jYS

Some usefull Jamovi procedures for researchers

• Correlation Clustering

  • corrplot (Taiyun Wei et al.)
  • Partial & Semi-Partial Correlations: ppcor (Seongho Kim)
  • Graphical Lasso (GLASSO): glasso (Jerome Friedman et al.)
  • Network visualizations & layouts: qgraph (Sacha Epskamp et al.)

• Multi ROC Classification

  • pROC (Xavier Robin et al.)

• Missing Values Imputation (using the prediction power of Random Forests)

  • missForest (Daniel J. Stekhoven), randomForest (Leo Breiman et al.)
  • missRanger (Michael Mayer), ranger (Marvin N. Wright et al.)

• Classify missing data as missing completely at random (MCAR), missing at random (MAR) and missing not at random (MNAR)

  • missr (Noah Hellen)

• Visualizations for incomplete data

  • ggmice (Hanne Oberman et al.)

• Outliers identification and removal

  • car (John Fox, Sanford Weisberg)
  • MASS (Brian Ripley et al.)

• Three-Way threshold determination in test results

  • UncertainInterval (Hans Landsheer)

• Statistical Power and Sample Size Calculation Tools

  • pwrss (Metin Bulus, Sebastian Jentschke)

• MLP Classifier

  • custom implementation in R
  • pROC (Xavier Robin et al.)

• Random Forest Classifier

  • ranger (Marvin N. Wright et al.)
  • pROC (Xavier Robin et al.)
  • ggplot2 (Hadley Wickham et al.)

• Binomial Logistic Regression with LASSO L1 & L2 regularization, K-Fold cross-validation, and Forest Plot of Odds Ratios

  • glmnet (Jerome Friedman et al.)
  • nnet (Brian Ripley)
  • pROC (Xavier Robin et al.)
  • ggplot2 (Hadley Wickham et al.)

• PCA Principal Component Analysis

  • stats (R Core Team)
  • ggplot2 (Hadley Wickham et al.)
  • ggrepel (Kamil Slowikowski)
  • reshape2 (Hadley Wickham)

• Survival Analysis (Kaplan-Meier estimation, log-rank test, Cox regression, and time-dependent ROC curves)

  • survival (Terry M. Therneau)
  • ggsurvfit (Daniel D. Sjoberg)
  • pROC (Xavier Robin et al.)

• SNP Analysis (mSNP)

  • Hardy-Weinberg Equilibrium tests & de Finetti ternary diagram: HardyWeinberg (Jan Graffelman)
  • Genetic Association tests (allelic, genotypic, codominant, dominant, recessive, overdominant, log-additive) & Forest plot of Odds Ratios: ggplot2
  • Population genetics metrics (MAF, PIC, Shannon Index, Ne)
  • Multifactor Dimensionality Reduction (MDR) for epistasis/interaction detection: custom R6 implementation
  • Linkage Disequilibrium (LD) estimation (EM-algorithm for haplotype frequencies) & LD heatmap: custom R6 implementation

Author: Yuri Smolyakov