reproducible.
Methods
The model was successfully reproduced; however, there were indications that the residuals may exhibit slight heteroscedasticity. To further verify the findings, bootstrapped standardized regression coefficients and their 95% confidence intervals were examined. Percentage and absolute changes in estimates and confidence-interval bounds relative to the linear model were summarised using thresholds of 10% change and standardized coefficient differences of <0.10 and <0.20. Coefficient direction and statistical significance were assessed for consistency. Wild bootstrapping was used to account for potential heteroscedasticity.
Results
Bootstrapped results
Wild bootstrapping was performed with 10,000 iterations.
Change in regression coefficients
Term | B | boot.B | B_diff | %_Diff | Diff_10% | Diff_0.1 | Diff_0.2 |
|---|---|---|---|---|---|---|---|
Intercept | 0.0000 | −0.0005 | 0.0005 | 1,000.0000 | Yes | No | No |
z_Citations | 0.7992 | 0.7988 | 0.0003 | 0.0400 | No | No | No |
B = standardized regression coefficient reproduced B; boot.B = boostrapped standardized reproduced B; B_diff = change in B - boot.B; %_Diff = percentage difference, percentage changes were truncated at ±1000%; Diff_10% = difference ≥10% ; Diff_0.1 and Diff_0.2 = absolute difference ≥0.1 and ≥0.2, respectively. | |||||||
Change in lower 95% confidence interval
Term | Lower | boot.Lower | Lower_diff | %_Diff | Diff_10% | Diff_0.1 | Diff_0.2 |
|---|---|---|---|---|---|---|---|
Intercept | −0.2380 | −0.2165 | −0.0214 | −9.0100 | No | No | No |
z_Citations | 0.5568 | 0.5542 | 0.0026 | 0.4700 | No | No | No |
Lower = standardized reproduced lower CI; boot.Lower = boostrapped standardized reproduced lower CI; Lower_diff = change in Lower - boot.Lower; %_change = percentage difference, percentage changes were truncated at ±1000%; Diff_10% = difference ≥10% ; Diff_0.1 and Diff_0.2 = absolute difference ≥0.1 and ≥0.2, respectively. | |||||||
Change in upper 95% confidence interval
Term | Upper | boot.Upper | Upper_diff | %_Diff | Diff_10% | Diff_0.1 | Diff_0.2 |
|---|---|---|---|---|---|---|---|
Intercept | 0.2380 | 0.2207 | 0.0173 | 7.2600 | No | No | No |
z_Citations | 1.0415 | 1.0518 | −0.0104 | −0.9900 | No | No | No |
Upper = standardized reproduced upper CI; boot.Upper = boostrapped standardized reproduced upper CI; Upper_diff = change in Upper - boot.Upper; %_change = percentage difference, percentage changes were truncated at ±1000%; Diff_10% = difference ≥10% ; Diff_0.1 and Diff_0.2 = absolute difference ≥0.1 and ≥0.2, respectively. | |||||||
Change in Range of 95% confidence interval
Term | Range | boot.Range | Range_Diff | %_Diff | Diff_10% | Diff_0.1 | Diff_0.2 |
|---|---|---|---|---|---|---|---|
Intercept | 0.4759 | 0.4372 | −0.0387 | −8.1400 | No | No | No |
z_Citations | 0.4847 | 0.4976 | 0.0130 | 2.6700 | No | No | No |
Range = standardized reproduced CI range; boot.B = boostrapped standardized reproduced CI range; Range_diff = change in CI Range ; %_change = percentage difference, Diff_10% = difference ≥10% ; Diff_0.1 and Diff_0.2 = absolute difference ≥0.1 and ≥0.2, respectively. | |||||||
Change in p-value significance and regression coefficient direction
Term | p-value | boot.p-value | changep | SigChangeDirection |
|---|---|---|---|---|
Intercept | 1.0000 | 0.9961 | 0.0039 | Remains non-sig, B changes direction |
z_Citations | <0.001 | <0.001 | 0.0000 | Remains sig, B same direction |
p-value = standardized reproduced p-value; boot.p-value = boostrapped standardized reproduced p-value; changep = change in p-value - boot.p-value; SigChangeDirection = statistical significance and B change between reproduced and bootstrapped model. | ||||
Check the distribution of bootstrap estimates
The bootstrap distribution of each coefficient appeared approximately normal and centered near the original estimate (red dashed line), suggesting that the estimates are relatively stable. No strong skewness or multimodality was observed.
Conclusions based on the bootstrapped model
This model was inferentially reproducible. While some statistics changed by 10% or more, these differences were not meaningful, with a change in standardized regression coefficients of less than 0.1. The direction of effects and statistical significance remained consistent between the reproduced and bootstrapped models.
