{
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  "Package": "nestedcv",
  "Title": "Nested Cross-Validation with 'glmnet' and 'caret'",
  "Version": "0.8.2",
  "Authors@R": "c(person(given = \"Myles\",family = \"Lewis\",\nrole = c(\"aut\", \"cre\"),\nemail = \"myles.lewis@qmul.ac.uk\",\ncomment = c(ORCID = \"0000-0001-9365-5345\")),\nperson(given = \"Athina\",family = \"Spiliopoulou\",\nrole = c(\"aut\"),\ncomment = c(ORCID = \"0000-0002-5929-6585\")),\nperson(given = \"Cankut\",family = \"Cubuk\",\nrole = c(\"ctb\"),\nemail = \"c.cubuk@qmul.ac.uk\",\ncomment = c(ORCID = \"0000-0003-4646-0849\")),\nperson(given = \"Katriona\",family = \"Goldmann\",\nrole = c(\"ctb\"),\ncomment = c(ORCID = \"0000-0002-9073-6323\")),\nperson(given = \"Ryan C.\", family = \"Thompson\",\nrole=c(\"ctb\")))",
  "Maintainer": "Myles Lewis <myles.lewis@qmul.ac.uk>",
  "BugReports": "https://github.com/myles-lewis/nestedcv/issues",
  "URL": "https://github.com/myles-lewis/nestedcv",
  "Description": "Implements nested k*l-fold cross-validation for lasso and\nelastic-net regularised linear models via the 'glmnet' package\nand other machine learning models via the 'caret' package\n<doi:10.1093/bioadv/vbad048>. Cross-validation of 'glmnet'\nalpha mixing parameter and embedded fast filter functions for\nfeature selection are provided. Described as double\ncross-validation by Stone (1977)\n<doi:10.1111/j.2517-6161.1977.tb01603.x>. Also implemented is a\nmethod using outer CV to measure unbiased model performance\nmetrics when fitting Bayesian linear and logistic regression\nshrinkage models using the horseshoe prior over parameters to\nencourage a sparse model as described by Piironen & Vehtari\n(2017) <doi:10.1214/17-EJS1337SI>.",
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  "Repository": "https://cranhaven.r-universe.dev",
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    "anova_filter",
    "barplot_var_stability",
    "bin_stat_filter",
    "boot_anova",
    "boot_correl",
    "boot_filter",
    "boot_lm",
    "boot_ttest",
    "boot_wilcoxon",
    "boruta_filter",
    "boxplot_expression",
    "class_balance",
    "class_stat_filter",
    "collinear",
    "combo_filter",
    "cor_stat_filter",
    "correl_filter",
    "correls2",
    "cv_coef",
    "cv_varImp",
    "cva.glmnet",
    "glmnet_coefs",
    "glmnet_filter",
    "hist_var_ranks",
    "innercv_preds",
    "innercv_roc",
    "innercv_summary",
    "lm_filter",
    "mcc",
    "mcc_multi",
    "metrics",
    "model.hsstan",
    "nestcv.glmnet",
    "nestcv.SuperLearner",
    "nestcv.train",
    "one_hot",
    "outercv",
    "plot_alphas",
    "plot_caret",
    "plot_lambdas",
    "plot_shap_bar",
    "plot_shap_beeswarm",
    "plot_var_ranks",
    "plot_var_stability",
    "plot_varImp",
    "pls_filter",
    "prc",
    "pred_nestcv_glmnet",
    "pred_nestcv_glmnet_class",
    "pred_SuperLearner",
    "pred_train",
    "pred_train_class",
    "predSummary",
    "randomsample",
    "ranger_filter",
    "relieff_filter",
    "repeatcv",
    "repeatfolds",
    "rf_filter",
    "slim",
    "smote",
    "stat_filter",
    "summary_vars",
    "supervisedPCA",
    "train_preds",
    "train_roc",
    "train_summary",
    "ttest_filter",
    "txtProgressBar2",
    "var_direction",
    "var_stability",
    "weight",
    "wilcoxon_filter"
  ],
  "_help": [
    {
      "page": "barplot_var_stability",
      "title": "Barplot variable stability",
      "topics": [
        "barplot_var_stability"
      ]
    },
    {
      "page": "boot_filter",
      "title": "Bootstrap for filter functions",
      "topics": [
        "boot_filter"
      ]
    },
    {
      "page": "boot_ttest",
