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33 protocols using r software version 3

1

Diagnostic Accuracy of Deep Learning

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All statistical analyses were performed using R software, version 3.6.3 (Vienna, Austria) and IBM SPSS Statistics version 26. Because a few studies reported the number of true positives (TP), true negatives (TN), false positives (FP) and false negatives (FN). This study used the diagnostic odds ratios (DOR) as pooled outcome from the reported sensitivity and specificity to determine the diagnostic accuracy of the deep learning system [18 (link)], calculated as follows: DOR=Sensitivity×Specificity1-Sensitivity×1-Specificity
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2

Prognostic Factors for Lung Cancer Survival

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The receiver operating characteristic (ROC) curve was used to determine the optimal cutoff value of the PNI and CONUT. The chi-square test or Fisher’s exact test was applied to explore differences in categorical variables. The Kaplan–Meier method with log-rank test was used to construct survival curves. Univariable and multivariable Cox proportional hazards regression models were used to identify variables associated with OS and PFS. Hazard ratios (HR) and 95% confidence intervals (CI) were then calculated for OS and PFS. Candidate variables with a P value < 0.2 on univariable analyses were included in multivariable analysis. Further subgroup analysis was performed according to age, gender, smoking, TNM stage, histology, lesion and surgery, while we also recognized that these analyses are subject to limited statistical power. Interactions were evaluated using the Wald test. Time-dependent receiver operating characteristic curves for the prognostic values of NPS, PNI, CONUT and SIS were estimated using the R package survivalROC. All analyses were performed by IBM SPSS 25.0 and R software version 3.6.3. Two-sided P value < 0.05 was considered statistically significant.
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3

Radiomics-based Immune Factors Prediction

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After feature selection, a logistic regression model was developed to validate the efficacy of the selected radiomics features on the basis of radiomics signatures (Rad score), which was calculated via the linear combination of selected features weighted by their respective LASSO coefficients in the training group. Models based on clinical factors or combined clinical factors and radiomics features were constructed using logistic regression for immune factors expression prediction. The area under the curve (AUC) of the receiver operator characteristics (ROC) was calculated to estimate the predictive performance of the models.
Statistical analysis was performed using R software version 3.4.2 (Auckland, New Zealand) and SPSS version 22.0 for Windows (Chicago, USA). The “glment” package was used for executing the LASSO algorithm. The predictive values of radiomics features were performed by the “pROC” package in R software. The Chi-squared test or Fisher’s test was employed to analyze the categorical variables. The Mann–Whitney U-test was used to determine the continuous variable between these groups. All statistical analyses were two sided, and p-value < 0.05 was considered to be significant difference.
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4

Multivariate Analysis of Lymph Node Metastasis

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Continuous variables were compared using an independent-sample, unpaired two-tailed t test or Mann−Whitney H test, as appropriate. Differences in categorical variables were compared using the chi-square or Fisher’s exact test. A logistic regression model was used to estimate the odds ratio (OR) and 95% CI and identify the independent predictors of LN metastasis. Survival curves were generated by using Kaplan–Meier survival analysis, and the differences in survival distributions were tested using the log-rank test. The Cox proportional hazard model was used to determine the hazard ratio (HR) of preoperative variables for OS and DFS. All statistical analyses were conducted using the R software (version 3.4.2) and SPSS (version 19.0), and a two-sided P-value  < 0.05 was considered as statistically significant.
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5

Comparative Analysis of PD Prognosis

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T tests were used to compare age between the PD group and the non-PD group. Pearson chi-square tests were used to compare other clinicopathological variables. OS, BCSS and DFS were compared between the two groups using the Kaplan–Meier method. Univariate and multivariate Cox regression analyses were performed to identify prognostic factors.19 (link) A propensity score matching model was used to conduct the matched study.19 (link) All tests were two-sided, and a P-value of less than 0.05 was considered statistically significant. SPSS statistical software version 25.0 package (IBM Corporation, Armonk, NY, USA) and R software version 3.5.3. (The R Project for Statistical Computing, https://www.r-project.org/) were used for the calculations and analyses. The R packages “MatchIt”, “survminer”, “readr”, and “survival” with the appropriate libraries were used.
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6