Model 2
Model results for Health research funding per 100,000
Term | B | SE | Lower | Upper | t | p-value |
|---|---|---|---|---|---|---|
Intercept | ||||||
Average_GDP_PC | 18.41 | −3.64 | 40.46 | 0.097 | ||
DALY_per_100000 | −30.15 | −79.93 | 19.64 | 0.222 | ||
Citations | 100283 | 60269 | 140298 | <0.001 | ||
population_quartile: | ||||||
2nd quartile – 1st quartile | 673962 | 69270 | 1278655 | 0.031 | ||
3rd quartile – 1st quartile | 633305 | 6829 | 1259782 | 0.048 | ||
4th quartile – 1st quartile | 190753 | −436460 | 1352454 | 0.534 | ||
SE = Standard error; Lower = lower confidence interval; Upper = upper confidence interval. | ||||||
Fit statistics for Health research funding per 100,000
R | R2 | R2Adj | AIC | RMSE | F | DF1 | DF2 | p-value |
|---|---|---|---|---|---|---|---|---|
0.83 | ||||||||
R2 Adj = Adjusted R2; AIC = Akaike Information Criterion; RMSE = The Root Mean Squared Error; DF1 = Degrees of freedom for the model; DF2 = Degrees of freedom for the residuals. | ||||||||
ANOVA table for Health research funding per 100,000
Term | SS | DF | MS | F | p-value |
|---|---|---|---|---|---|
Average_GDP_PC | |||||
DALY_per_100000 | |||||
Citations | |||||
population_quartile | 0.082 | ||||
Residuals | |||||
SS = Sum of Squares; DF = Degrees of freedom; MS = Mean Square. | |||||
Model results Health research funding per 100,000
Term | B | SE | Lower | Upper | t | p-value |
|---|---|---|---|---|---|---|
Intercept | −692,099.707 | 986,584.344 | −2,743,814.168 | 1,359,614.754 | −0.702 | 0.4907 |
Average_GDP_PC | 18.498 | 10.642 | −3.633 | 40.628 | 1.738 | 0.0968 |
DALY_per_100000 | −29.848 | 24.084 | −79.934 | 20.237 | −1.239 | 0.2289 |
Citations | 100,211.969 | 19,259.752 | 60,159.122 | 140,264.816 | 5.203 | <0.001 |
population_quartile: | ||||||
2nd quartile – 1st quartile | 672,227.000 | 291,219.684 | 66,602.513 | 1,277,851.487 | 2.308 | 0.0313 |
3rd quartile – 1st quartile | 632,255.747 | 302,023.406 | 4,163.690 | 1,260,347.804 | 2.093 | 0.0486 |
4th quartile – 1st quartile | 189,682.956 | 302,507.429 | −439,415.682 | 818,781.594 | 0.627 | 0.5374 |
SE = Standard error; Lower = lower confidence interval; Upper = upper confidence interval. | ||||||
Model fit for Health research funding per 100,000
R | R2 | R2Adj | AIC | RMSE | F | DF1 | DF2 | p-value |
|---|---|---|---|---|---|---|---|---|
0.908 | 0.825 | 0.775 | 826.816 | 469,729.694 | 16.508 | 6 | 21 | <0.001 |
R2 Adj = Adjusted R2; AIC = Akaike Information Criterion; RMSE = The Root Mean Squared Error; DF1 = Degrees of freedom for the model; DF2 = Degrees of freedom for the residuals. | ||||||||
ANOVA table for Health research funding per 100,000
Term | SS | DF | MS | F | p-value |
|---|---|---|---|---|---|
Average_GDP_PC | 888,916,574,062.690 | 1 | 888,916,574,062.690 | 3.022 | 0.0968 |
DALY_per_100000 | 451,875,188,381.914 | 1 | 451,875,188,381.914 | 1.536 | 0.2289 |
Citations | 7,964,757,698,839.988 | 1 | 7,964,757,698,839.988 | 27.073 | <0.001 |
population_quartile | 2,247,263,386,569.635 | 3 | 749,087,795,523.212 | 2.546 | 0.0834 |
Residuals | 6,178,087,581,216.055 | 21 | 294,194,646,724.574 | ||
SS = Sum of Squares; DF = Degrees of freedom; MS = Mean Square; Calculated using type III SS. | |||||
Visualisation of regression model
The blue line shows the best line of fit with shading representing 95% confidence intervals, while holding all other covariates constant. The dots show partial residuals, which reflect the observed data adjusted for all other predictors except the one being plotted.
