Categorical variables were reported as the number of cases and percentages; quantitative variables were reported by their means and standard deviations, or by medians and IQRs, if their distribution was not normal. The normality of the quantitative variables was verified graphically. The percentage of patients with HCC in each LI-RADS category (LR-1 to LR-5, LR-M, LR-TIV) was calculated for each available imaging. Several combinations of categories (LR-4 + LR-5; LR-4 + LR-5 + LR-TIV) were created. The diagnostic performance was assessed based on the sensitivity and specificity of these various categories, as compared with histology. The kappa test was used to determine the agreement between the two radiologists for each item, using the Landis and Koch thresholds. Statistical analyses were performed using Jamovi v.1.8 software (The Jamovi project [2021] https://www.jamovi.org ) and R v.4.0 (Core Team, 2021, R Foundation for Statistical Computing, Vienna, Austria).
Jamovi v 1
Manufactured by Jamovi
Sourced in Australia, United States
Jamovi V 1.2 is a statistical software package designed for data analysis and visualization. It provides a user-friendly interface for conducting various statistical tests and creating informative graphical representations of data.
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Lab products found in correlation
10 protocols using jamovi v 1
1
Diagnostic Performance of LI-RADS in HCC Prediction
2
Comprehensive Analysis of TAVR Outcomes
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For the variables presented in this study, baseline patient information is reported as number (percentages) for categorical variables and mean ± standard deviation or median (interquartile range) for continuous variables depending on normality. Continuous variables were tested for normality using the Shapiro-Wilk test. Correlations between the continuous variables were performed using parametric Pearson’s r or nonparametric Spearman’s rho. Paired samples t-tests were performed on pre-post TAVR variables using Mann-Whitney U or Wilcoxon W depending on normality. Statistical significance based on the corresponding test’s p-value was considered as follows (medium p < 0.05; strong p < 0.01; very strong p < 0.001). All analyses were performed using Jamovi (v.1.8).
3
Quantitative Cardiac Imaging Analysis
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Appropriate statistical tests were performed using Jamovi v.1.8. Summaries of the variables and tests performed in (Figures 4,6 Tables 2-4 Figures 4,6A Appendix 1 (section Normalization of the metrics).
4
Analyzing Cell and Lung Function Data
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Cell measurements and lung function data were analysed using the non-parametric test Wilcoxon rank, for comparisons between pretreatment and post-treatment values. P value significance was set at <0.05. Descriptive statistics were used for calculation of median values and 25th–75th percentile. Additionally, correlation analysis was conducted using Spearman’s rank correlation test. All analyses were performed using Jamovi V.1.1.9.0 software (https://www.jamovi.org ). Graphs and tables were created with Microsoft Excel 2013 and Microsoft Word 2013, respectively.
5
Statistical Analysis of Research Data
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Descriptive statistics were used for calculation of median values, the Mann-Whitney U test for comparisons between groups and Spearman′s rank for correlations. P value significance was set at <0.05. All analyses were performed using Jamovi V.1.1.9.0 software (https://www.jamovi.org ).
6
Microbial Diversity and Metabolome Analysis
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Statistical analysis of microbial diversity and pathway differential abundance were performed as described in detail above in the “Alpha and beta diversity analyses ,” Metabolome data analysis ,” and “Differential abundance analyses ” sections. Other standard statistical tests (as stated in figure legends) were performed in Jamovi, v1.1.9.0 [117 ] using P values < .05 as the cutoff for significance. Typically, pairwise group comparisons were made within age groups between PBS-only and FMT-treated mice and for PBS-only mice between the age groups.
7
Comparative Analysis of ACL Loading
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The Friedman test with post hoc Nemenyi multiple comparison test was used to examine the differences in ACL loading and peak time between the 5 conditions. Statistical tests were performed with R, package “PMCMR”41 using jamovi V 1.2 (The jamovi project, https://www.jamovi.org ). Statistical significance was set at P < .05.
8
Sociodemographic Analysis of Study Cohort
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Descriptive and summary statistics were used to describe the study cohort’s sociodemographic parameters, with continuous variables presented as means (±SD) or median (IQR) as appropriate. Categorical variables were presented as numbers (percentages). The Shapiro-Wilk tests analysed the normality of the data. We used one-way ANOVA (Welch’s) for the parametric variables and Kruskal-Wallis for the non-parametric variables for the comparison. All data were analysed using Jamovi V.1.2 (created in 2020, Sydney, Australia).
9
Statistical Analysis of Quantitative Results
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Group analyses of quantitative results were performed with the unequal variance t-test (Welch´s test) as recommended by Ruxton (2006) , as it accounts for unequal variances and is equally robust as a Student-t test when variances are equal, or one-way or two-way analysis of variance (ANOVA). Whenever the normality assumption was violated, the Mann Whitney U test (or the appropriate correction) was performed (software JAMOVI v.1.2). P values lower than 0.05 (p<0.05) were considered statistically significant. Results are reported as mean ± standard deviation (SD) and effect size when applicable (Cohen´s d or eta-square).
10
Evaluating Inflammatory, Anxious, and Depressive States
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The nature of the distribution of variables will be evaluated by the Shapiro-Wilk test. The measures of central tendency and dispersion will be organized and variables with normal distribution will be described in mean and standard deviation, variables with non-normal distribution will be described in median and range of variation. The Levene test will be used to evaluate the homogeneity of the variables. The research models will be an analysis of the mean by the student's t-test (associated with Welch's factor if there is no homogeneity) or the median by the Mann-Whitney test, depending on the distribution of the sample. For analysis of the difference between time and group ANOVA two-way (normal distribution) will be used, or Kruskall-Wallis and Friedman tests (non-normal distribution), and the post hoc tests will be corresponding for each test. The accepted significance level will be α = 5%. The analyses will be made using the Graphpad Prism v.9.2 (Graphpad, CA., USA) and Jamovi v.1.2 (Jamovi Project, Sydney, Australia) programs. In addition, a linear correlation will be made in order to evaluate the relationship between the inflammatory profile and the anxious, depressive and stress states of the volunteers.
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