      "title": "Bootstrap univariate filters",
      "topics": [
        "boot_anova",
        "boot_correl",
        "boot_lm",
        "boot_ttest",
        "boot_wilcoxon"
      ]
    },
    {
      "page": "boruta_filter",
      "title": "Boruta filter",
      "topics": [
        "boruta_filter"
      ]
    },
    {
      "page": "boxplot_expression",
      "title": "Boxplot expression levels of model predictors",
      "topics": [
        "boxplot_expression"
      ]
    },
    {
      "page": "class_balance",
      "title": "Check class balance in training folds",
      "topics": [
        "class_balance",
        "class_balance.default",
        "class_balance.nestcv.train"
      ]
    },
    {
      "page": "coef.cva.glmnet",
      "title": "Extract coefficients from a cva.glmnet object",
      "topics": [
        "coef.cva.glmnet"
      ]
    },
    {
      "page": "coef.nestcv.glmnet",
      "title": "Extract coefficients from nestcv.glmnet object",
      "topics": [
        "coef.nestcv.glmnet"
      ]
    },
    {
      "page": "collinear",
      "title": "Filter to reduce collinearity in predictors",
      "topics": [
        "collinear"
      ]
    },
    {
      "page": "combo_filter",
      "title": "Combo filter",
      "topics": [
        "combo_filter"
      ]
    },
    {
      "page": "correls2",
      "title": "Correlation between a vector and a matrix",
      "topics": [
        "correls2"
      ]
    },
    {
      "page": "cv_coef",
      "title": "Coefficients from outer CV glmnet models",
      "topics": [
        "cv_coef"
      ]
    },
    {
      "page": "cv_varImp",
      "title": "Extract variable importance from outer CV caret models",
      "topics": [
        "cv_varImp"
      ]
    },
    {
      "page": "cva.glmnet",
      "title": "Cross-validation of alpha for glmnet",
      "topics": [
        "cva.glmnet"
      ]
    },
    {
      "page": "glmnet_coefs",
      "title": "glmnet coefficients",
      "topics": [
        "glmnet_coefs"
      ]
    },
    {
      "page": "glmnet_filter",
      "title": "glmnet filter",
      "topics": [
        "glmnet_filter"
      ]
    },
    {
      "page": "innercv_preds",
      "title": "Inner CV predictions",
      "topics": [
        "innercv_preds",
        "innercv_preds.nestcv.glmnet",
        "innercv_preds.nestcv.train"
      ]
    },
    {
      "page": "innercv_roc",
      "title": "Build ROC curve from left-out folds from inner CV",
      "topics": [
        "innercv_roc"
      ]
    },
    {
      "page": "innercv_summary",
      "title": "Summarise performance on inner CV test folds",
      "topics": [
        "innercv_summary"
      ]
    },
    {
      "page": "lines.prc",
      "title": "Add precision-recall curve to a plot",
      "topics": [
        "lines.prc"
      ]
    },
    {
      "page": "lm_filter",
      "title": "Linear model filter",
      "topics": [
        "lm_filter"
      ]
    },
    {
      "page": "mcc",
      "title": "Matthews correlation coefficient",
      "topics": [
        "mcc",
        "mcc_multi"
      ]
    },
    {
      "page": "metrics",
      "title": "Model performance metrics",
      "topics": [
        "metrics"
      ]
    },
    {
      "page": "model.hsstan",
      "title": "hsstan model for cross-validation",
      "topics": [
        "model.hsstan"
      ]
    },
    {
      "page": "nestcv.glmnet",
      "title": "Nested cross-validation with glmnet",
      "topics": [
        "nestcv.glmnet"
      ]
    },
    {
      "page": "nestcv.SuperLearner",
      "title": "Outer cross-validation of SuperLearner model",
      "topics": [
        "nestcv.SuperLearner"
      ]
    },
    {
      "page": "nestcv.train",