Forest plot showing Original and Reproduced coefficients and 95% confidence intervals for Health research funding per 100,000
Change in regression coefficients
term | O_B | R_B | Change.B | reproduce.B |
|---|---|---|---|---|
Intercept | −692,099.70702 | |||
Average_GDP_PC | 18.41 | 18.49765 | 0.0877 | Not Reproduced |
DALY_per_100000 | −30.15 | −29.84845 | 0.3016 | Not Reproduced |
Citations | 100283 | 100,211.96884 | −71.0312 | Not Reproduced |
population_quartile: | ||||
2nd quartile – 1st quartile | 673962 | 672,227.00026 | −1734.9997 | Not Reproduced |
3rd quartile – 1st quartile | 633305 | 632,255.74730 | −1049.2527 | Not Reproduced |
4th quartile – 1st quartile | 190753 | 189,682.95613 | −1070.0439 | Not Reproduced |
O_B = original B; R_B = reproduced B; Change.B = change in R_B - O_B; Reproduce.B = B reproduced. | ||||
Change in lower 95% confidence intervals for coefficients
term | O_lower | R_lower | Change.lci | Reproduce.lower |
|---|---|---|---|---|
Intercept | −2,743,814.168434 | |||
Average_GDP_PC | −3.64 | −3.632591 | 0.0074 | Incorrect Rounding |
DALY_per_100000 | −79.93 | −79.934011 | −0.0040 | Reproduced |
Citations | 60269 | 60,159.121670 | −109.8783 | Not Reproduced |
population_quartile: | ||||
2nd quartile – 1st quartile | 69270 | 66,602.513155 | −2667.4868 | Not Reproduced |
3rd quartile – 1st quartile | 6829 | 4,163.690195 | −2665.3098 | Not Reproduced |
4th quartile – 1st quartile | −436460 | −439,415.681550 | −2955.6815 | Not Reproduced |
O_lower = original lower confidence interval; R_lower = reproduced lower confidence interval; change.lci = change in R_lower - O_lower; Reproduce.lower = lower confidence interval reproduced. | ||||
Change in upper 95% confidence intervals for coefficients
term | O_upper | R_upper | Change.uci | Reproduce.upper |
|---|---|---|---|---|
Intercept | 1,359,614.75440 | |||
Average_GDP_PC | 40.46 | 40.62789 | 0.1679 | Not Reproduced |
DALY_per_100000 | 19.64 | 20.23712 | 0.5971 | Not Reproduced |
Citations | 140298 | 140,264.81600 | −33.1840 | Not Reproduced |
population_quartile: | ||||
2nd quartile – 1st quartile | 1278655 | 1,277,851.48736 | −803.5126 | Not Reproduced |
3rd quartile – 1st quartile | 1259782 | 1,260,347.80441 | 565.8044 | Not Reproduced |
4th quartile – 1st quartile | 1352454 | 818,781.59380 | −533672.4062 | Not Reproduced |
O_upper = original upper confidence interval; R_upper = reproduced upper confidence interval; change.uci = change in R_upper - O_upper; Reproduce.upper = upper confidence interval reproduced. | ||||
Change in R2
O_R2 | R_R2 | Change.R2 | Reproduce.R2 |
|---|---|---|---|
0.830 | 0.8251 | −0.0049 | Reproduced |
O_R2 = original R2; R_R2 = reproduced R2; Change.R2 = change in R_R2 - O_R2 | |||
Change in p-values
Term | O_p | R_p | Change.p | Reproduce.p | SigChangeDirection |
|---|---|---|---|---|---|
Intercept | 0.4907 | ||||
Average_GDP_PC | 0.097 | 0.0968 | −0.0002 | Reproduced | Remains non-sig, B same direction |
DALY_per_100000 | 0.222 | 0.2289 | 0.0069 | Not Reproduced | Remains non-sig, B same direction |
Citations | <0.001 | <0.001 | 0.0000 | Reproduced | Remains sig, B same direction |
population_quartile: | |||||
2nd quartile – 1st quartile | 0.031 | 0.0313 | 0.0003 | Reproduced | Remains sig, B same direction |
3rd quartile – 1st quartile | 0.048 | 0.0486 | 0.0006 | Incorrect Rounding | Remains sig, B same direction |
4th quartile – 1st quartile | 0.534 | 0.5374 | 0.0034 | Not Reproduced | Remains non-sig, B same direction |
O_p = original p-value; R_p = reproduced p-value; Changep = change in p-value R_p - O_p; Reproduce.p = p-values reproduced. SigChangeDirection = statistical significance and B change between original and reproduced models. Note, p-values that were <0.001 were set to 0.00099 for the purposes of comparison. | |||||
Bland Altman plot showing differences between original and reproduced p-values for Health research funding per 100,000
Results for p-values
Some p-values were reproduced, others were not.
Conclusion computational reproducibility
This model was not computationally reproducible.
As this model was not computationally reproducible, inferential reproducibility was not considered, since the original analyses could not be reproduced and therefore, statistical assumptions could not be meaningfully compared or interpreted.
