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195 protocols using r software

1

Statistical Analysis of Hepatic Microvascular Invasion

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Continuous variables that conformed to a normal distribution were expressed as the mean ± standard deviation (SD) and compared using an independent samples t test. Non-normally distributed continuous variables were represented as the median (25th, 75th percentile) and compared using the Mann–Whitney U test. Categorical variables were reported as frequencies and compared using the χ2 test. The interobserver agreement between two radiologists for imaging features was evaluated using the Cohen’s Kappa. The optimal cutoff points for NLR, PLR, LMR, AAPR, APRI, ANRI, GPRI, AGLR, NRPI, GAR, and GLR were determined using receiver operating characteristic (ROC) curves. Variables that reached statistical significance in the univariate analysis were included in a multivariate logistic regression analysis to investigate independent risk factors for MVI. A p value of less than 0.05 was considered statistically significant. All statistical analyses were performed using SPSS (version 26.0; IBM) and R software (version 3.6.1).
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2

Evaluating Gene Status Associations

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Mann–Whitney U test and Fisher exact test were used to evaluate whether age, gender and pathological types had statistical differences between different gene statuses. The rms package was used for nomograms, and the Hmisc package was used for calculation of C-index in R software. Statistical significance was set as p < 0.05. All statistical analyses were performed by using SPSS software version 22.0 (IBM Corp.) and R software.
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3

Factors Influencing Stenotic Ratio Analysis

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For univariate analysis, a chi-square test, t-test, and rank sum test were performed to explore the correlation between stenotic ratio and clinical factors. For multivariate analysis, binary logistic regression analysis and a linear regression model were used.
All statistical tests were conducted using R software version 4.0.5 and SPSS (version 23.0; IBM Corp., Armonk, NY, USA). The “glmnet” package was used to analyze the LASSO logistic model. The “pROC” and “car” were used to calculate the ROC curves and VIF. The C-index was calculated using the Kaplan–Meier “survival” package. The nomogram and calibration curve were built by using “rms” package. The Hosmer-Lemeshow test was calculated using the “generalhoslem” package in the R environment. Differences were considered statistically significant at p < 0.05.
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4

Severe HFMD Clinical Outcomes Analysis

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Statistical sofrware: All statistical analyses were performed using R software (version 4.04) and IBM SPSS Statistics (version 26).
Regression model: Univariate and multivariate logistics regression models were used to analyze the factors influencing the clinical outcomes of severe HFMD. The “Forward” method was used to select the factors into the logistic regression model. The influencing factors were first analyzed by the univariate analysis, then the variables with differences (p < 0.1) were included in the multivariate logistic regression model. Variables with significant differences (p ≤ 0.05) are considered in the final interpretation. All the comparisons were two-sided, and the p-value of < 0.05 was considered significant. The OR and 95%CI were compared between the survival group and the death groups.
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5

Factors Influencing Patient Health-Related Quality of Life

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The mean HRQoL questionnaire scores and the prevalence of associated symptoms will also be determined, together with their 95% confidence intervals. HRQoL will be compared with the baseline data using statistical analysis tests for paired data in order to determine the factors associated with a better HRQoL. We will test the normality of the quantitative variables using the Kolmogorov–Smirnov test and will apply Student t-tests or Mann–Whitney U tests as appropriate to compare numerical parameters between two groups. An analysis of variance or the Kruskall–Wallis test will be used to compare more than two groups. The association between qualitative variables will be contrasted using the chi-square statistic and associations between quantitative variables will be studied with Pearson correlation coefficients and Spearman’s rho. Linear regression and multiple logistic models will be used to control for the effect of several variables on HRQoL, perceived quality of care, and patient function. All the statistical analyses will be carried out with SPSS (version 21.0; IBM Corp., Armonk, NY) and R software for Windows.
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6

Pyonephrosis Diagnosis using Machine Learning

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Data were analyzed using the statistical software SPSS version 22.0 (IBM Corp., NY, USA) and R software (Version 3.6.0; https://www.R-project.org). In both the training and testing datasets, patients were assigned to the pyonephrosis group and non-pyonephrosis group. The Mann-Whitney U test and chi-square test or Fisher’s exact test were applied to compare the demographic data and laboratory parameters of the pyonephrosis and non-pyonephrosis groups. The following R packages were used in data analysis: “rms”, “glmnet”, “caret”, “rpart”, “randomForest”, “gplots”, “e1071”, “kernlab”, “pROC”, “nricens”, “xgboost”, “DiagrammeR”, “rsvg”, and “MachineShop”. Statistical significance was set as P<0.05.
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7

