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R statistics software

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R is an open-source software environment for statistical computing and graphics. It provides a wide variety of statistical and graphical techniques, and is highly extensible. R is a language and environment for statistical computing and graphics.

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17 protocols using r statistics software

1

Statistical Analysis of Biomechanical Factors

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Data were checked for normality using the Kolmogorov-Smirnov test. Group comparisons were conducted with the Wilcoxon rank-sum, Kruskal-Wallis, or Fisher exact test. The Spearman rank correlation coefficient was used to assess the association between 2 continuous variables. Variables that were significantly different between the LPD and PFPS groups were further analyzed in a multiple logistic regression model. A penalized Firth correction was employed in the model because of quasi-complete data separation. The significance level was set to a 2-sided alpha of 5% for all statistical tests. In cases involving multiple tests, raw P values were adjusted by the Holm-Bonferroni method.
A simulation-based power analysis was conducted for the correlation analysis to evaluate the power to detect significant Spearman correlations between 2 variables using 91 samples. The significance level was set to alpha = 5%/36 to maintain a family-wise error rate of 5% across 36 correlation tests (all pairwise comparisons between 9 variables). In 10,000 iterations, 2 Gaussian variables with a given correlation coefficient were simulated. In these settings, 91 samples were sufficient to uncover a correlation of 0.38, with a power of 80% considered significant. All analyses were performed with R statistics software (version 3.4.0; www.r-project.org).
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2

Univariate Cox Regression Analysis

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Univariate cox regression analysis was determined by “survival” package (version 3.1-8; https://cran.r-project.org/web/packages/survival/index.html) in R statistics software (version 3.5.0; https://www.r-project.org/). The “survival” package and the basic usage could be downloaded from bioconductor (http://www.bioconductor.org/). Log-rank test was used to calculate the p values. In the univariate cox regression analysis, the coefficient measured the impact of covariates. The exponentiated coefficients were known as hazard ratios (HR).
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3

Statistical Analysis of Gut Microbial Composition

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Non-parametric Mann–Whitney tests (also known as the Wilcoxon rank-sum test) and Kruskal–Wallis rank-sum tests were used to calculate the p-values and identify significant differences between the two groups of wild rice fed and control mice with an n = 4. These statistical analyses were also used to identify significant differences between time course measurements for each animal group when appropriate. Statistical analyses of fecal microbial composition differences were assessed by non-parametric tests, as described by White et al. 2009 [22 (link)]. The Venn diagrams of OTUs determined from these analyses were generated while using ‘R’ statistics software (version 3.6.1, https://www.r-project.org/) ‘Venn Diagram’ package to show the number of common OTUs in feces of control and wild rice diet groups. Data are presented as means and standard deviations, where p-values ≤ 0.05 were deemed to be significantly different based on the degrees of freedom for each sample group. All of the statistical analyses were performed, while using either Microsoft Office Excel (365, Microsoft, Redmond, USA) or the comprehensive ‘R’ Archive Network (CRAN) statistics software (version 3.6.1, https://www.r-project.org/), with the ‘PMCMR’ analysis package, using ‘kruskal.test’ and ‘wilcox.test’ functions.
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4

Microbial Community Diversity Analysis

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Statistical analyses were performed with the R statistics software (https://www.r-project.org). The species richness (observed species richness (species number in a sample) and Chao1 (the common species richness estimator)), the community diversity (Shannon index) and evenness (Simpson index) were all calculated using the alpha diversity function from the Phyloseq R package [76 (link)]. Non-metric multidimensional scaling (NMDS) ordination plot (Fig. 1) of Bray-Curtis community dissimilarities between samples was performed using the Phyloseq R package [76 (link)]. The resulting graphs were all constructed using ggplot2 R package [78 ]. Statistical tests are provided in Table S4 and diversity indices in Fig. S3 and Table S5. All error bars in figures correspond to standard deviations from triplicate measurements.
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5