Model 3
Model results for Health research funding per 100,000
Term | B | SE | Lower | Upper | t | p-value |
|---|---|---|---|---|---|---|
Intercept | ||||||
Average_GDP_PC | 27.55 | 11.32 | 43.79 | 0.002 | ||
Citations | 97560 | 57385 | 137736 | <0.001 | ||
population_quartile: | ||||||
2nd quartile – 1st quartile | 700203 | 90777 | 1309630 | 0.026 | ||
3rd quartile – 1st quartile | 721330 | 105599 | 1337061 | 0.024 | ||
4th quartile – 1st quartile | 293956 | −315950 | 903861 | 0.328 | ||
SE = Standard error; Lower = lower confidence interval; Upper = upper confidence interval. | ||||||
Fit Statistics Health research funding per 100,000
R | R2 | R2Adj | AIC | RMSE | F | DF1 | DF2 | p-value |
|---|---|---|---|---|---|---|---|---|
0.82 | ||||||||
R2 Adj = Adjusted R2; AIC = Akaike Information Criterion; RMSE = The Root Mean Squared Error; DF1 = Degrees of freedom for the model; DF2 = Degrees of freedom for the residuals. | ||||||||
ANOVA Table for Health research funding per 100,000
Term | SS | DF | MS | F | p-value |
|---|---|---|---|---|---|
Average_GDP_PC | |||||
Citations | |||||
population_quartile | 0.067 | ||||
Residuals | |||||
SS = Sum of Squares; DF = Degrees of freedom; MS = Mean Square. | |||||
Model results for Health research funding per 100,000
Term | B | SE | Lower | Upper | t | p-value |
|---|---|---|---|---|---|---|
Intercept | −1,826,305.610 | 372,998.828 | −2,599,857.834 | −1,052,753.386 | −4.896 | <0.001 |
Average_GDP_PC | 27.554 | 7.830 | 11.317 | 43.792 | 3.519 | 0.0019 |
Citations | 97,560.323 | 19,372.294 | 57,384.644 | 137,736.002 | 5.036 | <0.001 |
population_quartile: | ||||||
2nd quartile – 1st quartile | 700,203.348 | 293,858.942 | 90,777.201 | 1,309,629.494 | 2.383 | 0.0262 |
3rd quartile – 1st quartile | 721,329.701 | 296,899.014 | 105,598.833 | 1,337,060.569 | 2.430 | 0.0237 |
4th quartile – 1st quartile | 293,955.476 | 294,090.076 | −315,950.013 | 903,860.964 | 1.000 | 0.3284 |
SE = Standard error; Lower = lower confidence interval; Upper = upper confidence interval. | ||||||
Fit statistics for Health research funding per 100,000
R | R2 | R2Adj | AIC | RMSE | F | DF1 | DF2 | p-value |
|---|---|---|---|---|---|---|---|---|
0.901 | 0.812 | 0.770 | 826.792 | 486,604.957 | 19.039 | 5 | 22 | <0.001 |
R2 Adj = Adjusted R2; AIC = Akaike Information Criterion; RMSE = The Root Mean Squared Error; DF1 = Degrees of freedom for the model; DF2 = Degrees of freedom for the residuals. | ||||||||
ANOVA Table for Health research funding per 100,000
Term | SS | DF | MS | F | p-value |
|---|---|---|---|---|---|
Average_GDP_PC | 3,732,393,212,495.432 | 1 | 3,732,393,212,495.432 | 12.385 | 0.0019 |
Citations | 7,643,156,607,888.156 | 1 | 7,643,156,607,888.156 | 25.362 | <0.001 |
population_quartile | 2,482,817,319,025.463 | 3 | 827,605,773,008.488 | 2.746 | 0.0673 |
Residuals | 6,629,962,769,597.969 | 22 | 301,361,944,072.635 | ||
SS = Sum of Squares; DF = Degrees of freedom; MS = Mean Square; Calculated using type III SS. | |||||
Visualisation of regression model
The blue line shows the best line of fit with shading representing 95% confidence intervals, while holding all other covariates constant. The dots show partial residuals, which reflect the observed data adjusted for all other predictors except the one being plotted.
Checking residuals plots for patterns
Blue line showing quadratic fit for residuals
Testing residuals for non linear relationships
Term | Statistic | p-value | Results |
|---|---|---|---|
Average_GDP_PC | −1.765 | 0.0921 | No linearity violation |
Citations | 1.455 | 0.1604 | No linearity violation |
population_quartile | |||
Tukey test | 2.740 | 0.0061 | Linearity violation |
Specification test for predictors using quadratic tests, for fitted values curvature is tested through Tukey's one-degree-of-freedom test for nonadditivity. | |||
Checking univariate relationships with the dependent variable using scatterplots
Blue line shows linear relationship, red line indicates relationship inferred by GAM modelling
Linearity results
Plots and tests show an unaccounted non-linear relationship may be present.
Testing for homoscedasticity
Statistic | p-value | Parameter | Method |
|---|---|---|---|
6.416 | 0.2678 | 5 | studentized Breusch-Pagan test |
Homoscedasticity results
- The studentized Breusch-Pagan test supports homoscedasticity.
- Some heteroscedasticity is present in plots, and a sensitivity analysis using weighted or robust regression or wild bootstrapping is recommended.