Statistical Analyses for Continuous and Categorical Variables

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Continuous variables were reported as mean ± standard deviation if normally distributed, and as median (interquartile range) if non-normally distributed. Normality was examined by means of both Shapiro–Wilk and Kolmogorov–Smirnov tests. Continuous variables were compared using the paired t-test if normally distributed, and the Wilcoxon signed rank test if non-normally distributed. Categorical variables were compared with the χ2 test. All statistical tests were two-sided, with alpha set at 0.05 for statistical significance. All statistical analyses were conducted using SPSS (version 25.0, IBM, Armonk, NY) and R software, version 3.3.3. For the supplemental data (see Figures and Tables, Supplemental Digital Content 1, http://links.lww.com/ASAIO/A503), we performed propensity score matching by choosing the covariates based on the comparison between the original groups and also their clinical relevance. The selected variables were: age, body mass index, smoking, COPD, nonischemic cardiomyopathy, postcardiotomy shock, left ventricular ejection fraction, and central ECLS. We performed a one-to-one propensity score–matched analysis using nearest-neighbor matching within a caliper of 0.25 standard deviation of the logit of the propensity score. We examined balance in baseline variables using standardized differences, where more than 25.0% was regarded as imbalanced.
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8

Diabetes Mellitus Risk Assessment in Patients

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The clinicopathological characteristics were summarized with descriptive statistics. Survival probability was estimated using the Kaplan–Meier method. The comparisons between variables were performed using the t-test or chi-square test. The association between variables and cumulative incidence of DM was identified with univariable analysis using Fine-Gray competing risk regression, and multivariable analysis was conducted with a Cox proportional hazards model. The cutoff value for the risk score of the high- and low-risk group was the same as the DM risk score model, and a concordance index (c-index) using Cox proportional-hazards regression was conducted to estimate the model. The inverse probability of treatment weighting (IPTW) [18 (link)] was used to minimize the bias of the clinical features between the pairwise groups. The statistical analyses were performed by IBM SPSS Statistic (version 26.0, IBM Corp, Armonk, NY, USA) and R software (version 4.0.5, Vienna, Austria). A two-tailed p-value of <0.05 was considered statistically significant.
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9

Plasma-Lyte vs. Saline for Acute Kidney Injury in DKA

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Sample size was calculated with AKI as a composite outcome using multivariate Cox Proportional Hazard Analysis. A total of 60 subjects (nearly 30 in each group) were estimated, expecting that 30 out of them meet one or other composite AKI criteria. With an alpha error of 5% and power of 80%, we assumed that the hazards of AKI in Plasma-Lyte will be 0.3 times lower than saline and the hazard ratio is constant throughout the study.
Data was analyzed as per intention-to-treat principle. Unadjusted chi-square test was used to analyze the differences in primary outcome. Absolute and relative risks with 95% confidence intervals were calculated. Survival analysis for time to resolution of AKI and DKA were compared with log-rank test. A Cox proportional hazards regression model was used to evaluate the influence of potential confounders on outcome as age, new onset DKA, and severity of DKA. Quantitative variables with normal and non-normal distribution were expressed as mean (with standard deviation) or median (with inter-quartile range) respectively. Unpaired Student’s t test or Wilcoxon rank-sum test was used for intergroup comparisons. General linear model repeated measure ANCOVA was used to compare the trends of continuous variables over time. A P value (two-tailed) < 0.05 was taken as significant. IBM SPSS Version 21 and R software were used for data analysis.
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10

Prognostic Nomograms for Survival in uLMS

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All qualified uLMS patients were randomly assigned to a training set and a validation set in a 7: 3 split ratio. The chi-square test was performed to compare the demographics and clinical statistics between the 2 sets. Survival analysis of different subgroups was performed using Kaplan-Meier curves. Based on Cox proportional-hazard regression models, we performed univariate and multivariate analysis to identify the prognostic variables.
Prognostic nomograms were constructed by combining all these predictors to predict 3- and 5-year OS and SCC. To validate these nomograms, we performed measurements both internally and externally. We used the C-index to assess the discrimination ability of the developed nomograms. A C-index of 0.5 indicates poor discrimination ability and 1.0 indicates excellent discrimination ability [18 (link)]. The calibration plots were applied using a bootstrap approach with 1000 resamples to show the consistency between observation and prediction.
SPSS software (version 21.0; IBM Corporation, NY, USA) and R software (version 3.6.1) were used to perform all statistical analyses. P value <0.05 was deemed statistically significant.
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