      "title": "Nested cross-validation for caret",
      "topics": [
        "nestcv.train"
      ]
    },
    {
      "page": "one_hot",
      "title": "One-hot encode",
      "topics": [
        "one_hot"
      ]
    },
    {
      "page": "outercv",
      "title": "Outer cross-validation of selected models",
      "topics": [
        "outercv",
        "outercv.default",
        "outercv.formula"
      ]
    },
    {
      "page": "plot_alphas",
      "title": "Plot cross-validated glmnet alpha",
      "topics": [
        "plot_alphas"
      ]
    },
    {
      "page": "plot_caret",
      "title": "Plot caret tuning",
      "topics": [
        "plot_caret"
      ]
    },
    {
      "page": "plot_lambdas",
      "title": "Plot cross-validated glmnet lambdas across outer folds",
      "topics": [
        "plot_lambdas"
      ]
    },
    {
      "page": "plot_shap_bar",
      "title": "SHAP importance bar plot",
      "topics": [
        "plot_shap_bar"
      ]
    },
    {
      "page": "plot_shap_beeswarm",
      "title": "SHAP importance beeswarm plot",
      "topics": [
        "plot_shap_beeswarm"
      ]
    },
    {
      "page": "plot_var_ranks",
      "title": "Plot variable importance rankings",
      "topics": [
        "hist_var_ranks",
        "plot_var_ranks"
      ]
    },
    {
      "page": "plot_var_stability",
      "title": "Plot variable stability",
      "topics": [
        "plot_var_stability"
      ]
    },
    {
      "page": "plot_varImp",
      "title": "Variable importance plot",
      "topics": [
        "plot_varImp"
      ]
    },
    {
      "page": "plot.cva.glmnet",
      "title": "Plot lambda across range of alphas",
      "topics": [
        "plot.cva.glmnet"
      ]
    },
    {
      "page": "plot.prc",
      "title": "Plot precision-recall curve",
      "topics": [
        "plot.prc"
      ]
    },
    {
      "page": "pls_filter",
      "title": "Partial Least Squares filter",
      "topics": [
        "pls_filter"
      ]
    },
    {
      "page": "prc",
      "title": "Build precision-recall curve",
      "topics": [
        "prc",
        "prc.data.frame",
        "prc.default",
        "prc.nestcv.glmnet",
        "prc.nestcv.SuperLearner",
        "prc.nestcv.train",
        "prc.outercv",
        "prc.repeatcv"
      ]
    },
    {
      "page": "pred_nestcv_glmnet",
      "title": "Prediction wrappers to use fastshap with nestedcv",
      "topics": [
        "pred_nestcv_glmnet",
        "pred_nestcv_glmnet_class",
        "pred_SuperLearner",
        "pred_train",
        "pred_train_class"
      ]
    },
    {
      "page": "predict.cva.glmnet",
      "title": "Predict method for cva.glmnet models",
      "topics": [
        "predict.cva.glmnet"
      ]
    },
    {
      "page": "predict.hsstan",
      "title": "Predict from hsstan model fitted within cross-validation",
      "topics": [
        "predict.hsstan"
      ]
    },
    {
      "page": "predict.nestcv.glmnet",
      "title": "Predict method for nestcv.glmnet fits",
      "topics": [
        "predict.nestcv.glmnet"
      ]
    },
    {
      "page": "predSummary",
      "title": "Summarise prediction performance metrics",
      "topics": [
        "predSummary"
      ]
    },
    {
      "page": "randomsample",
      "title": "Oversampling and undersampling",
      "topics": [
        "randomsample"
      ]
    },
    {
      "page": "ranger_filter",
      "title": "Random forest ranger filter",
      "topics": [
        "ranger_filter"
      ]
    },
    {
      "page": "relieff_filter",
      "title": "ReliefF filter",
      "topics": [
        "relieff_filter"
      ]
    },
    {
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