Model descriptives including cook’s distance and leverage to understand outliers
Term | N | Mean | SD | Median | Min | Max | Skewness | Kurtosis |
|---|---|---|---|---|---|---|---|---|
Health research funding per 100,000 | 28 | 1,167,902.821 | 1,143,700.373 | 782,287.500 | 54,627.000 | 4,074,757.000 | 0.984 | −0.178 |
Average_GDP_PC | 28 | 24,617.461 | 15,978.688 | 20,416.670 | 5,388.890 | 79,566.670 | 1.366 | 2.479 |
Citations | 28 | 19.342 | 6.573 | 18.230 | 8.600 | 32.250 | 0.144 | −1.090 |
population_quartile* | 28 | 2.500 | 1.139 | 2.500 | 1.000 | 4.000 | 0.000 | −1.475 |
.fitted | 28 | 1,167,902.821 | 1,030,774.644 | 955,108.840 | −470,784.916 | 2,981,548.152 | 0.333 | −1.208 |
.resid | 28 | 0.000 | 495,534.234 | −37,693.413 | −757,719.152 | 1,295,335.078 | 0.474 | −0.364 |
.leverage | 28 | 0.214 | 0.120 | 0.180 | 0.146 | 0.786 | 3.886 | 15.730 |
.sigma | 28 | 546,365.025 | 23,828.707 | 554,394.043 | 464,893.826 | 561,881.093 | −2.446 | 5.305 |
.cooksd | 28 | 0.183 | 0.743 | 0.022 | 0.000 | 3.959 | 4.681 | 20.843 |
.std.resid | 28 | −0.047 | 1.096 | −0.075 | −2.542 | 2.634 | 0.072 | −0.099 |
dfb.1_ | 28 | −0.042 | 0.372 | −0.015 | −1.512 | 0.661 | −1.970 | 6.563 |
dfb.A_GD | 28 | −0.136 | 0.988 | 0.006 | −5.124 | 0.601 | −4.571 | 20.211 |
dfb.Cttn | 28 | 0.074 | 0.593 | −0.009 | −0.803 | 2.825 | 3.395 | 13.760 |
dfb.p_2q | 28 | 0.053 | 0.417 | 0.000 | −0.537 | 1.920 | 3.087 | 11.660 |
dfb.p_3q | 28 | 0.046 | 0.352 | 0.002 | −0.351 | 1.314 | 1.970 | 4.272 |
dfb.p_4q | 28 | 0.052 | 0.373 | 0.008 | −0.381 | 1.757 | 3.317 | 12.726 |
dffit | 28 | −0.182 | 1.201 | −0.032 | −5.666 | 1.544 | −3.267 | 12.706 |
cov.r | 28 | 1.292 | 0.338 | 1.377 | 0.170 | 1.720 | −1.332 | 2.005 |
* categorical variable | ||||||||
Cooks threshold
Cook’s distance measures the overall change in fit, if the ith observation is removed. Potentially influential observations are identified by \(\text{Cook's Distance}_i > \frac{4}{n}\), where n is the number of observations. In practice, a threshold of 0.5 to 1 is often used to identify influential observations.
DFFIT threshold
DFFIT measures how many standard deviations the fitted values will change when the ith observation is removed. Potential influential observations \(\left| \text{DFFITS}_i \right| > \frac{2\sqrt{p}}{\sqrt{n}}\) where p is the number of predictors (including the intercept), and n is the number of observations. In practice, this can result in a large number of points identified, a practical cut-off of 1 was used to flag observations with meaningful impact.
DFBETA threshold
DFBETAS quantify the influence of the ith observation on the jth regression coefficient as the change in that coefficient when the observation is omitted, expressed in units of the coefficient’s estimated standard error. There is a DFBETA for each model parameter. Potential influential observations \(|\text{DFBETA}_{ij}| > \frac{2}{\sqrt{n}}\), where n is the number of observations. In larger datasets, this threshold can flag a high number of observations with only minor influence on the model. A practical cut-off of 1 was used to flag observations with meaningful impact.
Influence plot
Observations with high leverage (horizontal) and large residuals (vertical, typically at ±2 or ±3 studentized residuals) are concerning, as they may disproportionately influence the model. This combination is reflected by large bubbles with high Cook’s distance indicated by darker shadings of blue.
COVRATIO plot
COVRATIO measures the overall change in the precision (covariance matrix) of the estimated regression coefficients when the ith observation is removed. Values close to 1 indicate little influence on the model’s precision. Values below 1 suggest that an observation inflates the variances and reduces precision, resulting in wider confidence intervals, whereas values above 1 suggest deflated variances and narrower confidence intervals. A commonly cited guideline is \(\left|\mathrm{COVRATIO}_i - 1\right| > \frac{3p}{n}\), where p is the number of parameters and n is the number of observations. A practical cut-off between 0.9 to 1.1 was used to flag observations with meaningful impact on precision, although there is no agreed universal alternative cut-off.