Prognostic risk score analysis

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The χ2 test was used to compare the distribution of clinicopathological parameters between the two risk groups. The Mann-Whitney U test and one-way analysis of variance followed by Bonferroni's post hoc test were used to compare the risk scores of patients with different clinicopathological and molecular pathological characteristics. Univariate and multivariate Cox regression analyses were used to determine the prognostic value of the risk score. To analyze the prediction efficiency, receiver operating characteristic (ROC) curve analysis with the R package ‘survival ROC’ was employed. The OS of the patients was compared using the Kaplan-Meier method with a two-sided log-rank test. R software (version 3.5.3) and SPSS20.0 software (IBM Corp.) were used to perform statistical analysis.
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7

Gender Differences in Ischemic Stroke DALY

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The detailed methods for the assessment of disease DALYs have been described previously9 (link),10 (link). Differences in DALYs number (men minus women) and ASDR (men to women’s ASDR ratio) were used to compare the relative levels of IS DALYS between sexes. We used percentage changes and estimated annual percentage change (EAPC) to assess the trends in DALYs number and ASDR. It is assumed that the natural logarithm of ASDR follows a regression line. Thus, Y = α + βX + ε, where Y denotes ln (ASDR), X means a calendar year, and ε refers to the error term. Herein, β determines the positive or negative trends of ASDR. Then, EAPC = 100*(exp(β)− 1). Its 95% confidence intervals are also obtained from the linear model. When the EAPC value and its upper boundary of the confidence interval are positive, the trend in ASDR is increasing. Instead, when the EAPC value and its lower boundary of the confidence interval are negative, the trend in ASDR is decreasing. Pearson correlation and linear regression analyses were conducted to identify the correlations between ASDR ratio and SDI. R software version 3.5.2 (https://cran.r-project.org/doc/FAQ/R-FAQ.html#Citing-R) and SPSS software version 21.0 (https://www.ibm.com/products/spss-statistics) were used for charting and analysis. A two-tailed P value less than 0.05 was considered statistically significant.
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8

Physical Activity and Health-Related Quality of Life

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The QoLR package was used to calculate the HRQoL scores and determine the TTD events in EORTC QLQ-C30 and EORTC QLQ-LC13. Median and interquartile range were used to describe the HRQoL scores and TTD. And chi-squared test was performed to assess the differences in sociodemographic, clinical characteristics, and incidence rate of TTD events between patients with different levels of physical activity. Baseline HRQoL scores of three physical activity levels were compared using the Kruskal-Wallis test. Survival analysis was performed using the univariate and multiple Cox regression analysis after controlling for confounding factors; the results are shown as hazard ratios (HRs) with 95% confidence intervals (CIs). All statistical analyses were performed using R software (version 3.5.2) and Statistical Product and Service Solutions version 20.0 (SPSS 20.0).
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9

Comprehensive Statistical Analysis of Experimental Data

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Statistical significance of differences among variables with normal distribution was estimated by Student's t-test, while non-normal distribution variables were analyzed by Mann-Whitney U test. Qualitative variables were analyzed by Pearson χ2 test or Fisher’s exact test. Correlation was calculated using Pearson’s and distance correlation analysis. Survival probability was calculated by Kaplan–Meier method, and Log-rank test was used to test the significance of differences in survival curves. Multivariate analysis adopted Cox proportional hazards regression model, and methods of variable filtering were likelihood ratio test of maximum partial likelihood estimation (both forward: LR and backward: LR). Accuracy of survival prediction was evaluated by receiver operating characteristic curve (ROC) analysis and Harrell's concordance index (C-index) analysis. All statistical analyses were performed using R software (version 3.6.2) and SPSS software (version 26.0). Tow-tailed P < 0.05 was considered statistically significant.
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10

Comparative Statistical Analysis of Nominal, Ordinal, and Continuous Variables

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Nominal variables were analyzed using a two-tailed Fisher's exact test or chi-square test followed by post hoc two-tailed Fisher's exact tests when applicable. Ordinal and continuous variables were analyzed with the Mann–Whitney U test. P-values with corresponding odds ratios (OR) were presented in the tables. P < 0.05 was considered statistically significant. Tests were performed using R software version 3.6.2 and SPSS software (v24.0).
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