Gene Expression Analysis Pipeline

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All of the statistical analyses were performed with the R statistics software (version 3.2.3; available from https://www.r-project.org) (28 September 2021) and with R packages developed by the BioConductor project (available from https://www.bioconductor.org/) (28 September 2021) [24 (link)]. The expression level of each gene was summarized and normalized using the DESeq2 R/Bioconductor package [25 (link)]. Differential expression analysis was performed using the DESeq2 pipeline [25 (link)]. p-values were adjusted to control the global FDR across all comparisons with the default option of the DESeq2 package. Genes were considered differentially expressed with an adjusted p-value < 0.05 and a fold change > 1.5. For the Montpellier cohort, Affymetrix U133P chips were also used, as previously described [22 (link),26 (link)], to analyze GEP and to calculate previously published risk scores, including the RS score [8 (link)], UAMS HRS score [5 (link)], and IFM score [7 (link)].
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6

Negative Binomial Regression Analysis of AUDIT

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The baseline data from the three previous cohort studies were pooled into a single dataset and analysed using negative binomial regression to compute adjusted relative risks (RRs) and 95% confidence intervals (95%CI) for the three dimensions of the AUDIT test. Generalised negative binomial regression models were chosen for this analysis because they are more flexible than traditional models and, thus, permit the analysis of correlated data. The study period was introduced into the model as a random variable. In addition, a chi-square test was used to compare the differences between samples. Pseudo R2 by Nalgelkerke were calculated. Data were analysed using generalised negative binomial models in R Statistics software (The R Foundation for Statistical Computing c/o Institute for Statistics and Mathematics, Vienna, Austria) [31 ].
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7

Analysis of PIGD-N and TD-N Phenotypes

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The R statistics software (v.3.6.2, R Foundation for Statistical Computing, Vienna, Austria) were used for statistical analysis [45 (link)]. Normality assumptions were evaluated based on the residuals using the Shapiro-Wilk test. Clinic and neuropsychological tests between PIGD-N and TD-N phenotypes were analyzed using paired-sample two-tailed t-test (p < 0.05). The categorical variables were calculated by fisher test.
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8

Factors Associated with Early HAV Seroreversion

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Statistical analyses were performed using R statistics software (version 3.3.2; R Foundation for Statistical Computing, Vienna, Austria). Noncategorical variables were compared using the Mann‐Whitney U test, and categorical variables were compared using Fisher’s exact test. In the case‐control study, variables with P < 0.2 were entered into a multivariable general linear regression model with backward selection and missing values treated by imputation with mean to identify factors associated with early HAV seroreversion and determine the adjusted odds ratio (aOR) of each variable. Before being entered into multivariable analysis, variables with apparent correlation, such as weight, BMI, and obesity, were compared and only the variable with the smallest P value was selected into the model. A sensitivity analysis was carried out using another multivariable model that included only those matched patients from the hospitals using the CLIA method for determination of anti‐HAV IgG titers. Variables with a P value <0.05 were deemed statistically significant throughout the analyses.
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9

Microarray Printing, Scanning, and Analysis Protocol

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ArrayJet® Printer Marathon v1.4, JetSpyder™ 12 samples, JetStar™ (ArrayJet, Roslin, UK); Scanner SensoSpot Fluorescence (Miltenyi Imaging GmbH, Radolfzell, Germany); Orbital shaker (FALC Instruments S.r.l.; Treviglio, Italy); Fisherbrand™ Microplate Vortex Mixers (Fisherbrand™, EEUU); T100 Thermal Cycler (Biorad, Hercules/CA, USA); Magnetic 96-Well Separator, Digital Dry Block Heater (Thermo Scientific, Rockford/IL, USA); GenePix® Pro Microarray Analysis Software (Molecular Devices, San Jose/CA, USA); R statistics software (R Foundation for Statistical Computing, Vienna, Austria. http://www.R-project.org/); MAGPIX® System of xMAP® instruments and xPONENT® Software (Luminex Corporation, Austin, Texas, USA).
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10

Vibration-Assisted Canine Retraction Protocol

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The calculation of sample size was based on the data evaluating canine movement49 (link). Deguchi et al.49 (link) conducted a randomized controlled trial using a split-mouth design similar to the present study to evaluate the effects of low-friction attachment during canine retraction. According to their study, a 20% increase in the amount of tooth movement due to the application of vibration was assumed, with 90% power and a 5% significance level; it was calculated that 23 subjects were needed using R statistics software (R version 3.0.3, R Foundation for Statistical Computing, Vienna, Austria).
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