Observations of interest identified by the influence plot
ID | StudRes | Leverage | CookD | dfb.1_ | dfb.A_GD | dfb.Cttn | dfb.p_2q | dfb.p_3q | dfb.p_4q | dffit | cov.r |
|---|---|---|---|---|---|---|---|---|---|---|---|
9 | −1.727 | 0.304 | 0.199 | 0.661 | 0.250 | −0.803 | −0.537 | 0.125 | −0.055 | −1.140 | 0.856 |
20 | 3.111 | 0.198 | 0.285 | −0.657 | 0.178 | 0.578 | −0.034 | 0.822 | 0.051 | 1.544 | 0.170 |
18 | −2.955 | 0.786 | 3.959 | −1.512 | −5.124 | 2.825 | 1.920 | 1.314 | 1.757 | −5.666 | 0.767 |
StudRes = studentized residuals; CookD = Cook's Distance a combined measure of leverage and influence. DFBETAS (dfb.*) measures how much a specific regression coefficient changes (in standard errors) when an observation is removed; DFFITS measures how much the fitted (predicted) value for an observation changes (in standard deviations) when that observation is removed; cov.r = coefficient covariance ratio which measures how much the overall variance (precision) of the coefficients changes when that observation is removed. | |||||||||||
Results for outliers and influential points
Two observations had studentized residuals near 3. One of these observations was an inflential outlier with Cook’s distance of approximately 4, with DFBETAS and DFFITS also outside conventional ranges. COVRATIO values substantially < 1, suggesting the observation may effect point estimates but potential inflation of standard errors (wider confidence intervals).
Checking for normality of the residuals using a Q–Q plot
Normality of residuals using Shapiro-Wilk and Kolmogorov-Smirnov tests
Statistic | p-value | Method |
|---|---|---|
0.107 | 0.8713 | Exact one-sample Kolmogorov-Smirnov test |
Statistic | p-value | Method |
|---|---|---|
0.986 | 0.9608 | Shapiro-Wilk normality test |
Normality results
- The Kolmogorov-Smirnov supports residuals being normally distributed.
- The Shapiro-Wilk supports residuals being normally distributed.
- QQ-plot looks roughly normal.
Assessing collinearity with VIF
Term | VIF | Tolerance |
|---|---|---|
Average_GDP_PC | 1.184 | 0.844 |
Citations | 1.205 | 0.830 |
population_quartile | 1.009 | 0.991 |
VIF = Variance Inflation Factor. | ||
Collinearity results
- All VIF values are under three, indicating no collinearity issues.
- Overall, when taking into account VIF and SE, the model does not have collinearity issues.
Assessing independence with the Durbin–Watson test for autocorrelation
AutoCorrelation | Statistic | p-value |
|---|---|---|
−0.007 | 2.001 | 0.9440 |
Independence results
- The Durbin–Watson test suggests there are no auto-correlation issues.
- The study design seems to be independent.
Assumption conclusions
No meaningful departures from the assumptions of normality or independence were observed. However, residual plots and diagnostic tests indicated potential issues with linearity, suggesting that a non-linear relationship may not have been adequately captured, and residuals may be mildly heteroscedastic. Additionally, the presence of observations with high DFBETA, DFFIT and COVRatio indicates that further investigation of potential influential points is warranted.
Forest plot showing original and reproduced coefficients and 95% confidence intervals for Health research funding per 100,000
Change in regression coefficients
term | O_B | R_B | Change.B | reproduce.B |
|---|---|---|---|---|
Intercept | −1,826,305.60981 | |||
Average_GDP_PC | 27.55 | 27.55404 | 0.0040 | Reproduced |
Citations | 97560 | 97,560.32327 | 0.3233 | Reproduced |
population_quartile: | ||||
2nd quartile – 1st quartile | 700203 | 700,203.34761 | 0.3476 | Reproduced |
3rd quartile – 1st quartile | 721330 | 721,329.70087 | −0.2991 | Reproduced |
4th quartile – 1st quartile | 293956 | 293,955.47583 | −0.5242 | Incorrect Rounding |
O_B = original B; R_B = reproduced B; Change.B = change in R_B - O_B; Reproduce.B = B reproduced. | ||||
Change in lower 95% confidence intervals for coefficients
term | O_lower | R_lower | Change.lci | Reproduce.lower |
|---|---|---|---|---|
Intercept | −2,599,857.83390 | |||
Average_GDP_PC | 11.32 | 11.31659 | −0.0034 | Reproduced |
Citations | 57385 | 57,384.64406 | −0.3559 | Reproduced |
population_quartile: | ||||
2nd quartile – 1st quartile | 90777 | 90,777.20122 | 0.2012 | Reproduced |
3rd quartile – 1st quartile | 105599 | 105,598.83287 | −0.1671 | Reproduced |
4th quartile – 1st quartile | −315950 | −315,950.01284 | −0.0128 | Reproduced |
O_lower = original lower confidence interval; R_lower = reproduced lower confidence interval; change.lci = change in R_lower - O_lower; Reproduce.lower = lower confidence interval reproduced. | ||||
Change in upper 95% confidence intervals for coefficients
term | O_upper | R_upper | Change.uci | Reproduce.upper |
|---|---|---|---|---|
Intercept | −1,052,753.3857 | |||
Average_GDP_PC | 43.79 | 43.7915 | 0.0015 | Reproduced |
Citations | 137736 | 137,736.0025 | 0.0025 | Reproduced |
population_quartile: | ||||
2nd quartile – 1st quartile | 1309630 | 1,309,629.4940 | −0.5060 | Incorrect Rounding |
3rd quartile – 1st quartile | 1337061 | 1,337,060.5689 | −0.4311 | Reproduced |
4th quartile – 1st quartile | 903861 | 903,860.9645 | −0.0355 | Reproduced |
O_upper = original upper confidence interval; R_upper = reproduced upper confidence interval; change.uci = change in R_upper - O_upper; Reproduce.upper = upper confidence interval reproduced. | ||||
Change in R2
O_R2 | R_R2 | Change.R2 | Reproduce.R2 |
|---|---|---|---|
0.820 | 0.8123 | −0.0077 | Incorrect Rounding |
O_R2 = original R2; R_R2 = reproduced R2; Change.R2 = change in R_R2 - O_R2 | |||
Change in p-values
Term | O_p | R_p | Change.p | Reproduce.p | SigChangeDirection |
|---|---|---|---|---|---|
Intercept | <0.001 | ||||
Average_GDP_PC | 0.002 | 0.0019 | −0.0001 | Reproduced | Remains sig, B same direction |
Citations | <0.001 | <0.001 | 0.0000 | Reproduced | Remains sig, B same direction |
population_quartile: | |||||
2nd quartile – 1st quartile | 0.026 | 0.0262 | 0.0002 | Reproduced | Remains sig, B same direction |
3rd quartile – 1st quartile | 0.024 | 0.0237 | −0.0003 | Reproduced | Remains sig, B same direction |
4th quartile – 1st quartile | 0.328 | 0.3284 | 0.0004 | Reproduced | Remains non-sig, B same direction |
O_p = original p-value; R_p = reproduced p-value; Changep = change in p-value R_p - O_p; Reproduce.p = p-values reproduced. SigChangeDirection = statistical significance and B change between original and reproduced models. Note, p-values that were <0.001 were set to 0.00099 for the purposes of comparison. | |||||
Bland Altman Plot showing differences between original and reproduced p-values for Health research funding per 100,000
Results for p-values
P-values were reproduced with all differences close to zero.
Conclusion computational reproducibility
This model was mostly computationally reproducible, with minor rounding errors. P-values were reproduced and had the same interpretation, and regression coefficients did not change direction.
Methods
The model was successfully reproduced; however, residual diagnostics indicated potential heteroscedasticity, nonlinearity, and observations that may influence point estimates or confidence-interval widths. Evidence of non-linearity was primarily associated with GDP. To assess the impact of influential observations, a sensitivity analysis was conducted in which all continuous variables were standardized, and models were fitted with and without the influential observation to evaluate changes in effect size.
To further examine departures from linearity, models fitted on the original scale were visualised by comparing linear, quadratic, and cubic specifications, both with and without the influential observation. As the apparent polynomial relationship was driven by the influential observation, an additional sensitivity analysis was undertaken in which both the outcome and GDP were log-transformed to assess whether this specification improved linearity and model assumptions.
Results
This model was not inferentially reproducible with outliers and linearity issue substantially changing the results.
Standardized z_Funding_per_100000 showing with and without outlier
The authors identified an outlying value for Average_GDP_PC corresponding to Luxembourg; however, this observation was retained in the analysis without a sensitivity assessment. Removal of this observation resulted in substantial changes in coefficient estimates, with GDP more than doubling without the outlier, consistent with being an influential point identified by a large Cook’s distance. Although it is generally appropriate not to exclude outliers without strong justification, influential observations should be explicitly examined through sensitivity analyses to assess their impact on model estimates and inference.
| Characteristic |
All_data
|
Outlier Removed
|
||||||
|---|---|---|---|---|---|---|---|---|
| N | Beta | 95% CI1 | p-value | N | Beta | 95% CI1 | p-value | |
| (Intercept) | 28 | -0.37 | -0.75, 0.00 | 0.051 | 27 | -0.10 | -0.48, 0.28 | 0.594 |
| z_Citations | 28 | 0.56 | 0.33, 0.79 | <0.001 | 27 | 0.29 | 0.01, 0.57 | 0.040 |
| z_Average_GDP_PC | 28 | 0.38 | 0.16, 0.61 | 0.002 | 27 | 0.64 | 0.35, 0.93 | <0.001 |
| population_quartile | 28 | 27 | ||||||
| 1st quartile | — | — | — | — | ||||
| 2nd quartile | 0.61 | 0.08, 1.1 | 0.026 | 0.18 | -0.35, 0.72 | 0.484 | ||
| 3rd quartile | 0.63 | 0.09, 1.2 | 0.024 | 0.33 | -0.17, 0.83 | 0.182 | ||
| 4th quartile | 0.26 | -0.28, 0.79 | 0.328 | -0.13 | -0.66, 0.40 | 0.614 | ||
| 1 CI = Confidence Interval | ||||||||
Comparison of Funding_per_100000 with non-linear terms for Average_GDP_PC with outlier included
It can be seen that linear, quadratic and cubic models do not fit the data well, all models are heavily impacted by the outlier.
Comparison of Funding_per_100000 with non-linear terms for Average_GDP_PC without outlier included
After excluding the influential observation, a quadratic association between funding and GDP was evident. Although this sensitivity analysis is informative for understanding the underlying functional form, the observation should be retained in the primary analysis and modelled appropriately. Given that a single observation can exert disproportionate influence, the data were log-transformed to stabilise the variance and reduce the impact of extreme values.
To mitigate the influence of an extreme observation, funding and GDP per capita were log-transformed, while citations were retained on the original scale.
Back transformed coefficients
| Characteristic | exp(β) | 95% CI1 | p-value |
|---|---|---|---|
| (Intercept) | 0.841 | 0.020, 34.665 | 0.924 |
| Citations | 1.082 | 1.037, 1.129 | <0.001 |
| log_Average_GDP_PC | 3.301 | 2.162, 5.042 | <0.001 |
| population_quartile | |||
| 1st quartile | — | — | |
| 2nd quartile | 1.213 | 0.676, 2.176 | 0.501 |
| 3rd quartile | 1.387 | 0.770, 2.498 | 0.261 |
| 4th quartile | 1.059 | 0.588, 1.907 | 0.842 |
| 1 CI = Confidence Interval | |||
Each additional citation was associated with an 8.2% increase in funding (95% CI: 3.7% to 12.9%, p < 0.001). There were no statistically significant differences in funding between population quartiles. For example, countries in the second population quartile had 1.2 times the funding as those in the first quartile (95% CI: 0.68 to 2.18, p = 0.501).
The exponentiated coefficient for log(GDP) (3.3) represents the change in funding associated with an approximately 2.7-fold increase in GDP (because natural logarithms are used) and is therefore difficult to interpret directly. Because both funding and GDP were log-transformed, the coefficient for log(GDP) represents an elasticity. The coefficient (1.194; see table below) indicates that funding is proportional to GDP raised to the power of 1.194, meaning funding increases with GDP according to this power relationship. For example, a 10% increase in GDP corresponds to an estimated 12% increase in funding (1.101.194 - 1).
As the model was fitted on the log scale, fit statistics (e.g. R2, AIC, BIC) are not directly comparable with those from models on the original scale. The focus was therefore on obtaining a valid inferential model, assessed through residual diagnostics to ensure that the log transformation improved adherence to model assumptions and mitigated the impact of outliers. Although the influential observation continued to have some impact, its influence was substantially reduced, with Cook’s distance below 0.5. On the log scale, Residual diagnostics did not indicate evidence of non-linearity between GDP per capita and funding.
Residual plots
Residual diagnostics indicated mild heteroscedasticity. As a sensitivity analysis, heteroscedasticity-robust standard errors were applied, leading to inflated standard errors relative to the conventional OLS estimates and was therefore appropriate.
Comparison of OLS and robust standard errors with log coefficients
Ordinary least squares | Robust SE (HC3) | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|
Variable | Estimate | SE | Lower | Upper | p-value | Estimate | SE | Lower | Upper | p-value |
(Intercept) | −0.173 | 1.793 | −3.892 | 3.546 | 0.9239 | −0.173 | 2.621 | −5.310 | 4.963 | 0.9478 |
Citations | 0.079 | 0.020 | 0.037 | 0.122 | <0.001 | 0.079 | 0.032 | 0.016 | 0.142 | 0.0228 |
log_Average_GDP_PC | 1.194 | 0.204 | 0.771 | 1.618 | <0.001 | 1.194 | 0.317 | 0.572 | 1.816 | 0.0011 |
population_quartile2nd quartile | 0.193 | 0.282 | −0.392 | 0.777 | 0.5011 | 0.193 | 0.446 | −0.682 | 1.067 | 0.6699 |
population_quartile3rd quartile | 0.327 | 0.284 | −0.261 | 0.916 | 0.2613 | 0.327 | 0.383 | −0.424 | 1.078 | 0.4026 |
population_quartile4th quartile | 0.057 | 0.284 | −0.531 | 0.646 | 0.8417 | 0.057 | 0.393 | −0.713 | 0.828 | 0.8854 |